National Park Service 

U.S. Department of the Interior 

Natural Resources Program Center 

Diatom Monitoring Protocol 

Great Lakes Inventory and Monitoring Network 

Natural Resource Report NPS/GLKN/NRR—2008/068 
ON THE COVER 

Surface sediment sample collected with a Wiegner corer at Voyageurs National Park. Photograph by: Ray Wise.
Diatom Monitoring Protocol

Version 1.0 

National Park Service 

Great Lakes Inventory and Monitoring Network

Natural Resource Report NPS/GLKN/NRR—2008/068 

Prepared by: Joy Ramstack1, Mark Edlund1, Daniel Engstrom1, Brenda Moraska Lafrancois2, and 

Joan Elias*3

1

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, MN 55047 

2

National Park Service 

St. Croix Watershed Research Station 

16910 152nd Street North 

Marine on St. Croix, MN 55047 

3

National Park Service 

Great Lakes Inventory and Monitoring Network 

2800 Lake Shore Drive East 

Ashland, WI 54806 

* Author contact 

August 2008 

U.S. Department of the Interior 

National Park Service 

Natural Resources Program Center 

Fort Collins, Colorado 
Diatom Monitoring Protocol, Version 1.0 August 2008 

ii 

The Natural Resource Publication series addresses natural resource topics that are of interest and 

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of management applicability. Examples of the diverse array of reports published in this series 

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Internet or by sending a request to the address on the back cover. 

Please cite this publication as: 

Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. E. Elias. 2008. Diatom 

monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort Collins, Colorado. 

NPS D-85, August 2008 
Diatom Monitoring Protocol, Version 1.0 August 2008 

iii 

Contents 

 Page 

Figures..............................................................................................................................................v 

Standard Operating Procedures..................................................................................................... vii 

Revision History Log................................................................................................................... viii 

Acknowledgements........................................................................................................................ ix 

1.0 Background and Objectives .......................................................................................................1 

 1.1. Rationale for Selecting this Resource to Monitor.........................................................1 

 1.2. Measurable Objectives..................................................................................................2 

2.0 Sampling Design........................................................................................................................5 

 2.1. Number and Location of Sampling Sites......................................................................5 

 2.2. Frequency and Timing of Sampling .............................................................................5 

 2.3. Level of Change that can be Detected Given the Sampling Design.............................5 

3.0 Field Methods ............................................................................................................................7 

 3.1. Field Season Preparations and Equipment Setup..........................................................7 

 3.2. Sample Collection.........................................................................................................7 

 3.3. Post-Collection Processing of Samples ........................................................................8 

 3.4. End-of-Season Procedures............................................................................................8 

4.0 Data Handling, Analysis, and Reporting ...................................................................................9 

 4.1. Metadata Procedures.....................................................................................................9 

 4.2. Overview of Database Design ......................................................................................9 

 4.3. Data Entry, Verification, and Editing .........................................................................10 

 4.4. Routine Data Summaries and Statistical Analyses .....................................................10 

 4.5. Reporting Schedule.....................................................................................................11

 4.6. Recommended Report Format ....................................................................................11 

 4.7. Data Archival Procedures ...........................................................................................14 

5.0 Personnel Requirements and Training.....................................................................................15 

 5.1. Roles, Responsibilities, and Qualifications ................................................................15 

6.0 Operational Requirements .......................................................................................................17 

 6.1. Annual Workload and Field Schedule ........................................................................17 

 6.2. Facility and Equipment Needs....................................................................................17 

 6.3. Startup Costs and Budget Considerations...................................................................17

7.0 Literature Cited ........................................................................................................................19 

Diatom Monitoring Protocol, Version 1.0 August 2008 

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Figures 

 Page 

Figure 1. Sediment accumulation rate over time at Manitou Lake, Sleeping Bear Dunes National 

Lakeshore........................................................................................................................12 

Figure 2. Correspondence analysis of downcore samples from Shell Lake, Sleeping Bear Dunes 

National Lakeshore .........................................................................................................13 

Figure 3. Principal components analysis of environmental data from 145 Minnesota lakes ........14 

Diatom Monitoring Protocol, Version 1.0 August 2008 

vii 

Standard Operating Procedures 

SOP #1: Pre-season Preparation 

SOP #2: Training and Safety 

SOP #3: Using a GPS 

SOP #4: Field Methods 

SOP #5: Cleaning Sediment Samples 

SOP #6: Preparation of Diatom Slides 

SOP #7: Analysis of Slides 

SOP #8: Archiving Sediment and Diatom Slides 

SOP #9: Data Analysis 

SOP #10: Reporting 

SOP #11: Post-season Procedures 

SOP #12: Quality Assurance and Quality Control 

SOP #13: Procedure for Revising the Protocol 
Diatom Monitoring Protocol, Version 1.0 August 2008 

viii 

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this protocol 

narrative will promptly notify the project manager and/or the Great Lakes Network (GLKN) data 

manager about recommended and required changes. The project manager must review and 

incorporate all changes, complete the revision history log, and change the date and version 

number on the title page and in the footer of the document file. For complete instructions, please 

refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Diatom Monitoring Protocol, Version 1.0 August 2008 

ix 

Acknowledgements 

The diatom monitoring project will be closely tied to the water quality monitoring protocols for 

inland lakes and large rivers. See Elias et al. (2008) and Magdalene et al. (2007), respectively, 

for additional details on these projects. 

Diatom Monitoring Protocol, Version 1.0 August 2008 

1 

1.0 Background and Objectives 

This protocol is designed to use diatoms as bioindicators to monitor lakes and large rivers within 

the National Park Service Great Lakes Inventory and Monitoring Network (Network or GLKN) 

park units. Network parks encompass a variety of aquatic habitats and biota, including 129 

named lakes, totaling nearly 41,000 ha (101,000 acres) (Lafrancois and Glase 2005). Monitoring 

of diatoms will occur in the lakes selected for GLKN’s monitoring of water quality in inland 

lakes (Elias et al. 2008) and at select sites that are part of monitoring in large rivers (Magdalene 

et al. 2007). The lakes selected for monitoring span gradients of surface area, depth, visitor use, 

water chemistry, and spatial distribution within each park. The few river sites selected for 

diatom monitoring will be lake-like, where sediment deposition occurs. Aquatic resources at 

each of the parks are described in Elias et al. (2008), Magdalene et al. (2007), and Route and 

Elias (2005). Throughout the remainder of this protocol we will refer only to the inland lakes 

protocol to simplify the description, although diatom monitoring also will occur at several sites 

that are part of the large rivers protocol. 

Because diatom monitoring will be conducted in close collaboration between GLKN staff and 

contracted cooperators, this protocol is intended to address the essential aspects required of the 

project partners. 

1.1 Rationale for Selecting this Resource to Monitor 

A variety of stressors such as climate change, environmental contaminants, exotic species, and 

land and resource uses including shoreline and urban development, recreation, water level 

management, logging, and agriculture in and near GLKN park units influence the parks' 

resources. Park managers seek information to make considered decisions in a future certain to 

bring change. 

Bioindicators are critical to long-term monitoring of water quality because (1) they provide an 

assessment of the actual ecological impact of environmental stressors, (2) it is not possible to 

measure directly all of the water quality parameters needed to detect unexpected environmental 

change, and (3) they serve as integrators of changes in water quality that may be missed during 

routine water chemistry sampling. Physical and chemical measures of water quality provide only 

a partial picture of ecological impact, and even the full suite of proposed water quality indicators 

(Elias et al. 2008; Water Quality Monitoring Protocol for Inland Lakes) is likely to miss stressors 

that are not currently identified or anticipated. 

Diatoms (Class Bacillariophyceae) are among the most powerful groups of biological indicators 

of environmental conditions in aquatic systems (lakes, rivers, wetlands, estuaries; Stoermer and 

Smol 1999). Diatoms make excellent bioindicators because they are generally abundant in 

aquatic systems and respond rapidly to changes in their environment. They form a cell wall 

made of silica, which preserves well in the sediments, and different species can be identified by 

unique patterns in this silica cell wall. Diatoms sensitively register environmental changes at the 

base of the food chain and are thus critical to all ‘bottom-up’ ecological processes. As primary 

producers, their relationship to environmental stressors is more direct and traceable than those at 

higher trophic levels (e.g., invertebrates, fish, amphibians). The recent discovery that increases 

in chloride concentration from road-salt application have had a pronounced effect on diatom 
Diatom Monitoring Protocol, Version 1.0 August 2008 

2 

assemblages in the Minneapolis/St. Paul metropolitan area as well as more rural parts of 

Minnesota (Ramstack et al. 2004) is a case in point. Today chloride concentrations in many of 

these lakes are 1-2 orders of magnitude greater than those in pre-European times. What is 

unexpected about this finding is not the increase in chloride, although there was no way of 

assessing the magnitude of the increase without diatoms, but that a conservative anion had 

produced such a large impact on algal communities and that this change had gone unnoticed. 

Analysis of diatoms in surficial lake sediments is a powerful tool to detect recent environmental 

change, or to place modern conditions in a regional or historical context (Cumming et al. 1992; 

Ramstack et al. 2003, 2004; Smol and Douglas 2007). We will integrate diatom monitoring in 

GLKN park units with paleolimnological efforts on a subset of the lakes. Paleolimnology offers 

unique opportunities for aquatic and terrestrial biomonitoring programs, primarily by providing 

historical data with which to contextualize modern monitoring in the absence of long-term 

monitoring data. Paleolimnology is often the only available or practical means for reconstructing 

ecosystem conditions, because historical water quality records are rarely available and if they 

are, records do not extend beyond the influence of European settlement. Many, if not most, 

modern lakes are significantly altered from their natural state; thus the use of reference lakes or 

computer models to simulate reference conditions may produce questionable results. 

By coordinating the diatom monitoring and paleolimnology efforts, it will be possible to place 

the current lake conditions in a historical perspective. The results will provide a management 

foundation by determining the natural variability or reference condition of national park lakes 

and by reconstructing a detailed history of lake response to ecological changes that have 

occurred in and around the lakes during the last 150 years. Lake-sediment records integrate 

across both spatial and temporal scales; therefore, the results of the paleolimnological analyses 

can be used in conjunction with the biomonitoring efforts to quantify modern environmental 

conditions relative to historical conditions, to detect early ecological change and recent trends, 

and to evaluate success of management actions. 

At the time of this writing, the Network and the St. Croix Watershed Research Station (SCWRS) 

are collaborating on a paleolimnological project that includes several GLKN park units. As part 

of this project, a select subset of GLKN lakes will be cored for diatom and geochemical analysis 

to determine the timing and magnitude of historical environmental change. Results of this 

project will be available to help interpret and place into context data gathered through diatom 

monitoring. 

1.2 Measurable Objectives 

The analysis of diatoms in surficial lake sediments will address the following questions: 

• What is the current ecosystem status of a particular lake in relation to other regional 

lakes? 

• Are similar ecological trends occurring across regional lakes? (e.g., related to climate 

change or atmospheric deposition) 

• What is the ecosystem status of this lake in relation to historical environmental change 

noted in regional sediment cores? 

• Has this lake changed since the last time it was sampled? If so, what are the magnitude 

and direction of that change? 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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To answer these questions the following steps will be taken: 

1. Analyze diatom communities in surficial lake sediments to complement the routine physical 

and chemical water quality sampling and enhance the potential for detecting long-term changes 

in water quality. 

Rationale for using diatoms as bioindicators include: 

• The sensitivity and tolerance of diatoms to environmental variables – including nutrients, 

organic pollutants, pesticides, heavy metals, salinity (and major ion chemistry), pH, 

alkalinity, light, temperature, substrate, and depth – are known to vary among species 

(Battarbee et al. 2001). These species-specific responses can be used to infer 

environmental conditions and to provide an early-warning of the cumulative impacts of 

environmental change at the base of aquatic foodwebs. Early detection of change may 

facilitate park management decisions such that irreversible changes may be avoided.

• Diatoms occur in highly diverse assemblages, and species are relatively easily 

distinguished. The taxonomic diversity of diatom communities provides a high level of 

redundancy (confirmation by responses from multiple species) for robust tracking of 

environmental conditions. 

• The combined cost of diatom sampling and analysis is relatively low when compared to 

other biological indicators (Stevenson and Pan 1999), and diatom samples are easily 

archived and preserved semi-indefinitely, allowing samples to be re-examined at future 

dates, if desirable. 

• In lake environments, the deep-water sediments provide a highly integrated sample of 

diatom community structure for the lake as a whole. This means that only a single 

sample of surface sediment is needed to characterize the entire lake (Anderson 1990), as 

compared to the numerous samples required to overcome spatial heterogeneity for other 

bioindicators (e.g., benthic invertebrates). 

• Diatoms have been used extensively to assess environmental conditions in freshwaters. 

Literally dozens of papers are published each year in peer-reviewed journals describing 

analytical and numerical (statistical) methods, taxonomic refinements, environmental 

requirements, paleo-environmental constructions, and applications in water-quality issues 

and policy development (Stoermer and Smol 1999). Diatoms are currently being used in 

both state (e.g., Minnesota, Montana) and nation-wide (Environmental Monitoring and 

Assessmeny Program [EMAP], National Water-Quality Assessment [NAQWA]) 

assessments of water quality. 

2. Analyze contemporary changes in the community composition of diatoms within the context of 

the range of natural variability, as determined by diatoms present in cores dating back to the 

time of European settlement. 

The question of natural variability is particularly important to environmental monitoring, which 

in the final analysis aims to distinguish significant human perturbations from background 

conditions. Ecological systems are often naturally variable (seasonally and inter-annually), and 

decades of careful water monitoring may be needed to detect significant trends. Even where 

long-term datasets are available, it is often difficult to know whether the observed trends are of 

concern or within the range of natural variation. Comparing the current community composition 
Diatom Monitoring Protocol, Version 1.0 August 2008 

4 

of diatoms to the species compositions dating back 150-200 years will allow us to determine 

whether the current conditions are outside of the range of natural variability of GLKN park lakes. 

3. Compare diatom species assemblages in surficial lake sediments with recent water chemistry 

measurements to continue to improve our understanding of diatom response to 

physical/chemical variables. 

Diatom communities are readily compared using multivariate techniques such as ordination 

because the assemblages are taxonomically diverse. Differences among samples (in space or 

time) are summarized by dissimilarity metrics such as chord distance or by arraying them along 

one or a few major axes in multivariate space (using principal components analysis [PCA], 

correspondence analysis [CA], or similar techniques). If independent water quality 

measurements have been taken (e.g., pH, total phosphorus, Secchi depth), the ordination can be 

constrained so that the major axes of diatom variability are aligned with the most explanatory 

environmental gradients (canonical correspondence analysis); the strength of these relationships 

can then be summarized statistically as an objective measure of explained variance (Battarbee et 

al. 2001). 
Diatom Monitoring Protocol, Version 1.0 August 2008 

5 

2.0 Sampling Design 

Because analysis of diatoms in surficial sediments will be used to augment and integrate water 

quality monitoring of inland lakes and large rivers, the sampling design is based on these projects 

(Elias et al. 2008; Magdalene et al. 2007, respectively) and known sedimentation rates. 

Approximately 30-35 lakes and 5-8 river sites will comprise the routine diatom monitoring sites. 

2.1 Number and Location of Sampling Sites 

The deep-water sediments of lakes provide a highly integrated sample of diatom community 

structure from the lake as a whole. Therefore, only a single sample of surface sediment is 

needed to characterize an entire lake (Anderson 1990). The diatom surface sediment sample at 

each lake will be collected at the deepest part of the lake, where routine water quality monitoring 

is conducted (Elias et al. 2008). 

2.2 Frequency and Timing of Sampling 

Sediment samples for diatom analysis will be collected from lakes selected for water quality 

monitoring approximately once every five years, depending primarily on sedimentation rate. 

Although lakes will be sampled annually as part of the water quality monitoring protocol, diatom 

analysis in surficial sediments will be rotated across parks on an approximate 5-year cycle in an 

attempt to spread the costs evenly. Additional lakes will be sampled for diatoms and routine 

water chemistry as funding permits (see Elias et al. 2008 for details). 

Surface sediment samples will be collected during the final water quality monitoring event of the 

season, usually in September or October. Only one sediment sampling event at the end of the 

field season is necessary because that sample will represent the diatoms that have settled out of 

the water column over the previous approximately 3-5 years. At each site the top 0-1 cm and 1-2 

cm of sediment will be collected, and kept as two separate samples. In most cases only the 0-1 

cm sample will be analyzed; however, in lakes that are found to have a high sedimentation rate 

(this will be determined from the analysis of long cores), the 0-1 and 1-2 cm samples will be 

combined for analysis. This combined sample will then represent the previous 3-5 years. 

2.3 Level of Change that Can Be Detected Given the Sampling Design 

Sediment cores collected and analyzed for diatoms as part of the GLKN monitoring program will 

provide a historical framework for interpreting variability in the samples. Comparing the current 

community composition of diatoms to the species compositions dating back 150-200 years will 

demonstrate if the current conditions are outside of the range of natural variability of GLKN park 

lakes. 

Change will be evaluated in two ways; first, the amount of floristic change in the diatom 

community composition will be measured using a chord distance dissimilarity measure. Second, 

the change in diatom-inferred water quality estimates will be evaluated using the root mean 

square error of prediction. 

The chord distance dissimilarity measure will be used to quantify the floristic change in diatom 

community composition between subsequent sampling events. Meaningful change can be 

assessed using percentile cutoffs (Bennion et al. 2004), or by using the chord distance between 
Diatom Monitoring Protocol, Version 1.0 August 2008 

6 

samples from sediment cores as a framework (refer to SOP #9 [Data Analysis] for more 

information on chord distance). 

Methods for evaluating the certainty of inferred water quality estimates are well established. 

Generally error bars are reported as model error estimates, the jack-knifed or bootstrapped root 

mean square error of prediction (RMSEPboot/jack) of the calibration model (Fritz et al. 1999; 

Ramstack et al. 2003; Köster et al. 2004) (refer to SOP #9 [Data Analysis] for more information 

on the diatom calibration model being used for this project). Variability or change in inferred 

water quality parameters greater than the RMSEPboot/jack represents a measure of significant 

change. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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3.0 Field Methods 

This section summarizes the information presented in greater detail in the standard operating 

procedures (SOPs) #1 (Pre-season Preparation), #4 (Field Methods and Surface Sediment 

Collection), #7 (Analysis of Diatoms on Microscope Slides), and #9 (Data Analysis). Refer to 

these SOPs for more information. 

 

3.1 Field Season Preparations and Equipment Setup 

Prior to the field season, many preparations must be completed to ensure sampling can be 

undertaken according to schedule. The field season for collecting surface sediment samples for 

diatom analysis in GLKN park units is generally late summer/early fall. Because the surface 

sediment samples will be collected during the final water quality sampling event of the year it 

will be necessary to coordinate with personnel conducting water quality monitoring of inland 

lakes. 

All details for the season need to be planned well in advance. Field preparations should begin in 

January to allow enough time for ordering new supplies and equipment and making repairs if 

necessary. Field equipment should be checked to ensure proper functioning; supplies should be 

inventoried and orders placed. Refer to SOP #1 (Pre-season Preparation) for a complete list of 

field season preparations. 

For sampling stations located within park boundaries, a Research and Collecting Permit must be 

obtained before any work can be done. Refer to SOP #1 for details on renewing or obtaining 

new permits. Permanent diatom slides are considered U.S. government property, and as such, 

must be curated properly. Consult with the appropriate park representative for advice on 

compliance with government curation mandates. 

Agreements for diatom analysis with cooperators should be reviewed and modified, if necessary. 

Both parties (NPS and cooperating organization) should agree on the number of samples to be 

collected in the year, annual timelines, and other expectations. 

3.2 Sample Collection 

A line-operated gravity corer will be used to collect the upper 0-1 cm and 1-2 cm of sediment for 

an integrated assessment of lake conditions during the previous approximately 3-5 years (see 

SOP #4 for details). Collection sites will be precisely located by GPS to allow re-sampling in the 

same location in subsequent years; sampling sites will target central depositional basins in each 

lake. Sediment samples can be collected by water quality monitoring personnel during the final 

round of water quality sampling of the season. 

Surface sediment samples will be processed in the field according to SOP #4 and kept 

refrigerated until they are sent to the analytical laboratory for further processing and analysis. 

Upon receipt by the analytical laboratory, samples will be homogenized and subsampled for 

diatom analyses. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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3.3 Post-Collection Processing of Samples 

Diatom microscope slides will be prepared using standard oxidation and mounting techniques 

(see SOPs #5 and #6). A total of 400 diatom valves will be counted in each sample using a light 

microscope fitted with full immersion optics capable of 875-1250X magnification and numerical 

aperture (N.A.) >1.30. Analyses will follow the enumeration criteria used in the Minnesota 

calibration set (Ramstack et al. 2003; Edlund and Kingston 2004; Edlund 2005). 

Approximately 10% of the samples will be recounted by another analyst. Refer to SOP #12 for 

details on QA/QC. 

 

Diatoms will be identified using floras and monographs by Hustedt (1927-1966, 1930); Patrick 

and Reimer (1966, 1975); Collins and Kalinsky (1977); Camburn et al. (1978, 1984-1986); 

Krammer and Lange-Bertalot (1986, 1988, 1991a, b); Cumming et al. (1995); Reavie and Smol 

(1998); Camburn and Charles (2000); and Fallu et al. (2000) as well as all other pertinent 

literature. Diatom taxonomy should be harmonized with the Minnesota (MN) diatom calibration 

set (Ramstack et al. 2003; Edlund and Kingston 2004; Edlund 2005) because analysis of the 

GLKN samples will be overlaid on the Minnesota set. 

3.4 End-of-Season Procedures 

Before storing the gravity corer, be sure it is clean and dry and that all removable parts have been 

returned to the storage case. Inventory all field and laboratory supplies and replace as necessary 

as soon as possible. Refer to SOP #11 (Post-season Procedures) for a complete list of end-ofseason procedures. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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4.0 Data Handling, Analysis, and Reporting 

 

4.1 Metadata Procedures 

Metadata allows potential data users to evaluate the quality and usefulness of the data based on 

an understanding of the complete process under which it was collected and maintained. All of 

the protocol documentation, including standard operating procedures (SOPs), is part of a 

dataset’s metadata for this reason. A reference to the appropriate version of these documents is 

part of the metadata for any particular element of a dataset. All data must have associated values 

for the dates and times they were collected. 

Additional metadata associated with diatom monitoring includes geospatial data (location) and 

biological (species identification). For metadata associated with geospatial data, Executive 

Order 12906 will be abided by, which mandates that every federal agency document all new 

geospatial data it collects or produces using the Federal Geographic Data Committee (FGDC) 

Content Standard for Digital Geospatial Metadata (CSDGM; 

www.fgdc.gov/metadata/constan.html). 

Although not currently required, GLKN will make every effort to complete Biological Data 

Profiles (www.fgdc.gov/standards/status/sub5_2.html) for diatom datasets and add associated 

metadata to the National Biological Information Infrastructure Clearinghouse (NBII; 

www.nbii.gov/datainfo/metadata). 

For more details on the Great Lakes Network’s overall strategy for metadata generation, 

management, and distribution see Chapter 8, Data Documentation, of GLKN’s Data 

Management Plan (Hart and Gafvert 2005) and the appendices of that document. 

4.2 Overview of Database Design 

The NPS-Water Resources Division (WRD) has established a policy that all Inventory and 

Monitoring (I&M) water quality monitoring data will be made compatible with, and be uploaded 

to, the Environmental Protection Agency’s (EPA) STORET database. The WRD developed a 

Microsoft Access database tool, NPSTORET, which duplicates most of the data and table 

structures in EPA STORET, to facilitate easier movement of I&M networks’ water quality data 

into EPA STORET format. We will use NPSTORET as the primary data entry tool and data 

transfer mechanism to WRD. 

To meet the data flow requirements of NPS-WRD, the Network’s version of NPSTORET will be 

able to export and import water quality data from the master version of STORET maintained by 

WRD. In addition, GLKN uses the Vital Signs Internet Mapping Service (VSIMS) for data 

distribution. This service allows users to explore and query monitoring data using spatial and 

non-spatial parameters. Network versions of NPSTORET are used to update a master version of 

STORET maintained by NPS WRD. The WRD master copy of STORET data is the data source 

that is used by the VSIMS to serve water quality data collected by GLKN and other I&M 

networks. 

The Great Lakes Network will maintain one master copy of NPSTORET for each park at the 

Ashland office on a central server. This is the only copy of NPSTORET that can be used to 
Diatom Monitoring Protocol, Version 1.0 August 2008 

10 

export data to other locations (WRD, GLKN’s SQL Server). Additional copies of NPSTORET 

can be used by GLKN personnel stationed at parks, but they can only be used as a conduit for 

data entry and the importation of data to GLKN’s master version of NPSTORET. For analysis, 

the data from the master copy of NPSTORET, that has passed all QA/QC procedures, must be 

used. 

4.3 Data Entry, Verification, and Editing 

Each diatom species will be described by an 8-character species code; all of the codes used in the 

145 lake MN calibration set are listed in Appendix 1 of SOP #7 (Analysis of Slides). These 

codes follow the format used by the Great Lakes Environmental Indicators (GLEI) project (E. 

Reavie, Natural Resources Research Institute, University of Minnesota, Duluth). The GLEI list 

will be used as a starting point; however, many taxa and codes will need to be added as the 

project progresses. A complete and up-to-date list of codes for this project will be maintained by 

GLKN and the cooperators. 

After each sediment sample has been processed and diatoms have been identified, the following 

information will be recorded: 

• The full name, including authority(ies) of each diatom taxon identified 

• The appropriate 8-character code for each taxon 

• The raw number of valves of each taxon (refer to SOP #7 for details on counting) 

• The percentage abundance (relative frequency) of each taxon (number of times a taxon is 

observed, divided by the total number of diatoms observed) 

The cooperators, as subject experts, will verify the data prior to providing them to GLKN. 

Network personnel will upload the diatom data to NPSTORET and conduct quality 

assurance/quality control checks prior to transfer to WRD. These procedures protect the integrity 

of the data and allow the history of each data record to be traced. 

4.4 Routine Data Summaries and Statistical Analyses 

Multivariate statistical analysis of the diatom data will occur annually, following diatom 

enumeration. Comparisons of diatom species assemblages with water chemistry measurements 

will be used to derive an understanding of diatom response to physical/chemical variables. 

During the 2004-2009 diatom project (Task Agreement #J2105040028), surface sediment 

samples will be collected from approximately 50-60 lakes within the Great Lakes Network parks. 

The diatom assemblages from these samples will be appended to the MN diatom calibration set 

(Ramstack et al. 2003; Edlund and Kingston 2004; Edlund 2005). Subsequent surface sediment 

samples that are analyzed for diatoms will be plotted passively on this calibration set to look for 

changes in the lakes. The diatom taxonomy must be harmonized with the MN calibration set 

prior to statistical analyses. 

Changes in the community composition of diatoms will be analyzed in relation to other lakes as 

well as within the context of the range of natural variability, as determined by diatoms present in 

sediment cores dating back before the time of European settlement. Refer to SOP #9 Data 

Analysis, for a detailed discussion of the multivariate statistical methods that will be used in this 

project. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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4.5 Reporting Schedule 

One of the Network’s goals is to ensure that the results and knowledge acquired through the 

monitoring programs are shared with all appropriate parties, especially the parks and their natural 

resource managers. Park managers will be provided in a timely manner with clear, meaningful 

products. Because the monitoring data will be of interest to a broader scientific community, 

reports will be provided to the states in which the national park units reside, the NPS I&M 

Program, and when appropriate, articles will be submitted to peer-reviewed journals for 

publication. Findings will also be presented orally and in poster format at regional and national 

meetings. In particular, the Western Great Lakes Research Conference, which is sponsored in 

part by GLKN, will be a valuable venue for presenting the results of this program. 

 

Annual reports will be prepared by the diatom cooperators in collaboration with the Network’s 

aquatic ecologist. As parks are monitored repeatedly, the reports will become progressively 

more in-depth and will include syntheses and analyses of data over time. The reports will place 

the observed results in both a regional and historical context by relating them to other published 

literature, the significance of the results will be discussed in terms of environmental change, and 

management recommendations will be provided based on the findings. See SOP #10, Reporting, 

for more details. 

4.6 Recommended Report Format 

Reports should follow the format of a typical peer-reviewed journal article. The following 

outline is a good example of the type of report to be produced. 

 TITLE PAGE 

(Title, Author(s), Participating Institutions, For Whom Prepared, and Date) 

 TABLE OF CONTENTS PAGE 

 EXECUTIVE SUMMARY PAGE (abstract) 

 1.0 INTRODUCTION 

 1.1 Background 

 1.2 Justification for Study 

 1.3 Objectives 

 2.0 METHODS 

 2.1 Study area(s) 

 2.2 Field methods(s) 

 2.3 Analytical method(s) 

 3.0 RESULTS 

 4.0 DISCUSSION 

 5.0 MANAGEMENT IMPLICATIONS 

 6.0 ACKNOWLEDGEMENTS 

 7.0 LITERATURE CITED (if any) 

 8.0 TABLES 

 9.0 FIGURES 

 1.0 APPENDICES (if any) 
Diatom Monitoring Protocol, Version 1.0 August 2008 

12 

Reports should include tabular and graphic displays of data. Tables are appropriate for displaying 

simple data summaries, but can also be used to show results of more comprehensive analyses. 

Graphical display of data is especially useful for depicting trends across years (e.g., Figures 1 

and 2) or the correlations among multiple variables or lakes (e.g., Figure 3). See SOP # 9, Data 

Analysis, for more details on presentation of data. 

 

Lake Manitou (SLBE)

1800

1820

1840

1860

1880

1900

1920

1940

1960

1980

2000

2020

0.00 0.01 0.02 0.03 0.04 0.05 0.06

Sediment Accumulation (g/cm2 yr)

210-Pb Date

Figure 1. Sediment accumulation rate over time at Lake Manitou, Sleeping Bear Dunes National 

Lakeshore. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

13 

-3 -2 -1 0 1

-2 -1 0 1 2

CA1

CA2

X2003 X1997

X1991

X1980 X1968

X1953

X1941

X1925

X1912

X1889

X1870

X1841

X1810

X1771

X1727

Figure 2. Correspondence analysis of downcore samples from Shell Lake (Sleeping Bear Dunes 

National Lakeshore) based on diatom species assemblages, from sediments dating from 1727 to 

2003. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

14 

-1.5 -1.0 -0.5 0.0 0.5 1.0

-1.0 -0.5 0.0 0.5 1.0

PC1

PC2

ANC

Chla

Cl

Color

Cond

LakeArea

pH

Secchi

TN

TP

WshdArea

DepthMax

DepthAvg

Figure 3. Principal components analysis of environmental data from 145 Minnesota lakes. 

4.7 Data Archival Procedures 

Data archiving serves two primary functions: it provides a source to retrieve a copy of any 

dataset when the primary dataset is lost or destroyed, and it provides a data record that is an 

essential part of the QA/QC process. The cooperators will house the original copies of the 

diatom count data and will provide copies to the Network. 

Both freeze-dried sediment samples and diatom slides will be archived (refer to SOP #8 

[Archiving] for details). Researchers will coordinate with each park unit to decide where the 

collections for each park will be housed. Representatives from each park will also work with 

researchers to ensure that the archived materials are entered into the appropriate NPS database. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

15 

5.0 Personnel Requirements and Training

The requirements of GLKN personnel and cooperators differ; both will be addressed in the 

following section. 

5.1 Roles, Responsibilities, and Qualifications 

Field personnel for the GLKN water quality monitoring project will collect the surficial sediment 

samples. Qualifications of GLKN field staff are detailed in the protocol for monitoring water 

quality of inland lakes (Elias et al. 2008). 

The project manager (GLKN aquatic ecologist) will oversee all aspects of the NPS involvement 

with the diatom monitoring project. Specific responsibilities of the project manager will be to: 

• Hire and train field personnel 

• Coordinate field logistics with park staff 

• Administer the contract with cooperators for diatom analysis 

• Collaborate closely with cooperators on data summaries, reports, and publications 

• Ensure collaborators receive water quality monitoring data in a timely manner 

• Work with Network data manager to ensure data are entered into NPSTORET, verified, 

and validated 

• Ensure parks and other interested parties are informed of project results 

The GLKN will contract with an organization or institution experienced with all aspects of 

diatom identification, enumeration, and analyses of species assemblages. The cooperators should 

have the following specific qualifications: 

• Experience in multivariate data analysis and paleoecology 

• Experience using lake sediment records to explain long-term environmental change, 

including the effects of human activities on water quality, atmospheric chemistry, and 

biogeochemical processes 

• Extensive experience in diatom taxonomy 

• Facilities that include: 

o Research-grade light microscopes with bright field and DIC optics, 875-1200X 

magnification, numerical aperture (N.A.) >1.3, and image capture 

o Computing facilities with software for multivariate statistical analysis 

o Analytical laboratory 

o Extensive literature on diatom taxonomy 

o Diatom reference collection or stated intent to use specific diatom herbarium (or 

herbaria) for checking collected specimens against voucher specimens 

Specific requirements of the cooperators may vary with the contract language, but in general the 

cooperators will be responsible for: 

• Hiring and training of laboratory and analytical personnel 

• Processing sediment samples 

• Enumerating and analyzing diatom communities 

• Collaborating with GLKN on data summaries, reports, and publications 

• Providing raw data to GLKN in a timely manner 
Diatom Monitoring Protocol, Version 1.0 August 2008 

16 

• Collaborating with GLKN to ensure parks and other interested parties are informed of 

results 
Diatom Monitoring Protocol, Version 1.0 August 2008 

17 

6.0 Operational Requirements

 

6.1 Annual Workload and Field Schedule 

Surficial sediment samples will be collected annually by GLKN field crews, on a rotational basis 

across parks such that sampling is repeated on a given lake approximately every 5 years. 

Approximately 10 sites will be sampled each year. Because the sampling will be conducted 

during the final round of water quality sampling for the season, little additional field time or 

travel by GLKN staff is required. 

The GLKN project manager will provide cooperators with raw and summarized water quality 

data in a timely manner and will collaborate on annual reports. The project manager will ensure 

parks and other interested parties are informed of progress and results. The cooperators will 

process the sediment samples collected by NPS personnel each year, identify the diatoms, and 

analyze the species assemblages relative to the GLKN-MN calibration set. Changes in species 

since the last sampling will be related to changes in water quality. Annual reports will be 

prepared in collaboration with the Network aquatic ecologist. 

6.2 Facility and Equipment Needs 

Equipment required by GLKN for collection and storage of sediment samples consists of the 

following: 

• Gravity corers (Wiegner corer), two or more to ensure availability at all parks 

• Sample containers 

• Container labels 

• Pipettes 

• Refrigerator space for storing samples 

The collaborators will need all laboratory supplies and equipment required for processing of 

sediment samples, preparation of microscope slides, identification and enumeration of diatoms, 

and computing facilities with software for multivariate statistical analysis. 

6.3 Startup Costs and Budget Considerations 

The costs of collecting surficial sediment samples for diatom analysis are minimal if combined 

with the routine water quality monitoring. Because the Network will make use of water quality 

monitoring personnel, no additional staff costs are anticipated. Similarly, no additional travel 

costs are anticipated. The equipment required for collecting the samples is minimal, consisting 

of a gravity corer, specimen cups, pipettes, and labels. The Network currently has two gravity 

corers, which cost approximately $1200 each. We expect these corers to remain functional for 

many years, with annual costs consisting of consumables amounting to approximately $200. 

The majority of the costs will be associated with a contract with the cooperators for processing 

samples, microscopy, analysis, report-writing, supplies, and travel. Because the Network will 

request bids from interested contractors, the exact cost is not known. However, we expect the 

cost of the contract to be approximately $15-20,000 annually. 

Diatom Monitoring Protocol, Version 1.0 August 2008 

19 

7.0 Literature Cited 

Anderson, N. J. 1990. Variability of diatom concentrations and accumulation rates in sediments 

of a small lake basin. Limnology and Oceanography 35:497-508. 

Battarbee, R. W., V. J. Jones, R. J. Flower, N. G. Cameron, H. Bennion, L. Carvalho, and S. 

Juggins. 2001. Diatoms. Pages 155-202 In Smol, J. P., H. J. B. Birks, and W. M. Last, 

editors. Tracking Environmental Change Using Lake Sediments. Volume 3: Terrestrial, 

Algal, and Siliceous Indicators, Kluwer Academic Publisherss, Dordrecht, The 

Netherlands. 

Camburn, K. E., and D. F. Charles. 2000. Diatoms of low-alkalinity lakes in the northeastern 

United States. Academy of Natural Sciences of Philadelphia, Special Publication 18. 

Camburn, K. E., J. C. Kingston, and D. F. Charles (editors). 1984-1986. PIRLA Diatom 

Iconograph. PIRLA Unpublished Report Series, Report 3. - Electric Power Research 

Institute, Palo Alto, California. 

Camburn, K. E., R. L. Lowe, and D. L. Stoneburner. 1978. The haptobenthic diatom flora of 

Long Branch Creek, South Carolina. Nova Hedwigia 30:149-279. 

Collins, G. B., and R. G. Kalinsky. 1977. Studies on Ohio Diatoms: I. Diatoms of the Scioto 

River Basin. II. Referenced Checklist of Diatoms from Ohio. Bull. of the Ohio Biological 

Survey-New Series 5(3). 

Cumming, B. F., J. P. Smol, J. C. Kingston, D. F. Charles, H. J. B. Birks, K. E. Camburn, S. S. 

Dixit, A. J. Uutala, and A. R. Selle. 1992. How much acidification has occurred in 

Adirondack region lakes (New York, USA) since preindustrial times? Canadian Journal 

of Fisheries and Aquatic Sciences 49:128-141. 

Cumming, B. F., S. E. Wilson, R. I. Hall, and J. P. Smol. 1995. Diatoms from British Columbia 

(Canada) lakes and their relationship to salinity, nutrients and other limnological 

variables. Bibliotheca Diatomologica 31:1-207. 

Edlund, M. B. 2005. Using diatom-based analysis of sediment records from central Minnesota 

lakes for TMDL and nutrient criteria development. Final report to the Minnesota 

Pollution Control Agency. 

Edlund, M. B., and J. C. Kingston. 2004. Expanding sediment diatom reconstruction model to 

eutrophic southern Minnesota lakes. Final report to Minnesota Pollution Control Agency, 

CFMS Contract No. A45276. 

Elias, J., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol for inland lakes, 

Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. Natural 

Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. National Park 

Service, Fort Collins, Colorado.
Diatom Monitoring Protocol, Version 1.0 August 2008 

20 

Fritz, S. C., B. F. Cumming, F. Gasse, and K. Laird. 1999. Diatoms as indicators of hydrologic 

and climatic change in saline lakes. Pages 41-72 In Stoermer, E. F., and J. P. Smol, 

editors. The Diatoms: Applications for the environmental and earth sciences, Cambridge 

University Press, Cambridge, United Kingdom. 

Fallu, M. -A., N. Allaire, and R. Peinitz. 2000. Freshwater diatoms from northern Québec and 

Labrador (Canada). Species-environment relationships in lakes of boreal forest, foresttundra and tundra regions. Bibliotheca Diatomologica 45:1-200. 

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20. 

Hustedt, F. 1927-1966. Die Kieselalgen Deutschlands, Österreichs und der Schweiz mit 

Berücksichtigung der übrigen Länder Europas sowie der angrenzenden Meeresgebeite. in 

Dr. L. Rabenhorst's Kryptogramen-Flora von Deutschland, Österreich und der Schweiz. 

Band VII. Teil 1: Lieferung 1, seite 1-272, 1927: Lieferung 2, seite 273-464, 1928: 

Lieferung 3, seite 465-608, 1929: Lieferung 4, seite 609-784, 1930: Lieferung 5, seite 

785-920, 1930: Teil 2: Lieferung 1, seite 1-176, 1931: Lieferung 2, seite 177-320, 

1932: Lieferung 3, seite 321-432, 1933: Lieferung 4, seite 433-576, 1933: Lieferung 5, 

seite 577-736, 1937: Lieferung 6, seite 737-845, 1959: Teil 3: Lieferung 1, seite 1-160, 

1961: Lieferung 2, seite 161-348, 1962: Lieferung 3, seite 349-556, 1964: Lieferung 4, 

seite 557-816, 1966. Leipzig, Akademische Verlagsgesellschaft Geest und Portig K.-G. 

 

Hustedt, F. 1930. Die Süsswasserflora Mitteleuropas. Heft 10. 2nd Edition. Bacillariophyta 

(Diatomeae). A. Pascher (ed.) Verlag von Gustav Fischer, Germany. 

Köster, D., J. M. J. Racca, and R. Peinitz. 2004. Diatom-based inference models and 

reconstructions: methods and transformations. Journal of Paleolimnology 32:23-246. 

Krammer, K., and H. Lange-Bertalot. 1986. Bacillariophyceae. 1. Teil: Naviculaceae. in Ettl, H., 

J. Gerloff, H. Heynig, and D. Mollenhauer. (eds) Süsswasser flora von Mitteleuropa, 

Band 2/1. Gustav Fischer Verlag: Stuttgart, New York. 

Krammer, K., and H. Lange-Bertalot. 1988. Bacillariophyceae. 2. Teil: Bacillariaceae, 

Epithemiaceae, Surirellaceae. in Ettl, H., J. Gerloff, H. Heynig, and D. Mollenhauer. 

(eds) Süsswasserflora von Mitteleuropa, Band 2/2. VEB Gustav Fischer Verlag: Jena. 

Krammer, K., and H. Lange-Bertalot. 1991a. Bacillariophyceae. 3. Teil: Centrales, 

Fragilariaceae, Eunotiaceae. in Ettl, H., J. Gerloff, H. Heynig, and D. Mollenhauer. (eds) 

Süsswasserflora von Mitteleuropa, Band 2/3. Gustav Fischer Verlag: Stuttgart, Jena. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

21 

Krammer, K., and H. Lange-Bertalot. 1991b. Bacillariophyceae. 4. Teil: Achnanthaceae, 

Kritische Ergänzungen zu Navicula (Lineolatae) und Gomphonema, 

Gesamtliteraturverzeichnis Teil 1-4. In Ettl, H., G. Gärtner, J. Gerloff, H. Heynig, and D. 

Mollenhauer. (eds) Süsswasserflora von Mitteleuropa, Band 2/4. Gustav Fischer Verlag: 

Stuttgart, Jena.. 

Lafrancois, B. Moraska, and J. Glase. 2005. Aquatic studies in National Parks of the upper Great 

Lakes States: past efforts and future directions. Water Resources Division Technical 

Report, NPS/NRWRD/NRTR-2005/334. National Park Service, Denver, Colorado. 

Magdalene, S., D. R. Engstrom, and J. Elias. 2008. Large rivers water quality monitoring 

protocol, Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. 

NPS/GLKN/NRR—2008/060. National Park Service, Fort Collins, Colorado. 

Patrick, R., and C. W. Reimer. 1966. The diatoms of the United States, exclusive of Alaska and 

Hawaii, Volume 1-Fragilariaceae, Eunotiaceae, Achnanthaceae, Naviculaceae. Academy 

of Natural Sciences of Philadelphia Monograph No. 13. 

Patrick, R., and C. W. Reimer. 1975. The diatoms of the United States, exclusive of Alaska and 

Hawaii, Volume 2, Part 1-Entomoneidaceae, Cymbellaceae, Gomphonemaceae, 

Epithemaceae. Academy of Natural Sciences of Philadelphia Monograph No. 13. 

Ramstack, J. M., S. C. Fritz, D. R. Engstrom, and S. A. Heiskary. 2003. The application of a 

diatom-based transfer function to evaluate regional water-quality trends in Minnesota 

since 1970. Journal of Paleolimnology 29:79-94. 

Ramstack, J. M., S. C. Fritz, and D. R. Engstrom. 2004. Twentieth-century water-quality trends 

in Minnesota lakes compared with pre-settlement variability. Canadian Journal of 

Fisheries and Aquatic Sciences 61:561-576. 

Reavie, E. D., and J. P. Smol. 1998. Freshwater diatoms from the St. Lawrence River. 

Bibliotheca Diatomologica 41:1-137. 

Route, B., and J. Elias (editors). 2005. Draft. Long-term ecological monitoring plan: Phase III 

report. U.S. National Park Service, Great Lakes Inventory and Monitoring Network. 

Technical Report GLKN/05/19. 

Smol, J. P., and M. S. V. Douglas. 2007. From controversy to consensus: Making the case for 

recent climate change in the Arctic using lake sediments. Frontiers in Ecology and the 

Environment 5:466-474. 

Stevenson, R. J., and Y. Pan. 1999. Assessing environmental conditions in rivers and streams 

with diatoms. Pages 11-40 In Stoermer, E. F., and J. P. Smol, editors. The Diatoms: 

Applications for the environmental and earth sciences, Cambridge University Press, 

Cambridge, United Kingdom. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

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Stoermer, E. F., and J. P. Smol (editors). 1999. The Diatoms: Applications for the environmental 

and earth sciences. Cambridge University Press, Cambridge, United Kingdom. 
Diatom Monitoring Protocol, Version 1.0 August 2008 

23 

Standard Operating Procedures 

SOP #1: Pre-season Preparation 

SOP #2: Training and Safety 

SOP #3: Using a GPS 

SOP #4: Field Methods 

SOP #5: Cleaning Sediment Samples 

SOP #6: Preparation of Diatom Slides 

SOP #7: Analysis of Slides 

SOP #8: Archiving Sediment and Diatom Slides 

SOP #9: Data Analysis 

SOP #10: Reporting 

SOP #11: Post-season Procedures 

SOP #12: Quality Assurance and Quality Control 

SOP #13: Procedure for Revising the Protocol 

Standard Operating Procedure #1: 

Pre-Season Preparation 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation:

Ramstack, J. M., M. B. Edlund , and D. R. Engstrom. 2008. Standard operating procedure #1, 

Pre-season preparation. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, 

and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great 

Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page ii

Contents 

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

1.0 Introduction..........................................................................................................................1 

1.1 Read the Entire Protocol ......................................................................................................2 

1.2 Prepare Calendar of Planned Field Sampling ......................................................................2 

1.3 Review Checklists of Equipment and Supplies ...................................................................2 

1.4 Confirm/Apply/Renew Research and Collecting Permits ...................................................2 

1.5 Review Sample Collection, Processing, and Documentation..............................................3 

1.6 Clean and Test Equipment...................................................................................................3 

1.7 Vehicle, Boat, and Safety Gear............................................................................................4

1.8 Training and Safety..............................................................................................................4 

1.9 Field Reconnaissance...........................................................................................................4 

1.10 Travel Arrangements ...........................................................................................................4 

1.11 Communicate with Supervisor.............................................................................................4 

1.12 Literature Cited ....................................................................................................................4 

Tables 

 Page 

Table 1. Checklist of activities to be conducted prior to collecting surface 

 sediments for diatom analysis...........................................................................................1 

Table 2. Example of calendar of planned field sampling ...............................................................2 

Table 3. Checklists of equipment and supplies for diatom monitoring ..........................................2 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page iv

Acknowledgements 

This standard operating procedure is based on SOP #1, Pre-season Preparation, by Axler et al. 

(2008), from the Water Quality Monitoring Protocol for Inland Lakes (Elias et al. 2008).
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 1

1.0 Introduction

Prior to the field season, many preparations must be completed to ensure sampling can be 

undertaken according to schedule. The field season for collecting surface sediment samples for 

diatoms from the Great Lakes Network parks is generally late summer/early fall. Coordination 

with personnel from the inland lakes water quality monitoring program will be necessary 

because surface sediment samples will be collected during the final inland lakes monitoring of 

the year. All details for the season should be planned well in advance. Field preparations should 

begin in January to allow enough time to order new supplies and equipment, as needed. Table 1 

provides a checklist and general guidance for activities conducted prior to sampling. Many of 

these activities are discussed in more detail in other SOPs. 

Table 1. Checklist of activities to be conducted prior to collecting surface sediments for diatom 

analysis. 

 Pre-Sampling Activities Checklist. Date: 

Prepare calendar of planned field trips 

Includes sampling dates, locations, and personnel. 

It will be necessary to coordinate with personnel 

from the inland lakes water quality monitoring 

program. 

Review sampling methods to determine 

if revision is needed 

Check web reference to see if method has been 

updated from version currently used 

Review checklists of equipment and 

supplies required; prepare list of items 

to be ordered 

Check each SOP for detailed equipment lists; check 

expiration dates of chemicals 

Order supplies 

Includes specimen cups, centrifuge tubes, 

chemicals for sediment sample cleaning, 

microscope slides and coverslips, slide mounting 

medium 

Clean and test equipment; charge or 

replace batteries as needed 

Includes surface sediment corer, camera, GPS unit, 

depth finder, cell phone or radio 

Obtain permission for site access, if 

necessary 

Confirm research and collection permits 

for in-park sites 

Check field vehicle and boat for safety 

equipment and supplies Includes flares, flashlight, extra specimen cups, etc. 

Update field folder Include maps, site information, field forms, 

sampling procedures 

Prepare headers on field data forms, and 

specimen cup labels 

Header information should be cross-checked with 

metadata to permit entry into NPSTORET 

Review sample collection, processing, 

and documentation information 

Includes methods, sample collection and processing 

procedures, and quality control samples 

Make travel reservations and 

arrangements as needed 

Provide supervisor with field trip and 

call-in (check-in) schedule 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 2

1.1 Read the Entire Protocol 

Periodically read through the entire protocol, including all standard operating procedures (SOPs). 

Be sure to understand the purpose for which the various types of data will be collected and 

review the SOPs for the types of measurements and samples needed. Be alert for portions of the 

protocol or SOPs that may be in need of revision, and bring them to the attention of the 

appropriate supervisor. 

1.2 Prepare Calendar of Planned Field Sampling

Well in advance of the field season, prepare a calendar of sampling dates for the entire season. 

Coordinate with personnel from the inland lakes water quality monitoring program because the 

surface sediment sampling for the diatom monitoring will be done during the last round of water 

quality sampling of the year. Allow for the possibility of unsuitable weather; sampling may have 

to be postponed. Include the location of sampling, dates, personnel, and any additional relevant 

notes (Table 2). 

Table 2. Example of calendar of planned field sampling. 

Location Sampling Dates Personnel Notes 

Indiana Dunes NL September 15-20 Elias, Wise 

Voyageurs NP October 1-5 Nauertz, Elias 

1.3 Review Checklists of Equipment and Supplies

Checklists help ensure that equipment and supplies will be ordered on time, data collection 

activities will be completed appropriately, and data quality objectives will be met. Review the 

detailed equipment lists that are included with each SOP (Table 3). Note expiration dates on all 

chemicals. Prepare a list of equipment and supplies that must be ordered and present it to the 

project manager. 

Table 3. Checklists of equipment and supplies for diatom monitoring. 

Checklist Location 

Safety equipment SOP #2 

Field supplies and equipment SOP #4 

Laboratory equipment and supplies SOPs #5 and 6 

1.4 Confirm/Apply/Renew Research and Collecting Permits

For sampling stations located within park boundaries, a Research and Collecting Permit must be 

obtained from each park separately before field work can be done. Submit an application or 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 3

renewal application online to: http://science.nature.nps.gov/research/ac/apps/appInstructions. 

Each park has a research coordinator who will issue a permit from that park. For samples that 

will be archived, curatorial paperwork may be required by the parks. Work with the appropriate 

park representative to ensure all necessary archival forms are completed. 

1.5 Update Field Folder

Field folders should contain reference information relevant to each sampling station, including 

maps of site locations and sampling collection and processing procedures. The field folder 

should be taken along on each sampling trip. Each year, prior to the sampling season, the field 

folder for each site should be reviewed and the following information updated as needed: 

• Location of sample-collection sites. Review field notes for any indication that the 

location for sample collection may need revision. Update protocol if necessary.

• Name of landowner, tenant, or other responsible party. If the site is located on private 

land, ownership may change. Verify.

• Current copy of research and collection permits (if site is located within NPS 

boundaries). Check dates on permits. Renew/apply as described above.

• Site access instructions (for example, call owner or site operator before arrival at site, 

obtain key to unlock security gate). Confirm contact person, procedure, and phone 

numbers.

• Photographs to document site conditions. Take new digital photographs annually.

• Maps to site (state and local). Review map for accuracy; update if necessary.

• Safety information (SOP #2). Verify/update “Medical Information Form for Field 

Personnel” and “Emergency Contact Form.”

• Field forms, including data collection field forms and specimen cup labels. Prepare as 

much of the field forms as possible in advance (see SOP #4, Appendix A for a field data 

sheet). For each station, complete the header information, including the park code, lake 

name, date, etc. Place enough field forms in field folder to last the entire field season.

• Ensure that copies of the current field procedures are included in the field folder. Copies 

of procedures should be on waterproof paper. Use tabs to identify each procedure for ease 

of access while conducting field activities. 

1.6 Clean and Test Equipment

Clean and test all sampling equipment, including surface corer, depth finder, camera, and GPS 

unit. Start each new field season with fresh batteries and replace spares from the field tool kit. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #1, page 4

1.7 Vehicle, Boat, and Safety Gear

Check maintenance schedule of field vehicle and arrange maintenance, if needed. Check boats 

and vehicle for safety equipment such as flares, spare tires, triangles, cones, and first aid kit. 

Prepare a list of supplies needed and present list to supervisor. If using a trailer, ensure that taillights are in working order. Check that the field tool-kit is complete and replace tools, as needed. 

1.8 Training and Safety

Keep current with training and the laboratory requirements associated with your data collection 

activities. New technicians will need basic skills training, including hands-on training and pilottesting of equipment. 

1.9 Field Reconnaissance

Field reconnaissance trips will not be necessary because water quality sampling will have 

occurred at least twice at each site before the surface sediment sample is collected. Be sure to 

check with personnel from the inland lakes water quality monitoring program to get information 

on boat access, road or trail closings, and any site access peculiarities. 

1.10 Travel Arrangements 

Make travel arrangements. Because hotel and campground reservations may be difficult-toimpossible to obtain at certain times of the year, it is important to review the sampling schedule 

and plan ahead. Submit park housing requests well in advance of the sampling season. 

1.11 Communicate with Supervisor 

Ensure the project manager is informed of supply needs, problems with equipment, changes in 

sampling schedule, changes in sampling site conditions, and other needs that may have an impact 

on the program budget, data collection, schedule, or sampling design. 

1.12 Literature Cited

Axler, R., E. Ruzycki, and J. E. Elias. 2008. Standard operating procedure #1: Pre-season 

preparation. In Elias, J.E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring 

protocol for inland lakes, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. NPS/MWR/GLKN/NRTR—2008/109. National Park Service, Fort 

Collins, Colorado. 

Elias, J. E, R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol for inland lakes. 

Version 1.0. National Park Service, Great Lakes Inventory and Monitoring Network. 

NaturalResources Technical Report NPS/MWR/GLKN/NRTR—2008/109. National Park 

Service, Fort Collins, Colorado.
Standard Operating Procedure #2: 

Training and Safety 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #2, 

Training and safety. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. 

E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

2.0 Introduction..........................................................................................................................1 

2.1 Pre-Season Classroom Training...........................................................................................1 

 2.1.1 Understanding the Protocol and Standard Operating Procedures...............................1 

 2.1.2 First Aid and Cardio-Pulmonary Resuscitation (CPR)...............................................1 

2.2 Hands-On Training ..............................................................................................................1 

 2.2.1 Use of the Weigner Corer ...........................................................................................1 

 2.2.2 Use of a Global Positioning System (GPS) ................................................................2 

 2.2.3 Field Data Sheets ........................................................................................................2 

 2.2.4 Boat Training ..............................................................................................................2 

2.3 Safety Procedures.................................................................................................................2 

 2.3.1 USGS Field Manual....................................................................................................2 

 2.3.2 Basic Safety Preparation.............................................................................................3 

 2.3.3 Medical Forms and Safety Equipment Checklists......................................................3 

 Emergency Contact Form ...........................................................................................4 

 Medical Information Form..........................................................................................5 

 General Safety Equipment Checklist..........................................................................6 

 Personal Protective Equipment Checklists .................................................................7 

 Checklists for Vehicles ...............................................................................................8 

 Watercraft Checklists..................................................................................................9 

2.4 Literature Cited ..................................................................................................................10 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page iv

Acknowledgements 

This SOP is based on SOP #2, Training and Safety, by Elias 2008, from the Water Quality 

Monitoring Protocol for Inland Lakes (Elias et al. 2008). 

The safety related portions of this standard operating procedure were adapted from the Greater 

Yellowstone Network’s SOP on safety (O’Ney 2005), with heavy reliance on the U.S. 

Geological Survey’s manual for collecting water quality data (Lane and Fay 1997). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 1

2.0 Introduction

Prior to collecting surface sediment samples in the field, the field crew members must be trained 

in the techniques and procedures that will be used throughout the season. Familiarity with the 

protocol and standard operating procedures (SOPs), as well as with boats, equipment, and basic 

safety standards, are critical to the success of the diatom monitoring program. The crew must be 

trained in specific safety procedures to ensure their safety and that of others. 

The project manager will conduct or arrange for all necessary training prior to the field season. 

2.1 Pre-Season Classroom Training

It is desirable to begin training well before the field season begins to allow adequate time for 

thorough understanding of field and laboratory procedures. 

2.1.1 Understanding the Protocol and Standard Operating Procedures 

Reading and understanding the entire protocol and all SOPs are crucial prior to initiating field 

work. The project manager will allow adequate time for all field crew members to complete this 

step to ensure success of the project. Field and laboratory related SOPs will also be covered as 

part of the hands-on training, described below. 

2.1.2 First Aid and Cardio-Pulmonary Resuscitation (CPR) 

Training in the basic medic/first aid and Heartsaver AED, which includes CPR and use of an 

automated external defribrillator (AED), is required for all crew members and will be paid for by 

the Network. Acceptable training should be through the American Red Cross or American Heart 

Association. Certification is valid for two years. Training and certification should be acquired 

prior to the field season. 

2.2 Hands-On Training

A variety of hands-on training and practice prior to the first sampling period will help ensure 

high quality sample collection. Familiarity with the use and maintenance of equipment, 

procedures for collecting and processing sediment samples, techniques for cleaning field and 

laboratory equipment, and safe use of watercraft are essential to the success of the diatom 

monitoring project. Field crew leaders are required to complete all of the following training; 

other field crew members should also complete the training, if possible, although it is not 

required. 

2.2.1 Use of the Wiegner Corer 

The Wiegner corer is used for the collection of a surface sediment sample. Refer to SOP #4 for 

instructions on use and maintenance of the corer. 

Crew members will have the opportunity to practice the skills learned prior to the actual 

sampling until they are comfortable with the use of the corer. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 2

2.2.2 Use of a Global Positioning System (GPS) 

Location information must be gathered via GPS for each site during each visit. Training in the 

use of a GPS will include navigation to a known location, acquiring location information, storing 

data, and downloading data. Details on the use of a GPS can be found in SOP #3. 

2.2.3 Field Data Sheets 

In addition to collecting a surface sediment sample, a field data sheet must be completed. Prior to 

the field season, the field crew will receive training in how to properly complete the field data 

sheet. 

2.2.4 Boat Training 

Prior to operating a NPS boat or canoe, training and certification are required. Since the diatom 

sampling will occur in conjunction with the last inland lakes water quality sampling of the year, 

the crew leader for the inland lakes project must receive the training and obtain certification; it is 

highly desirable for the remaining crew members to do so as well. 

2.3 Safety Procedures

Safety of field personnel should always be the first concern in conducting a sampling program 

and in the selection of sampling sites. Numerous safety issues and concerns are associated with 

implementing a program that includes fieldwork and sampling. Field personnel routinely come 

into direct and indirect contact with waterborne pathogens, chemicals, and potentially hazardous 

plants and animals. Fieldwork requires an awareness of potential hazards and knowledge of basic 

safety procedures. Advanced planning can reduce or eliminate many safety hazards. 

2.3.1 USGS Field Manual 

This SOP is meant to be used in conjunction with Chapter A9 of the USGS National Field 

Manual (Lane and Fay 1997), which contains more complete information about potential hazards 

that personnel may encounter during fieldwork in aquatic environments. The procedures in 

Chapter A9, when implemented properly, will help ensure the safety and health of field crew 

members. A copy of this manual is provided to the field crew and may be downloaded from 

http://water.usgs.gov/owq/FieldManual/Chap9/content.html and taken to the field as a reference. 

Topics addressed in the USGS document include: 

• General references for federal policies and Department of Interior (DOI) safety 

guidelines 

• Safety policies you are required to know and follow under the Occupational Safety and 

Health Act (OSHA), Environmental Protection Agency (EPA), and Department of 

Transportation (DOT) 

• Understanding and implementing a job hazard analysis (JHA) 

• Requirements related to the use of personal protective equipment (PPE) on the job 

• Safety training and certification requirements 

• Safety issues associated with transportation and operation of vehicles (road vehicles and 

trailers, watercraft, aircraft, etc.) used to reach sampling sites 

• Surface water activities (e.g., wading, working from bridges, boats and cableways, etc.) 

• Working around machinery, pumps, and other equipment 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 3

• Proper use, handling, transport, storage, and disposal of chemicals 

• Handling of contaminated water and limiting exposure to yourself and others 

• Environmental conditions caused by extremes in temperature; sun exposure; threats 

posed by storms, floods, fire, snow, ice, and various animals and plants 

In addition to consulting the USGS manual, the field crew should contact individual park’s 

safety officers or resource managers for information on park radio safety procedures and local 

problems and issues, such as dangerous or nuisance animals (e.g., black bears at VOYA, red fox 

at ISRO), insect- and tick-borne diseases (e.g., Lyme disease, encephalitis, West Nile disease), 

and other issues specific to each park. 

2.3.2 Basic Safety Preparation 

Basic preparations should become routine before every sampling activity. At a minimum, 

complete a trip plan for each field trip, and leave it at the designated location in the office. The 

trip plan should include the following information: 

• Field trip participants, including guests and observers, with emergency contact 

information 

• Departure and expected return time(s) and date(s) 

• Hotel and campground contact information (for overnight trips) 

• Basic itinerary, including where and when sampling will occur 

• Phone numbers for cellular phones or radio frequencies 

Fieldwork should be done in pairs. Always carry a park radio, or if reception is known to be 

available, a cellular telephone. Carry basic safety equipment, including a first aid kit, flashlight, 

boots, rain gear, antibacterial soap or hand cleaner, matches or lighter, etc. Be aware of changing 

weather conditions and the potential for storms. Be aware of potential hazards at a monitoring 

site. Carry general safety information in each vehicle or boat, including: 

• Basic first aid protocols 

• Emergency phone numbers 

• Locations of emergency facilities (hospitals, police and fire departments, U.S. Coast 

Guard) 

• Maps of the park, surrounding area, and nearest city 

2.3.3 Medical Forms and Safety Equipment Checklists 

The following pages contain medical forms and equipment checklists for field personnel 

(adapted from Lane and Fay 1997). Prior to the field season, complete as much of the medical 

information as possible. Confirm all contact information annually. Medical information sheets 

should be completed for each individual venturing into the field. 

Checklists are helpful for ensuring that personnel have the appropriate safety equipment 

available during field trips. Field crew members should consider their specific needs and should 

customize the checklists as necessary. The field crew and project manager will discuss the 

checklists and determine which items are necessary. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 4

Emergency Contact Form for: (name)__________________________________

Emergency Contacts

#1 Name: __________________________ Relationship: _____________________ 

Phone: (home) (work) _________________________________________________ 

#2 Name: __________________________ Relationship: _____________________ 

Phone: (home) (work) _________________________________________________ 

Great Lakes Network Contacts

Network Office _715-682-0631 x25___ Mississippi NRRA ________________ 

Apostle Islands ___________________ Pictured Rocks NL ________________ 

Grand Portage NM ________________ St. Croix NSR ___________________ 

Indiana Dunes NL_________________ Sleeping Bear Dunes NL ___________ 

Isle Royale NP ___________________ Voyageurs NP ___________________ 

Local Emergency Contacts (or call 911)

Hospital Phone: ______________________________________________________ 

Address: ____________________________________________________________ 

Other medical facility (24-hour care) Phone: _______________________________ 

Address: ____________________________________________________________ 

Police: _____________________________________________________________ 

Fire: _______________________________________________________________ 

Utility: _____________________________________________________________ 

Health Information Centers 

Centers for Disease Control: ____________________________________________ 

Information Hotline: __________________________________________________ 

Other: _____________________________________________________________ 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 5

Medical Information Form (retain in office)

Employee name: ___________________________ Home phone: ___________________ 

Treatment preference: medical ________________ other (specify) __________________ 

Doctor: __________________________________ Phone: ________________________ 

Other emergency contact: ____________________ Phone: ________________________ 

Allergies and other medical 

conditions Medications being taken Medications to avoid 

 

Relevant medical history: 

Special instructions: 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 6

General Safety Equipment Checklist

√ Basic Safety Equipment Checklist 

 Waders, hip boots, rubber knee boots 

 Personal flotation device (PFD) 

 First aid kit 

 Fire extinguisher 

 Flashlight and spare batteries 

 Park radio and cellular phone 

 Rain gear 

 Hat, sunscreen, and sunglasses 

 Drinking water or sports drinks 

 Tool box with basic tools 

 Antibacterial soap or hand cleaner 

 List of emergency phone numbers and office contacts 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 7

Personal Protective Equipment Checklists 

Personal Protective Equipment (PPE) must be selected based on the hazards likely to be 

encountered. The Great Lakes Network is required to supply appropriate PPE, and field 

personnel are required to use it. 

√ Chemical and disease protection

 Aprons 

 Eye/Face splash guards 

 Gloves (vinyl and/or latex or nitrile) 

 Protective suits 

 Respirators (certification required for use) 

 

√ Weather and UV protection

 Boots 

 Fluids (e.g., water, sports drinks) 

 Hat with a brim 

 Insect repellent 

 Rain gear 

 Sunglasses 

 Sunscreen 

 Temperature-modifying clothing 

 Work gloves 

√ Flotation and reflective protection 

 Orange flotation vests and jackets 

 Safety harness 

√ Protection for working around boat motors 

 Hearing protection 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 8

Checklists for Vehicles

√ Communications and Instructions

 Field folder (including maps, emergency phone numbers for medical facilities, 

office contacts, family contacts) 

 Cellular phone/communication equipment (check that the service is operational for 

the area to be traveled) 

√ First aid and protective equipment

 Complete change of clothes (stored in dry area) 

 Fire extinguisher (safely secured) 

 First aid kit and manual (check for missing or old, expired items and replace if 

necessary) 

 Orange reflective vest 

√ Miscellaneous equipment

 Bungie cords (to secure loose articles) 

 Flagging 

 Flares 

 Flashlight (including fresh batteries) 

 Flexible hose (to vent exhaust away from vehicle) 

 Safety cones 

 Tool kit 

 U.S. Geological Survey TWRI Book 9 Chapter A9 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 9

Watercraft Checklists

√ Instructions and navigation

 Field folder, with sampling plans 

 Charts and maps 

 Compass 

 Depth finder 

 Dead-man’s switch 

 Navigation lights 

√ Distress and external communication

 Radio (VHF, AM, FM, and WEATHER) 

 Special lighting/flagging (if boat activities might pose a hazard to the public, such 

as tag line measurements) 

 Visual distress signals (Coast Guard approved) 

 Whistles or horns 

 Type IV throwable rescue device 

 Personal flotation devices for each passenger (Coast Guard approved) 

 Anchor and lines (spare) 

 Bucket for use as a bailer 

 Paddle (extra paddle for each canoe or rowboat) 

 First aid kit (Coast Guard approved) 

 Flashlights and batteries 

 Fire extinguishers 

 Spare parts (anchor, fuel, propeller, extra lines, cotter pin, starter cord) 

 Tool and repair kits 

 Extra clothes (hat, foul-weather gear) 

 Food and water 

 Sunscreen 

 Conversion factors and abbreviations 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #2, page 10

2.4 Literature Cited

Elias, J. E. 2008. Standard operating procedure #2: Training and safety. In Elias, J. E., R. Axler, 

and E. Ruzycki. 2008. Water quality monitoring protocol for inland lakes, Version 1.0. 

National Park Service, Great Lakes Network, Ashland, Wisconsin. Natural Resources 

Technical Report NPS/MWR/GLKN/NRTR—2008/109. National Park Service, Fort 

Collins, Colorado. 

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol narrative for 

inland lakes, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. 

National Park Service, Fort Collins, Colorado. 

Lane, S. L., and R. G. Fey. 1997. Ch A9: Safety in field activities. In National field manual for 

the collection of water-quality data: U.S. Geological Survey techniques of waterresources investigations, Book 9. Available from: http://pubs.water.usgs.gov/twri9A9.

O’Ney, S. E. 2005. Standard operating procedure #3: Safety and health, Version 1.0. In

Regulatory water quality monitoring protocol, Version 1.0, Appendix E. Bozeman (MT): 

National Park Service, Greater Yellowstone Network. 
Standard Operating Procedure #3: Using a GPS 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #3, 

Using a GPS. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. E. 

Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

3.0 Introduction..........................................................................................................................1 

3.1 Role of GPS in Collecting Samples for Diatom Analysis ...................................................1 

3.2 Using Recreational-Grade GPS Units..................................................................................2 

3.3 QA/QC .................................................................................................................................2 

3.4 Literature Cited ....................................................................................................................3 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise Description 

of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page iv

Acknowledgements 

This standard operating procedure is adapted from SOP #3, Using the Global Positioning 

System, by VanderMeulen, D., and M. Hart (2008), in the Water Quality Monitoring Protocol for 

Inland Lakes (Elias et al. 2008). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 1

3.0 Introduction

This Standard Operating Procedure (SOP) provides guidance on some of the more common 

operations associated with global positioning systems (GPS) units. Although most GPS units are 

capable of multiple functions, only those operations relevant to the diatom monitoring protocol 

are discussed. 

GPS units currently (2007) used by water quality monitoring staff are the Trimble GeoXT and 

Garmin 76S. The Trimble GeoXT is an example of a mapping-grade GPS unit, while the Garmin 

76S is an example of a recreational-grade unit. Mapping-grade units record data with location 

accuracy ranging from sub-meter to less than five meters. Recreational-grade units generally are 

not as accurate, with spatial accuracy less than 15 meters. Mapping-grade units have greater 

ability to capture spatially referenced metadata (i.e., attributes) than recreational-grade GPS. 

Recreational-grade GPS units are sufficient for diatom monitoring; therefore a discussion of 

mapping-grade units is not included in this protocol (see Vandermeulen and Hart (2007) for a 

detailed discussion of mapping-grade units). 

Due to the rapid development of commercial software and hardware capabilities, it is likely that 

other GPS units or software will be utilized in the future. Therefore, this SOP is meant to act as a 

working document that is updated periodically as new technology becomes available. Although 

nomenclature may differ depending on what hard-software is utilized, this document should 

provide sufficient guidance on the general process of data collection using GPS tools until the 

SOP is revised. It is strongly recommended that water quality monitoring staff obtain unitspecific GPS training prior to deploying in the field. The training should include hands-on use, 

and should be designed to test all appropriate functions and operations prior to going out into the 

field. 

Additionally, this SOP is not intended to be exhaustive or simply a regurgitation of operating 

manuals, but a document that might be carried into the field or periodically reviewed by field 

technicians and project leaders. The objective of this document is to summarize GPS use 

guidelines applicable to the diatom monitoring efforts for lakes in GLKN parks. 

3.1 Role of GPS in Collecting Samples for Diatom Analysis

GPS units are primarily used in the following ways to support diatom monitoring on lakes: 

1) For diatom monitoring on lakes, navigating to and sampling at the position location of 

previously determined sampling sites is accomplished through a combination of: 

a. Using GPS units to navigate to previously established GPS point locations 

b. Using hardcopy maps and written notes with site descriptions (where available) 

c. Field experience of NPS staff conducting the monitoring 

2) Accurate station location descriptions must be recorded and carefully followed by 

sampling personnel on subsequent field visits. Therefore, once at the sampling location, 

GPS equipment is used to obtain the sampling coordinates, which allows the user to 

spatially reference diatom monitoring data to specific geo-referenced locations. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 2

Note that the diatom monitoring efforts will be coordinated with the final field sampling of the 

season for the inland lakes water quality monitoring program. Therefore, the field crew from the 

inland lakes monitoring project will have already visited the sites and will be able to assist with 

navigating to the correct sampling location. 

3.2 Using Recreational-Grade GPS Units 

Recreational-grade GPS units can be used to acquire location information (generally points) 

when spatial accuracy is not paramount to the project. Recreational GPS units do not have data 

dictionaries for storing attribute information with the point location. However, using a 

recreational-grade unit to capture a waypoint at each sampling site is a reliable means to verify 

the correct sampling site has been reached, even if a GPS location is not needed. 

Personnel that employ recreational-grade GPS units should become familiar with GLKN GPS 

collection procedures and relevant manufacturer’s user guides and operating manuals before 

GPS operation. For example, prior to using a Garmin 76S (recreational-grade) GPS unit, the 

following documents should be reviewed: 

• GPSMAP 76S Quick Start Guide 

• GPSMAP 76S Owner’s Manual and Reference Guide 

• Garmin MapSourceTM User’s Manual and Reference Guide 

The appropriate user guide and operating manual should be taken into the field during sampling 

in case the field crew needs to refer to them. 

Planning

The sediment sample for diatom analysis will be collected at the same location and at the same 

time as the final water sampling of the season for the inland lakes monitoring program. Enter the 

site location coordinates onto a GPS unit prior to departure to the field and use the GPS to 

navigate to the site. Some recreational grade GPS units have the ability to store and display 

topographic maps that can aid in navigation. Printed topographic maps of the waypoint locations 

can also be used to maximize field time and efficiently navigate between waypoints. 

Data Collection

Location data are captured by recreational-grade GPS units as waypoints. When taking a 

waypoint, enter the site ID or site designation in the text field provided. Collect reference points 

at regular intervals as good practice. These reference point positions should be taken at known 

locations (e.g., trailheads, parking lots, stream confluences) which can later be used in GIS to 

check the accuracy of waypoint data. Write the site location coordinates on the field data sheet as 

a backup, even if the data will be downloaded electronically. 

3.3 QA/QC

Long-term monitoring is only valuable if users have confidence in the data. Efforts to detect 

trends and patterns in ecosystem processes require high-quality, well-documented data that 

minimize error and bias. Data of inconsistent or poor quality can result in loss of sensitivity and 

lead to incorrect interpretations and conclusions. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #3, page 3

NPS Director’s Order #11B: Ensuring Quality of Information Disseminated by the National Park 

Service (www.nps.gov/policy/DOrders/11B-final.htm) specifies that information produced by 

the NPS must be of the highest quality and based on reliable data sources that are accurate, 

timely, and representative of the most current information available. Therefore, GLKN will 

establish and document procedures for quality assurance (QA) and quality control (QC) to 

identify and reduce the frequency and significance of errors at all stages in the data life cycle. 

Under these procedures, the progression from raw data to verified data to validated data implies 

increasing confidence in the quality of those data. Quality assurance and quality control 

procedures will document internal and external review processes and include guidance for 

addressing problems with data quality. 

Examples of general QA/QC practices include: 

• Standardized field data collection forms 

• Proper calibration and maintenance of equipment 

• Training of field crew and data technicians 

Examples of QA/QC practices pertaining to the use of a GPS unit include: 

• Ensure that GPS-related software is periodically updated as it becomes available and has 

been tested. 

• Record location data on field data forms as well as with the GPS unit. 

• For each monitoring station, compare location positions for different sampling events, 

including the position recorded during establishment of the monitoring station. This will 

allow for an assessment of position accuracy over time. 

• Ensure that the appropriate coordinate system is used when collecting and exporting data. 

3.4 Literature Cited

VanderMeulen, D., and M. Hart. 2008. Standard operating procedure #3, Using the Global 

Positioning System. In Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality 

monitoring protocol for inland lakes, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. Natural Resources Technical Report 

NPS/MWR/GLKN/NRTR—2008/109. National Park Service, Fort Collins, Colorado. 

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol for inland lakes, 

Version 1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. Natural 

Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. National Park 

Service, Fort Collins, Colorado.

Standard Operating Procedure #4: 

Field Methods 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008 

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #4, 

Field methods. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. E. 

Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page ii 

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

4.0 Introduction..........................................................................................................................1 

4.1 Where and When to Sample ................................................................................................1 

 4.1.1 Where to Sample.........................................................................................................1 

 4.1.2 When to Sample..........................................................................................................1 

4.2 Equipment and Supplies ......................................................................................................1 

4.3 Field Procedures...................................................................................................................1 

4.3.1 Operating the Wiegner Corer and Collecting a Surface Sample ................................2 

4.4 Sample Handling..................................................................................................................5 

4.5 Decontamination of Equipment Between Lakes..................................................................5 

4.6 Quality Assurance and Quality Control...............................................................................5 

4.7 Literature Cited ....................................................................................................................6 

Appendix A. Field data sheet for diatom monitoring ......................................................................7 

Tables

 Page 

Table 1. Field supplies and equipment checklist required for diatom monitoring ..........................2 

Figures 

 Page 

Figure 1. The Wiegner surface corer ...............................................................................................4 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page iii 

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page iv 

Acknowledgements 

Portions of this standard operating procedure were based on or modified from SOP #6, 

Procedures for Field Water Column Measurements and Water Sampling, by Axler et al. (2008), 

from the Water Quality Monitoring Protocol for Inland Lakes (Elias et al. 2008). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 1 

4.0 Introduction

Experience with and knowledge of the sampling equipment and the collection and storage of 

sediment samples for subsequent laboratory analysis is critical for collecting data of high quality. 

It is highly recommended that new personnel receive training on the operation of the Wiegner 

corer from an experienced technician. To ensure that consistent, high quality samples are 

collected, always: 

• Maintain a permanent log book for each field instrument for recording problems and 

repairs. Review the log book before leaving for the field. 

• Test each piece of equipment before leaving for the field. 

• Follow quality assurance/quality control procedures. Such protocols are mandatory, and 

include practicing good field procedures and implementing quality-control checks. 

4.1 Where and When to Sample

4.1.1 Where to Sample

Sampling locations for the diatom monitoring program will follow the sites selected for the 

GLKN water quality monitoring program (Elias et al. 2008; the deepest part of the lake is being 

used as the primary sampling site). Therefore, the GPS location of the water quality monitoring 

sample site for each lake, as well as the depth at each site, must be obtained before going into the 

field. 

When on the lake, use the GPS in conjunction with the handheld depth finder to navigate to the 

appropriate location in the lake basin (see SOP #3 Using a GPS). 

4.1.2 When to Sample

Sampling for the diatom monitoring program will be conducted in conjunction with the GLKN 

water quality monitoring program. Collect sediment samples during the final water quality 

monitoring event of the season, which will usually be in September or October. 

4.2 Equipment and Supplies

Refer to the checklist of supplies and equipment needed for field sampling (Table 1) 

conscientiously prior to each sampling trip. Keep on hand all necessary forms, logbooks, and 

field data sheets. Copy field data sheets onto waterproof paper. See Appendix A for an example 

of a blank field data sheet. 

4.3 Field Procedures

Use the lake bathymetry map (if available) to orient yourself in the lake basin and use the GPS 

unit, in conjunction with the handheld depth finder, to navigate to the sampling location (see 

SOP #3, Using a GPS). Include a note on the water quality monitoring field data sheet when a 

sediment sample was collected in addition to completing a diatom monitoring field data sheet. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 2 

Table 1. Field supplies and equipment checklist required for diatom monitoring. 

Field notebook, pencils, and pen (indelible ink) 

Sharpie® or other permanent markers 

Field data sheets (with header information completed) on waterproof paper 

Specimen cups (with appropriate labels) for collection of surface sediment 

Spatulas, pipettes, Kimwipes®, zip lock bag for garbage 

Tool kit for repairing boat motor and sampling equipment 

Weather radio or barometer 

Extra batteries for all equipment (GPS, etc.) 

Rain gear 

Personal flotation device(s) 

Field trip itinerary 

Cellular phone and/or park radio 

Wiegner corer and adequate length of line 

Anchor and line 

Cooler with ice or cold packs 

Digital camera with extra flash cards, fully charged battery, and extra batteries 

Handheld depth finder 

Map(s); lake bathymetry 

Global positioning system (GPS) and user manual 

GPS coordinates of sampling location (from water quality monitoring program) 

4.3.1 Operating the Wiegner Corer and Collecting a Surface Sample 

The Wiegner corer falls into the broad category of gravity corers. It is lowered in the set or open 

position into the lake sediments until penetration stops. The line to the boat is allowed to go 

slack, and upon retrieval, tension on the line is maintained to create a seal on the core tube. The 

corer recovers approximately the top 20-35 cm of sediment. The recovered core is extruded out 

of the top of the core barrel using the included extruder, tools, and sampling tray (optional). 

1. Take corer out of case. Locate nut driver, spatula for sampling, plastic sectioning tray 

(optional), and sectioning setup (the white PVC “X” on stainless steel rod). Unwrap 

enough line from spool to reach the lake bottom. 

2. Before using the corer, loosen the clamps and remove the black rubber protective piece 

from the top of the corer (this is only to protect the corer during storage, and must be 

removed before the corer is used). 

3. Additional brass plates can be added (or removed) from the corer to increase (or 

decrease) the weight. Increased weight is desirable when coring firm substrates. 

4. Prepare the corer by opening the black stopper and propping it open behind the black 

rubber band. Place the two arms of the small brass clip in the grooves of the PVC sleeve. 

Then pull the rope taut to maintain tension on the line and clip. The corer is now in the 

set position (Figures 1a and b). 

5. Lower the corer into the lake and continue lowering until it reaches AND penetrates the 

sediments. Use a controlled, moderate rate of descent to hit the sediment at about 0.5 m 

sec-1. Do not allow the corer to free fall. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 3 

6. Once the corer has penetrated the sediments and stopped, let the line go slack. The brass 

clip will slide out of the grooves on the white PVC sleeve (Figure 1c), which will allow 

the black stopper to close. While maintaining continuous and steady tension on the line, 

bring the corer back to the surface. As the brass plates break the surface, reach into water 

and cap the bottom of the corer with the palm of your hand. Keep the corer and core 

vertical! 

7. Bring the core and corer into the boat. Set up the sectioning mechanism as illustrated 

(Figure 1d), noting that the stopper is flush with the top of the gray PVC and that the 

small brass pin is inserted into the 3rd or 4th hole from the top of gray PVC. Slide bottom 

of corer across your hand and onto the black stopper. Push the corer down so the black 

stopper slides up into the corer until the core barrel hits the brass pin (Figure 1d). If you 

are using the corer alone, you will want to reach over the side of the boat with the 

sectioning mechanism and slide the stopper directly into the core barrel as the corer 

breaks the surface (skipping using your hand). 

8. Take the nutdriver and loosen the hose clamp that runs around the black rubber cylinder 

near the top of the corer. This will allow the black rubber cylinder and the brass plates to 

be separated from the core tube. 

9. Now you will slide the top of the sediments to the top of the core tube for sectioning. 

Inside one of the arms of the white PVC "X" on the sectioning mechanism is a stainless 

steel bar. As this stainless bar is depressed, the black stopper will slide up into the core 

tube and the sectioning mechanism will slide down the stainless rod. Do this slowly. 

Water will run out of the core tube top and eventually the top of the core will appear at 

the top of the core tube. Slowly align the top of the mud with the top of the core tube. If 

using a sectioning tray, place it over the top of the core tube. 

10. Reach down and move the brass pin down one or two centimeters (depending on how 

much mud you want to sample). Then slide the core tube down till it hits the brass pin 

again. One or two centimeters of sediment will come out of the top of the core tube onto 

the sectioning tray. Or, if you are not using a sectioning tray, move the core flush with the 

top of the tube and use a pipette to remove the top 1 cm (or a pipette cut in half such that 

the bulb portion can be used to scoop out the top 1 cm). If this approach is used, the tube 

must be pre-marked at 1 cm. Then move the core flush again with the top to collect the 

next cm. Scrape (or scoop) the sediment into your pre-labeled sampling cup, cap, and 

place sample in cooler. If additional samples are desired, you can continue to section the 

entire core. 

11. Rinse core tube and sectioning equipment when finished. Reassemble corer using 

nutdriver and prepare for next core. 

Troubleshooting

• Make sure nylon lines threaded through the top of the corer move freely and are not 

wrapped around anything. 

• The stopper on the sectioning mechanism can be tightened or loosened using the wingnut 

to get a good fit and snug travel up and down the core tube. Test the tightness prior to 

collecting the core. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 4 

Figure 1. The Wiegner surface corer. a) The corer in the set position, ready to be deployed. b) 

When deploying the corer, the black stopper must be in the open position, resting against the 

black rubber band. c) The corer being retrieved from the sediments (brass clip has been released 

from the white PVC sleeve, and the line has been pulled taut, allowing the black stopper to close. 

d) The sectioner with the brass pin in place. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 5 

4.4 Sample Handling

Place the sediment sample in a specimen cup that is pre-labeled with the date, lake name, GLKN 

park unit, and the core interval collected (e.g., 0-1 cm). Use a Sharpie marker to label the lid of 

the specimen cup with the lake name and core interval. On the field data sheet, record the GPS 

coordinates of the sampling location, the water depth at the sampling location, and the core 

intervals collected. 

Samples should be placed in a cooler while in the field and then transferred to 4°C laboratory 

storage. Samples should be processed within two weeks of collection. 

Upon return to the office, make a photocopy of the data sheet and send the copy to the contractor 

with the samples. Keep the original data sheet on file at the GLKN office with other field 

datasheets for the same sites. 

 

4.5 Decontamination of Equipment Between Lakes 

As we implement the diatom monitoring protocol we must take precautions against transferring 

aquatic invasive species from one lake to another. Because the diatom sample will be collected 

during the final round of water quality monitoring, decontamination of diatom sampling 

equipment should be coordinated with that of water quality monitoring equipment. The 

procedures for decontamination vary by species and are likely to change over time. Consult Elias 

(2008) for specific details regarding decontamination requirements and procedures. 

Decontamination to prevent the spread of exotic organisms will also prevent against crosscontamination of the equipment by diatom species from another site. 

4.6 Quality Assurance and Quality Control 

Quality assurance protocols are means to ensure data collected are as representative of the 

natural environment as possible. Quality assurance procedures are required in all data collection 

efforts as part of this monitoring protocol. Many of the key elements of quality assurance have 

been included in the SOPs where appropriate, as well as detailed in SOP #12. A summary of 

important QA/QC procedures follows. 

• Field staff must be trained in the use of the Wiegner corer. They will be given ample 

opportunity to practice collecting cores prior to actually collecting a sample. 

• Test the Wiegner corer prior to using it to collect a sample. Ensure it is functioning 

properly. 

• All manually recorded field measurement data will be collected on field forms. Hard and 

electronic copies will be made as soon as possible after sampling and kept at a separate 

location as backup. 

• Complete records will be maintained for each sampling station and all supporting 

metadata will be recorded appropriately. 

• Clean all equipment thoroughly between sampling sites to ensure no cross-contamination. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 6 

4.7 Literature Cited 

Axler, R., E. Ruzycki, and J. E. Elias. 2008. Standard operating procedure #6, Field water 

column measurements and water sampling. In Elias, J. E., R. Axler, and E. Ruzycki. 

2008. Water quality monitoring protocol for inland lakes, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. Natural Resources Technical Report 

NPS/MWR/GLKN/NRTR—2008/109. National Park Service, Fort Collins, Colorado. 

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol narrative for 

inland lakes, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. 

National Park Service, Fort Collins, Colorado. 

Elias, J. E. 2008. Standard operating procedure #5, Decontamination of equipment to remove 

exotic species. In Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring 

protocol for inland lakes, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—

2008/109. National Park Service, Fort Collins, Colorado.
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #4, page 7 

Appendix A. Field data sheet for diatom monitoring. 

NPS GLKN DIATOM MONITORING 

Date: 

Park Unit: 

Lake Name: 

Collector: 

GPS coordinates of 

sampling location 

Water depth at 

sampling location (m) 

Core interval(s) 

collected (e.g. 0-1 cm) 

Notes 

Standard Operating Procedure #5: 

Cleaning Sediment Samples 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008 

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #5, 

Cleaning sediment samples. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page ii 

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

5.0 Introduction..........................................................................................................................1 

5.1 Equipment and Supplies ......................................................................................................1 

 

5.2 Safety Precautions................................................................................................................1 

5.3 Methods................................................................................................................................2 

5.4 Quality Assurance/Quality Control......................................................................................3 

5.5 Literature Cited ....................................................................................................................3 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page iii 

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol SOP, #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page iv 

Acknowledgements 

We consulted Acker et al. (2002) while compiling information for this standard operating 

procedure. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 1 

5.0 Introduction

To accurately identify diatoms at the species level, all cellular organic matter, as well as other 

organic and carbonate material in the sample, must be removed. Removing the organic matter 

will allow the details in the structure of the siliceous cell wall to be visible with light microscopy. 

This protocol describes a method for removing organic material and carbonates from a sediment 

sample. 

5.1 Equipment and Supplies 

Refer to the checklists below and ensure adequate equipment and supplies are on hand for 

cleaning the sediment samples in a safe manner. 

√ Checklist of equipment needed for cleaning sediment samples 

 50 ml NUNC polypropylene fliptop conical centrifuge tubes (NUNC Catalog 

#362697; available through Fisher Scientific, www.fishersci.com/) 

 10% (by volume) reagent grade hydrochloric acid (HCl) 

 30% (by volume) reagent grade hydrogen peroxide (H2O2) 

 De-ionized (DI) water 

 Spatula 

 Permanent marker to label centrifuge tubes 

 Water bath set at 85°C 

 Centrifuge capable of holding 50 ml NUNC centrifuge tubes and spinning at 3500 

rpm 

 Positive-draw fume hood 

√ Checklist of personal protective equipment (PPE) needed for cleaning 

sediment samples 

 Acid-impervious gloves 

 Safety glasses and face shield 

 Laboratory coat or apron, acid resistant 

5.2 Safety Precautions

Personnel are required to wear the PPE listed in Section 5.1 of this SOP while performing this 

procedure. 

Hydrochloric acid (HCl) is used to oxidize carbonates in the sample; HCl is a corrosive acid and 

should be used under a fume hood while wearing safety glasses, gloves, and a lab coat. HCl is a 

corrosive acid; store in a cool, dry, well-ventilated area away from incompatible substances, and 

keep away from heat, sparks, and flame (refer to the Material Safety Data Sheets (MSDS) in 

your laboratory for complete storage and handling instructions). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 2 

Hydrogen peroxide (H2O2) is used to digest organic materials; it is a corrosive material and 

should be used under a fume hood while wearing a face shield, safety glasses, gloves, and a lab 

coat. H2O2 is corrosive and a strong oxidizer; store in a cool, dry, well-ventilated area away from 

incompatible substances, and keep away from heat, sparks, and flame (refer to the MSDS in your 

laboratory for complete storage and handling instructions). 

Consult the MSDS for additional information on any of the above chemicals. Be familiar with 

the location of the MSDS in your laboratory before proceeding with this analysis. 

5.3 Methods

1. Sediment samples should be stored in a dark, 4°C, relatively air-tight environment until 

processed. Process samples within two weeks of collection. 

2. Mix each sediment sample well with a spatula to ensure an accurate representation 

throughout the whole sample. 

3. Place approximately 0.5 to 1.0 ml of homogenized sediment in a labeled, 50 mL 

polypropylene centrifuge tube with a snap cap (tubes should be labeled with the date, 

GLKN park unit, core interval, and your initials). The samples will not be analyzed 

quantitatively for diatom concentration, so it is not necessary to record the volume of 

sample used. 

4. To remove carbonates, add 10% hydrochloric acid (HCl) by pipette (one drop at a time) 

until no further reaction occurs when more acid is added. Samples containing significant 

amounts of carbonate will bubble and sputter when HCl is added; therefore proceed 

cautiously with this step and add HCl slowly so that the reaction does not become too 

violent. 

5. Add 10 mL 30% peroxide (H2O2), and place in an 85°C water bath (with the centrifuge 

tube flip-top open) for 3 hours. Monitor the samples closely for the first 20 minutes to 

make sure the reaction is not too violent. If the samples come close to boiling over, 

remove them from the water bath and let the reaction proceed at room temperature under 

a positive-draw fume hood (the samples can be put back in the water bath after the 

reaction has slowed down, but watch them closely to make sure they do not boil over). 

Dense samples with lots of silts may need periodic homogenization with a glass stirring 

rod to ensure that buried organic material gets adequate exposure to peroxide. Samples 

are fully digested when the solution is clear and the reaction has stopped; if samples are 

not fully digested after 3 hours they can be left in the water bath for additional time, or 

left at room temperature under a positive-draw fume hood until the digestion is complete. 

6. When cool, fill each centrifuge tube to even levels (to approximately the 50 mL mark on 

the tube) with de-ionized (DI) water. 

7. Centrifuge each sample for 6 minutes at 3500 rpm. Repeat 5-6 times for each sample, 

decanting supernatant each time and re-filling with DI water. When decanting, pour off 

as much water as possible without losing any of the sediment. 

8. After the last centrifuge run, decant but do not re-fill the centrifuge tubes. 

9. The samples can now be used to prepare diatom slides (see SOP # 6). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #5, page 3 

5.4 Quality Assurance/Quality Control 

Diatom frustules are microscopic, and there is a possibility that samples can be contaminated. 

Laboratory areas where raw or processed samples are handled should be kept as clean as possible 

and lab bench tops should be kept free of debris. 

5.5 Literature Cited 

Acker, F., B. Russell, and E. Hagan. 2002. Protocol P-13-42, Diatom cleaning by nitric acid 

digestion with a microwave apparatus. In Protocols for the analysis of algal samples 

collected as part of the U.S. Geological Survey National Water-Quality Assessment 

Program. Charles, D. F., C. Knowles, and R. S. Davis (editors). Report No. 02-06, The 

Academy of Natural Sciences, Patrick Center for Environmental Research – Phycology 

Section, Philadelphia, Pennsylvania. 

 

Standard Operating Procedure #6: 

Preparation of Diatom Slides 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008 

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #6, 

Preparation of diatom slides. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/069. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #6, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

6.0 Introduction..........................................................................................................................1 

6.1 Equipment and Supplies ......................................................................................................1 

 

6.2 Safety Precautions................................................................................................................1 

6.3 Methods................................................................................................................................2 

 6.3.1 Preparing Coverslips...................................................................................................2

 6.3.2 Mounting Coverslips on Slides...................................................................................3 

6.4 Quality Assurance/Quality Control......................................................................................4 

6.5 Literature Cited ....................................................................................................................4 
SOP #6, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol SOP, #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
SOP #6, page iv

Acknowledgements 

We consulted Acker et al. (2002) while compiling information for this standard operating 

procedure. 
SOP #6, page 1

6.0 Introduction

This protocol outlines the steps to produce high-quality diatom microscope slides from sediment 

samples cleaned according to SOP #5. Identification of diatom valves under light microscopy 

requires mounting cleaned material between a glass coverslip and a microscope slide, using a 

medium that has a refractive index near that of glass. ZraxTM is a commercially available 

toluene-based mounting media with an appropriate refractive index (R.I. ~1.7). Slides prepared 

according to this protocol will last for many decades. 

6.1 Equipment and Supplies 

Refer to the checklists below and ensure adequate equipment and supplies are on hand for 

preparing diatom slides in a safe manner. 

√ Checklist of equipment needed for preparing diatom slides 

 10% (by volume) reagent grade hydrochloric acid (HCl) 

 Disposable plastic pipettes (approx. 3 ml) 

 Kimwipe® tissues 

 De-ionized (DI) water 

 Glass coverslips (22 mm x 22 mm) – No. 1 thickness 

 Aluminum drying plate (squares are etched onto the surface, each square is etched 

with an identifying number) 

 Hotplate with temperature control 

 Positive-draw fume hood 

 Glass microscope slides (1 x 3 inches; 2.5 x 7.5 cm) 

 Permanent marker 

 Toluene-based mounting medium (information on ZraxTM can be found at 

http://www.sas.upenn.edu/~dailey/zrax.pdf; Philadelphia, PA USA) 

 Forceps 

 Rounded toothpicks, disposable wooden stirring sticks, or pencil with eraser 

 Single-edged razor blade 

 Paper labels for slides 

√ Checklist of personal protective equipment (PPE) needed for preparing 

diatom slides 

 Acid-impervious gloves 

 Safety glasses 

 Laboratory coat or apron, acid resistant 

6.2 Safety Precautions 

Personnel are required to wear the PPE listed in Section 6.1 of this SOP while performing this 

procedure. 
SOP #6, page 2

Hydrochloric acid (HCl) is a corrosive material and should be used under a fume hood while 

wearing safety glasses, gloves, and a lab coat. 

The toluene-based mounting medium should be considered hazardous. Toluene is an organic 

solvent which volatilizes readily when heated. Therefore, only heat the mounting medium under 

a positive-draw fume hood and wear safety glasses and protective hand wear when working with 

the mounting medium (until the slides have cooled). 

Hotplate temperatures required for this procedure are high enough to cause severe burns; use 

extreme care when manipulating slides on the hotplate. 

Consult the Material Safety Data Sheets (MSDS) for additional information on any of the above 

chemicals. Be familiar with the location of MSDS in your laboratory before proceeding with this 

analysis. 

6.3 Methods 

Note that all slides will be prepared in duplicate, that is, two slides will be prepared from each 

cleaned sediment sample. The two slides should be designated with the letters ‘a’ and ‘b’. The 

remaining label information will be the same for the two slides (see section 6.3.2 part 9, below). 

6.3.1 Preparing Coverslips 

Coverslips will be prepared from sediment samples that have been cleaned according to SOP #5. 

Note that once the coverslip preparations begin, one will not be able to move the aluminum 

drying plate. Before beginning the following process, find a place in the laboratory where the 

aluminum drying plate can be left overnight (somewhere that will be undisturbed and free of 

vibrations and drafts). 

1. Use a Kimwipe® to wipe each coverslip as you remove it from the box. Place each 

coverslip on a marked space of the aluminum drying plate. Be sure the aluminum drying 

plate is clean and dry to avoid cross-contamination. NOTE: All slides will be made in 

duplicate, so prepare two coverslips for each sample. 

2. Under the fume hood, add one small drop of 10% HCl to each centrifuge tube to create a 

better distribution of diatoms. 

3. Add de-ionized (DI) water to each centrifuge tube until the liquid is a slightly translucent 

grey color. This means that more water will be added for samples with a high diatom 

abundance and less water for samples that have a lower density. 

4. If the solution is still overly saturated with diatoms (either the solution is still fairly dark 

grey or one has previously tried to make a slide from a similar sample that was too dense 

to count), put a large drop of distilled water on the coverslip before transferring the 

diatom suspension. 

5. Agitate the sample to a uniform dispersion and use a plastic pipette to add the diatom 

solution to each coverslip. Fill each slip corner-to-corner and to the maximum surface 
SOP #6, page 3

tension of the coverslip. If the coverslip overflows, discard it and repeat the procedure 

with a freshly cleaned coverslip. Use a new pipette for each sample. 

6. Once the aluminum drying plate is loaded with coverslip preparations, allow coverslips to 

dry undisturbed overnight at room temperature. The drying plate should be on a surface 

where vibrations from surrounding equipment are minimal and free of drafts so that the 

distribution of diatoms on the coverslip is even. It is highly recommended to draw a map 

of the sample locations on the drying plate to ensure that samples do not get mixed up. 

7. Once coverslips have dried, a diatom density check can be performed on unmounted 

coverslips. Coverslips can be placed, diatom side up, on a slide and observed at 400X 

under a microscope. If diatoms are too dense the coverslip can be discarded and remade 

(when remaking, dilute the sample either by adding more DI water to the centrifuge tube, 

or adding more DI water to the coverslip before transferring the diatom suspension). If 

the diatoms are not dense enough, more of the suspension can be added to the same 

coverslip and dried again. A final density check will be made after the coverslips are 

mounted, but performing this preliminary check before making permanent slides will 

save time and materials. 

6.3.2 Mounting Coverslips on Slides

1. After the coverslips have dried, place the aluminum drying plate full of coverslips on a 

hotplate to drive off hydroscopic water (for 1 hour at 225o

F). The hotplate should be 

under a fume hood in preparation for the following steps. 

2. Label slides and clean with a Kimwipe® (slides can be labeled with a Sharpie marker at 

this stage, a paper label will be added at the end of the process). 

3. Turn on the fan of the fume hood. Once coverslips have been dried, add a small drop of 

mounting medium to a slide by placing the slide over the top of the bottle and inverting, 

or by using a disposable pipette (the volume of mounting medium on the slide should be 

equivalent to approximately 2 to 4 drops of water). Place the drop of mounting medium 

just off-center of the slide to leave room for a label on the other side of the slide. Remove 

the appropriate coverslip from the aluminum plate with forceps, being careful to handle 

the coverslip only at the extreme corners. Invert the coverslip and place it gently on the 

portion of the slide that is covered with mounting medium. 

4. Place the slide (keep the coverslip-side up) on the hotplate (which is still set at 225o

F 

within the fume hood, with the fan turned on). Bubbles will soon result from the 

evaporation of the toluene; keep the slide on the hotplate until the bubbles significantly 

diminish. 

5. Remove the slide from the hotplate; using a rounded toothpick, wooden stirring stick, or 

eraser end of a pencil, gently position the coverslip and press down on it to form a thin 

layer of mounting medium beneath the entire coverslip. Press down firmly, but not so 

hard as to damage the coverslip. The mounting medium will harden quickly; if it is 

necessary to reposition the coverslip after the medium hardens, the slide will have to be 

put back on the hotplate for a few seconds to soften the mounting medium. 
SOP #6, page 4

6. If there are no bubbles under the coverslip and the mounting mediumsufficiently covers 

the area of the coverslip (i.e., no edges of the coverslip are free of mounting medium), 

then set the slide aside to cool. If you are unable to remove all of the bubbles, put the 

slide back on the hotplate for a few seconds and repeat step 5. If there is not enough 

mounting medium on the slide, put the slide back on the hotplate and add a small amount 

of mounting medium to the edge of the coverslip (it will be pulled underneath as it heats) 

with a disposable pipette and repeat steps 4 through 6. 

7. Once the slide has cooled, scrape the excess mounting medium from the edges of the 

coverslip with a razor blade. Always start in the center of the slide and work outward to 

avoid popping the coverslip loose from the slide; be sure that the blade is aimed away 

from your fingers. 

8. Look at the completed slides on the microscope under medium to low magnification 

(100x to 450x) to confirm that there is an even distribution of diatoms and that most the 

diatom frustules do not overlap, are not too dense, or too dilute. Remake any slides that 

have problems with the diatom dispersion or density that would interfere with the quality 

and accuracy of the analysis. 

9. Label all completed slides with a printed paper label that contains the name of the state, 

the county, the name of the park, the name of the lake, the GPS coordinates of the sample 

location, the core interval (e.g., 0-1 cm), the collector’s name, and the date (designate the 

duplicates of each sample as ‘a’ and ‘b’). Use a dating convention in which the day and 

month are readily distinguishable (e.g., 21 Sept 2008 or 21 IX 2008) to avoid confusion 

between European and North American abbreviation styles. A glass etching pen can also 

be used to label slides with the lake name and interval, in case the paper labels ever fall 

off. 

6.4 Quality Assurance/Quality Control 

Diatom frustules are microscopic, and there is a possibility that samples can be contaminated. 

Laboratory areas where raw or processed samples are handled should be kept as clean as 

possible, and lab bench tops should be kept free of debris. Disposable pipettes should be used 

when possible. 

All slides will be prepared in duplicate: set ‘a’ will be counted, set ‘b’ will be archived and 

available for loan to other laboratories. 

6.5 Literature Cited

Acker, F., B. Russell, and E. Morales. 2002. Protocol P-13-49, Preparation of diatom slides using 

NaphraxTM mounting medium. In Protocols for the analysis of algal samples collected as 

part of the U.S. Geological Survey National Water-Quality Assessment Program. 

Charles, D.F., C. Knowles, and R.S. Davis (editors). Report No. 02-06, The Academy of 

Natural Sciences, Patrick Center for Environmental Research – Phycology Section, 

Philadelphia, Pennsylvania. 
Standard Operating Procedure #7: 

Analysis of Slides 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #7, 

Analysis of slides. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. 

E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great Lakes 

Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

7.0 Introduction..........................................................................................................................1 

7.1 Scanning Slides....................................................................................................................1 

7.2 Counting and Taxonomy......................................................................................................1 

7.3 Entering Data .......................................................................................................................2 

7.4 Literature Cited ....................................................................................................................2 

Appendix A. Diatom codes used in the Minnesota calibration set..................................................5 

Appendix B. Diatom count sheet...................................................................................................11 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol SOP, #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page iv

Acknowledgements 

We consulted Clason et al. (2002) while compiling information for this standard operating 

procedure. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page 1

7.0 Introduction

The purpose of this SOP is to describe the procedure for analyzing diatoms on microscope slides. 

7.1 Preview Slides 

Permanent slides should be previewed before identifying and enumerating diatoms to ensure that 

an even distribution of diatoms exists and that the abundance of diatoms is neither too dense nor 

too sparse for counting. Overlapping of frustules should be minimal. The preferred density of 

diatoms will vary among analysts, however the valves should not be so dense that the details of 

individual valves are obscured, and should not be so sparse that it is not possible to identify 400 

valves. If the density or distribution of diatoms on the slide is not appropriate the slide must be 

remade according to SOP #6. 

7.2 Counting and Taxonomy 

A total of 400 diatom valves will be counted along random transects from the ‘a’ slide using a 

light microscope fitted with full immersion optics capable of magnification within the range of 

875-1250X and numerical aperture (N.A.) >1.30. Analyses will follow the enumeration criteria 

used in the Minnesota (MN) calibration set (Ramstack et al. 2003; Edlund and Kingston 2004; 

Edlund 2005), that is, diatoms will be counted when over 50% of the valve is present or visible 

within the field of view or when a distinct valve fragment is present (e.g., central area of 

Amphora libyca or head pole of Asterionella formosa). If a sample with poor diatom preservation 

is encountered, a maximum of 10 transects will be counted. Unknown taxa will be give a unique 

name and 8-character code, and photos will be taken. 

Diatoms will be identified to the lowest taxonomic unit using floras and monographs by Hustedt 

(1927-1966, 1930); Patrick and Reimer (1966, 1975); Collins and Kalinsky (1977); Camburn et 

al. (1978, 1984-1986); Krammer and Lange-Bertalot (1986, 1988, 1991a, b); Cumming et al. 

(1995); Reavie and Smol (1998); Camburn and Charles (2000); and Fallu et al. (2000); as well as 

all other pertinent literature. As slides are being counted, taxonomy should be harmonized with 

the MN diatom calibration set (Ramstack et al. 2003; Edlund and Kingston 2004; Edlund 2005), 

because these NPS samples will ultimately be combined with the MN set. 

Any new technicians introduced into the program will need to be trained by an experienced 

taxonomist. To ensure internal taxonomic consistency, photographic databases will be 

constructed for all predominant diatom taxa; this collection of photographs will be maintained at 

the St. Croix Watershed Research Station (SCWRS). (Note: should another contracting 

organization be conducting the work, replace all reference to SCWRS with the appropriate 

contractor’s name.) 

Each year, 10% of the samples collected will be recounted by another analyst in the program. 

The primary analyst will etch a line in the slide to mark the transect counted, and will etch circles 

at the start and end points of the area counted along the transect. The QC analyst will then use 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page 2

the etchings to count the exact same portion of the slide. Refer to SOP #12 (Quality Assurance 

and Quality Control) for details on assessing percent difference between the two counts. 

7.3 Entering Data 

Each taxon will be described by an 8-character code; all of the codes used in the 145 lake MN 

calibration set are listed in Appendix A. These codes follow the format used by the Great Lakes 

Environmental Indicators (GLEI) project (E. Reavie, Natural Resources Research Institute, 

University of Minnesota, Duluth); the GLEI list will be used as a starting point, however many 

taxa and codes will need to be added as the project progresses. A complete and up-to-date list of 

codes for this project will be maintained in a database at the SCWRS. 

After a sample has been analyzed, the following information should be entered into an Excel 

spreadsheet: 

• The park unit, lake name, sediment interval, transect counted, date, and the analyst 

• The full taxon name 

• The appropriate 8-character code for that taxon 

• The raw count for each taxon (number of valves of a taxon counted in a given sample) 

• The percentage abundance (relative frequency) of each taxon (number of valves of each 

taxon divided by the total number of valves counted in that sample) 

• Any relevant notes 

All of the Excel datasheets for this project will be housed at the St. Croix Watershed Research 

Station. Researchers will communicate with the individual parks to make these data available to 

them 

7.4 Literature Cited 

Camburn, K. E., and D. F. Charles. 2000. Diatoms of low-alkalinity lakes in the northeastern 

United States. Academy of Natural Sciences of Philadelphia, Special Publication 18, 

Camburn, K. E., J. C. Kingston, and D. F. Charles (editors). 1984-1986. PIRLA diatom 

iconograph. PIRLA Unpublished Report Series, Report 3. -Electric Power Research 

Institute, Palo Alto, California. 

Camburn, K. E., R. L. Lowe, and D. L. Stoneburner. 1978. The haptobenthic diatom flora of 

Long Branch Creek, South Carolina. Nova Hedwigia 30:149-279. 

Clason, T., F. Acker, E. Morales, and L. Marr. 2002. Protocol P-13-39, Analysis of diatoms on 

microscope slides prepared from USGS NAWQA program algae samples. In Protocols 

for the analysis of algal samples collected as part of the U.S. Geological Survey National 

Water-Quality Assessment Program. Charles, D. F., C. Knowles, and R. S. Davis 

(editors). Report No. 02-06, The Academy of Natural Sciences, Patrick Center for 

Environmental Research – Phycology Section, Philadelphia, Pennsylvania. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page 3

Collins, G. B., and R. G. Kalinsky. 1977. Studies on Ohio Diatoms: I. Diatoms of the Scioto 

River Basin. II. Referenced checklist of diatoms from Ohio. Bull. of the Ohio Biological 

Survey-New Series 5(3). 

Cumming, B. F., S. E. Wilson, R. I. Hall, and J. P. Smol. 1995. Diatoms from British Columbia 

(Canada) lakes and their relationship to salinity, nutrients and other limnological 

variables. Bibliotheca Diatomologica 31:1-207. 

Edlund, M. B. 2005. Using diatom-based analysis of sediment records from central Minnesota 

lakes for TMDL and nutrient criteria development. Final report to the Minnesota 

Pollution Control Agency. 

Edlund, M. B. and J. C. Kingston. 2004. Expanding sediment diatom reconstruction model to 

eutrophic southern Minnesota lakes. Final report to the Minnesota Pollution Control 

Agency. 

Fallu, M. -A., N. Allaire, and R. Peinitz. 2000. Freshwater diatoms from northern Québec and 

Labrador (Canada). Species-environment relationships in lakes of boreal forest, foresttundra and tundra regions. Bibliotheca Diatomologica 45:1-200. 

Hustedt, F. 1927-1966. Die Kieselalgen Deutschlands, Österreichs und der Schweiz mit 

Berücksichtigung der übrigen Länder Europas sowie der angrenzenden Meeresgebeite. In

Dr. L. Rabenhorst's Kryptogramen-Flora von Deutschland, Österreich und der Schweiz. 

Band VII. Teil 1: Lieferung 1, seite 1-272, 1927: Lieferung 2, seite 273-464, 1928: 

Lieferung 3, seite 465-608, 1929: Lieferung 4, seite 609-784, 1930: Lieferung 5, seite 

785-920, 1930: Teil 2: Lieferung 1, seite 1-176, 1931: Lieferung 2, seite 177-320, 

1932: Lieferung 3, seite 321-432, 1933: Lieferung 4, seite 433-576, 1933: Lieferung 5, 

seite 577-736, 1937: Lieferung 6, seite 737-845, 1959: Teil 3: Lieferung 1, seite 1-160, 

1961: Lieferung 2, seite 161-348, 1962: Lieferung 3, seite 349-556, 1964: Lieferung 4, 

seite 557-816, 1966. Leipzig, Akademische Verlagsgesellschaft Geest und Portig K.-G. 

 

Hustedt, F. 1930. Die Süsswasserflora Mitteleuropas. Heft 10. 2nd edition. Bacillariophyta 

(Diatomeae). A. Pascher (ed.) Verlag von Gustav Fischer, Germany. 

Krammer, K. and H. Lange-Bertalot. 1986. Bacillariophyceae. 1. Teil: Naviculaceae. In Ettl, H., 

J. Gerloff, H. Heynig, and D. Mollenhauer. (eds) Süsswasser flora von Mitteleuropa, 

Band 2/1. Gustav Fischer Verlag: Stuttgart, New York. 

Krammer, K. and H. Lange-Bertalot. 1988. Bacillariophyceae. 2. Teil: Bacillariaceae, 

Epithemiaceae, Surirellaceae. In Ettl, H., J. Gerloff, H. Heynig, and D. Mollenhauer. 

(editors) Süsswasserflora von Mitteleuropa, Band 2/2. VEB Gustav Fischer Verlag: Jena. 

Krammer, K. and H. Lange-Bertalot. 1991a. Bacillariophyceae. 3. Teil: Centrales, 

Fragilariaceae, Eunotiaceae. In Ettl, H., J. Gerloff, H. Heynig, and D. Mollenhauer. 

(editors) Süsswasserflora von Mitteleuropa, Band 2/3. Gustav Fischer Verlag: Stuttgart, 

Jena. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #7, page 4

Krammer, K. and H. Lange-Bertalot. 1991b. Bacillariophyceae. 4. Teil: Achnanthaceae, 

Kritische Ergänzungen zu Navicula (Lineolatae) und Gomphonema, 

Gesamtliteraturverzeichnis Teil 1-4. In Ettl, H., G. Gärtner, J. Gerloff, H. Heynig, and D. 

Mollenhauer. (editors) Süsswasserflora von Mitteleuropa, Band 2/4. Gustav Fischer 

Verlag: Stuttgart, Jena. 

Patrick, R. and C. W. Reimer. 1966. The diatoms of the United States, exclusive of Alaska and 

Hawaii, Volume 1-Fragilariaceae, Eunotiaceae, Achnanthaceae, Naviculaceae. Academy 

of Natural Sciences of Philadelphia Monograph No. 13. 

Patrick, R., and C. W. Reimer. 1975. The diatoms of the United States, exclusive of Alaska and 

Hawaii, Volume 2, Part 1-Entomoneidaceae, Cymbellaceae, Gomphonemaceae, 

Epithemaceae. Academy of Natural Sciences of Philadelphia Monograph No. 13. 

Ramstack, J. M., S. C. Fritz, D. R. Engstrom, and S. A. Heiskary. 2003. The application of a 

diatom-based transfer function to evaluate regional water-quality trends in Minnesota 

since 1970. Journal of Paleolimnology 29:79-94. 

Reavie, E. D., and J. P. Smol. 1998. Freshwater diatoms from the St. Lawrence River. 

Bibliotheca Diatomologica 41:1-137. 
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SOP #7, page 5

Appendix A. Diatom codes used in the Minnesota calibration set. 

Code Genus Species Variety Author ACEGRANA Achnanthes grana Hohn & Hellerman ACECONSP Achnanthes conspicua A. Mayer ACECATEN Achnanthes catenata Bily & Marvan ACHMINUT Achnanthidium minutissimum (Kütz.) Czarn. AMPSUBCO Amphora subcostulata Stoermer & J.J.Yang AMPINARI Amphora inariensis Krammer AMPLIBYC Amphora libyca Ehrenb. AMPPEDIC Amphora pediculus (Kütz.) Grunow AMPVENET Amphora veneta Kütz. AMPOVALI Amphora ovalis (Kütz.) Kütz. ANOSPHCO Anomoeoneis sphaerophora fo. costata (Kütz.) A.M.Schmid ASTFORMO Asterionella formosa Hass. AULSUBAR Aulacoseira subarctica (O.Müll.) E.Y.Haw. AULPFAFF Aulacoseira pfaffiana (Reinsch) Krammer AULLIRBI Aulacoseira lirata biseriata (Grunow) E.Y.Haw. AULITATE Aulacoseira italica tenuissima (Grunow) Simonsen AULITALI Aulacoseira italica (Ehrenb.) Simonsen AULGRANU Aulacoseira granulata (Ehrenb.) Simonsen AULDISTA Aulacoseira distans (Ehrenb.) Simonsen AULCCREN Aulacoseira crenulata (Ehrenb.) Thwaites AULAMBIG Aulacoseira ambigua (Grunow) Simonsen BELBEROL Belonastrum berolinensis (Lemmermann) Round & Maidana BRABREBI Brachysira brebissonii R.Ross in B.Hartley BRAVITRE Brachysira vitrea (Grunow) R.Ross in B.Hartley COCPLACE Cocconeis placentula Ehrenb. COCPEDIC Cocconeis pediculus Ehrenb. COCPLAEU Cocconeis placentula euglypta (Ehrenb.) Grunow COCPLALI Cocconeis placentula lineata (Ehrenb.) VanHeurck COCNEODI Cocconeis neodiminuta Krammer in Krammer & Lange-Bert. 
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Code Genus Species Variety Author COCNEOTH Cocconeis neothumensis Krammer CRAHALOP Craticula halophila (Grunow) D.G. Mann in Round, Crawford & ManCRACUSPI Craticula cuspidata (Kütz.) D.G.Mann in Round, Crawford & Man CSPINVIS Cyclostephanos invisitatus (Hohn et Hellermann) Theriot, Stoermer et Håk. CSPTHOLI Cyclostephanos tholiformis Stoermer, Håk. & Theroit CSPDUBIU Cyclostephanos dubius (Fricke) Round in Theriot, Håkansson, Kociolek, RCYCCOMRA Cyclotella comta radiosa Grunow CYCCOMEN Cyclotella comensis Grunow CYCBODLE Cyclotella bodanica lemanica (O.Müll. ex Schroter) Bachmann CYCSTELL Cyclotella stelligera (Cleve & Grunow) VanHeurck CYCROSSI Cyclotella rossii Håk. CYCPSEUD Cyclotella pseudostelligera Hust. CYCOCELL Cyclotella ocellata Pant. CYCMENEG Cyclotella meneghiniana Kütz. CYCMICHI Cyclotella michiganiana Skvortsov CYCDISTI Cyclotella distinguenda Hust. CYCKRAMM Cyclotella krammeri Håk. CYCGORDO Cyclotella gordonensis Kling & Håk. CYTELLIP Cymatopleura elliptica (Bréb. & Godey) W.Sm. CYMAFFIN Cymbella affinis Kütz. CYMCISTU Cymbella cistula (Ehrenb. in Hemprich & Ehrenb.) Kirchn. in Cohn DIATENEL Diatoma tenue elongatum Lyngb. ENCSILES Encyonema silesiacum (Bleisch in Rabenh.) D.G.Mann ENCTRIAL Encyonema triangulum (Ehrenb.) Kütz. ENPMICRO Encyonopsis microcephala (Grunow) Krammer EPIARGUS Epithemia argus (Ehrenb.) Kütz. EPIADNAT Epithemia adnata (Kütz.) Bréb. EUNBILUN Eunotia bilunaris (Ehrenberg) Mills EUNZASUM Eunotia zasuminensis (Cab.) Körner FRACAPUC Fragilaria capucina Desm. FRACROTO Fragilaria crotonensis Kitton 
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Code Genus Species Variety Author FRACONV2 Fragilaria construens var. 2 provisional name FRACAPVR Fragilaria capucina rumpens (Kütz.) Lange-Bertalot FRACAPGR Fragilaria capucina gracilis (Oestrup) Hust. FRAVAUCH Fragilaria vaucheriae (Kütz.) J.B.Petersen FRAEXIGU Fragilaria exigua Grunow in Cl. & Möll. FRANANAN Fragilaria nanana Lange-Bert. FRATENER Fragilaria tenera (W. Smith) Lange-Bert. FRACAPME Fragilaria capucina mesolepta Rabenh. GOMPUMIL Gomphonema pumilum (Grunow) Reich. & Lange-Bert. GOMPARVU Gomphonema parvulum (Kütz.) Kütz. GOMTRUNC Gomphonema truncatum Ehrenb. GOMINSIG Gomphonema insigne Gregory GOMINTRI Gomphonema intricatum Kütz. GOMGRACI Gomphonema gracile Ehrenb. emend. VanHeurck GOMDICHO Gomphonema dichotomum Kütz. GOMANGUS Gomphonema angustatum (Kütz.) Rabenh. HANAMPHI Hantzschia amphioxys (Ehrenb.) Grunow HIPCAPIT Hippodonta capitata (Grunow) Lange-Bert., Metzelin & Witkowski HIPHUNGA Hippodonta hungarica (Grunow) Lange-Bert., Metzeltin & Witkowski KARCLEVE Karayevia clevei (Grunow in Cleve & Grunow) Round & Bukht. MARMARTY Martyana martyii (Héribaud) F.E.Round in Round, Crawford & ManNAVVITIO Navicula vitiosa Schimanski NAVTRIVI Navicula trivialis Lange-Bert. NAVSUBMA Navicula subminuscula Manguin NAVSEMIN Navicula seminulum Hust. NAVREINH Navicula reinhardtii Grunow NAVRADIO Navicula radiosa Kütz. NAVPHYLL Navicula phyllepta Kütz. NAVMINUS Navicula minuscula Grunow NAVMINIM Navicula minima Grunow in Van Heurck NAVLUNDI Navicula lundii Reichardt 
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Code Genus Species Variety Author NAVLIBON Navicula libonensis Schoeman 1970 NAVLEPTO Navicula leptostriata Jorgensen NAVPSEUV Navicula pseudoventralis Hust. NAVCRYPT Navicula cryptotenella Lange-Bert. NAVCRYCP Navicula cryptocephala Kütz. NAVCINCT Navicula cincta (Ehrenb.) Ralfs NAVCAPRA Navicula capitatoradiata Germain NAVACCOM Navicula accomoda Hustedt NAVDENSL Navicula densilineolata (Lange-Bert.) Lange-Bert. NITINCOG Nitzschia incognita Krasske NITPERMI Nitzschia perminuta (Grunow) M.Perag. NITSUBLI Nitzschia sublinearis Hust. NITSUBAC Nitzschia subacicularis Hust. NITPUSIL Nitzschia pusilla Grunow NITPALEC Nitzschia paleacea Grunow NITPALEA Nitzschia palea (Kütz.) W.Sm. NITLINVS Nitzschia linearis subtilis (Grunow) Hustedt NITLIEBE Nitzschia liebetruthii Rabenh. NITACICO Nitzschia acicularioides Hust. NITFONTI Nitzschia fonticola Grunow NITDENTI Nitzschia denticula Grunow NITARCHI Nitzschia archibaldii Lange-Bert. NITAMPHI Nitzschia amphibia Grunow NITRADIC Nitzschia radicula Hust. NITAGNIT Nitzschia agnita Hust. NITACICU Nitzschia acicularis (Kütz.) W.Sm. NITGRACI Nitzschia gracilis Hantzsch PINVIRID Pinnularia viridis (Nitzsch) Ehrenb. PINBICPU Pinnularia biceps pusilla Camburn & Charles PINBRAUN Pinnularia brauniana (Grunow) Cleve PLAROSTR Planothidium rostratum (Østrup) Round et L.Bukhtiyarova 
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Code Genus Species Variety Author PLAFREQU Planothidium frequentissimum (Lange-Bertalot) Round et L.Bukhtiyarova PLALANCE Planothidium lanceolatum (Bréb.) Round & Bukht. PSASUBAT Psammothidium subatomoides (Hust.) L.Bukhtiyarova et Round PRABREVT Pseudostaurosira brevistriata "triangular" provisional name PRABREVI Pseudostaurosira brevistriata (Grunow in Van Heurck) D.M.Williams et Round PRABREBC Pseudostaurosira brevistriata capitata (Héribaud) N.A.Andresen & Kreis PRABREIN Pseudostaurosira brevistriata inflata (Pant.) M.B.Edlund PRAMICRO Pseudostaurosira microstriata (Marciniak) provisional placement in genus RHOCURVA Rhoicosphenia curvata (Kütz.) Grunow RHPGIBBA Rhopalodia gibba (Ehrenb.) O.Müll. ROSLINEA Rossithidium linearis (W.Sm.) Round & Bukht. ROSLINCU Rossithidium linearis fo. curta provisional name SELPUPUL Sellaphora pupula (Kütz.) Mereschk. SELLAEVI Sellaphora laevissima (Kütz.) D.G.Mann SELVITAB Sellaphora vitabunda (Hust.) D.G.Mann STAANCEP Stauroneis anceps Ehrenb. STAANCGR Stauroneis anceps fo. gracilis Rabenh. SRACONVE Staurosira construens venter (Ehrenb.) Hamilton SRACONBI Staurosira construens binodis (Ehrenberg) P.B. Hamilton in Hamilton, Poulin, CSRACONPU Staurosira construens pumila (Grunow in Van Heurck) Kingston SRAELLIP Staurosira elliptica (Schum.) D. M. Williams & Round SRACONST Staurosira construens (Ehrenb.) D.M.Williams et Round SLLPINVA Staurosirella pinnata acuminata A. Mayer SLLANSAT Staurosirella ansata (M.H.Hohn & Hellerm.) Kingston SLLPINNA Staurosirella pinnata (Ehrenb.) D.M.Williams & Round SLLPINLA Staurosirella pinnata lancettula (Schumann) E.Y.Haw. et M.G.Kelly SUSMINUS Stephanodiscus minutulus (Kütz.) Cleve & J.D.Möll. SUSALPIN Stephanodiscus alpinus Hust. SUSHANTZ Stephanodiscus hantzschii Grunow SUSHANTE Stephanodiscus hantzschii fo. tenuis (Hust.) Håk. & Stoermer SUSMEDIU Stephanodiscus medius Håk. 
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SOP #7, page 10

Code Genus Species Variety Author SUSNIAGA Stephanodiscus niagarae Ehrenb. SUSPARVU Stephanodiscus parvus Stoermer & Håk. SUSVESTI Stephanodiscus vestibulus Håk., Stoermer & Theriot SUSOREGO Stephanodiscus oregonicus (Ehrenb.) Håkansson SUROVALI Surirella ovalis Bréb. SYNDELIC Synedra delicatissima W.Sm. SYNACUAN Synedra delicatissima angustissima Grunow SYNRADIA Synedra radians Kütz. SYNRUMFA Synedra rumpens familiaris (Kütz.) Hust. SYNULNA Synedra ulna (Nitzsch) Ehrenb. SYNACUS Synedra acus Kütz. SYLPARAS Synedrella parasitica (W. Smith) Round & Maidana TABFLOC4 Tabellaria flocculosa IV Koppen TABFLOC3 Tabellaria flocculosa III Koppen TABQUADR Tabellaria quadriseptata Knuds. TRYHUNGA Tryblionella hungarica (Grunow) D.G.Mann TRYANGUS Tryblionella angustata W.Sm. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 

SOP #7, page 11

Appendix B. Diatom count sheet. 

NPS I&M Diatom Monitoring Program 

Park Unit Lake Interval Transect Counted Date Analyst Taxon Code Taxon Name # of Valves 

Relative Abundance Notes 

Standard Operating Procedure #8: 

Archiving Sediment and Diatom Slides 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #8, 

Archiving sediment and diatom slides. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #8, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

8.0 Introduction..........................................................................................................................1 

8.1 Freeze Drying Sediment Samples........................................................................................1 

8.2 Archiving Freeze Dried Sediment Samples and Diatom Slides ..........................................1 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #8, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol SOP, #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #8, page 1

8.0 Introduction

The purpose of this SOP is to outline the procedure for preserving surface sediment samples and 

archiving sediment samples and diatom slides. 

8.1 Freeze-Drying Sediment Samples

After diatom slides have been made, the remaining sediment should be freeze-dried and placed 

into a vial labeled with: the project name, the lake name, the GLKN park unit, the GPS 

coordinates of the sample location, the sediment interval (e.g., 0-1 cm), the collector’s name, and 

the date. 

Note that if for any reason microscope slides need to be remade at some time in the future, freeze 

dried sediment can be cleaned following the same procedure that was used for wet sediment 

(SOP #5). When cleaning freeze dried sediment, approximately 100-200 mg of dry sediment 

should be used. 

8.2 Archiving Freeze-Dried Sediment and Diatom Slides

Both freeze-dried sediment samples and diatom slides will be archived. Freeze-dried sediment 

samples will be stored in vials and labeled as described above (Section 8.1); diatom slides will be 

labeled as described in SOP #6, Section 6.3.2. Researchers will coordinate with each park unit to 

decide where the collections for each park will be housed. Representatives from each park will 

also work with researchers to ensure that the archived materials are entered into the appropriate 

NPS database. 

All freeze-dried sediment samples from a given year will be stored together, and all slides from a 

given year will be stored together. Vials containing freeze-dried samples will be stored in boxes, 

with the tops and sides of the boxes clearly labeled for easy retrieval from storage. Slides will be 

stored in labeled microscope slide boxes and in the dark. Both freeze-dried samples and slides 

will be stored at room temperature. Archived slides and samples will be checked periodically to 

be sure that they have not been damaged while in storage. 

 

 
Standard Operating Procedure #9: 

Data Analysis 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack1

, Mark Edlund1, Daniel Engstrom1, Brenda Moraska Lafrancois2 

1

St Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

2

National Park Service 

St. Croix Watershed Research Station 

16910 152nd Street North 

Marine on St. Croix, MN 55047 

August 2008 

Suggested citation: 

Ramstack, J. M., M. B. Edlund, B. M. Lafrancois, and D. R. Engstrom. 2008. Standard operating 

procedure #9, Data analysis. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iv 

Acknowledgements..........................................................................................................................v 

9.0 Introduction..........................................................................................................................1 

 9.0.1 Recommended Reading ..............................................................................................1 

 9.0.2 Software Suggestions..................................................................................................2 

9.1 The GLKN Diatom Calibration Set .....................................................................................2 

 9.1.1 Species Data................................................................................................................2 

 9.1.2 Environmental Data ....................................................................................................3 

9.2 Multivariate Analyses ..........................................................................................................3 

 9.2.1 Principal Components Analysis (PCA) ......................................................................3 

9.2.2 Correspondence Analysis (CA) and Detrended Correspondence Analysis (DCA)....4 

 9.2.3 Canonical Correspondence Analysis (CCA) ..............................................................4 

9.3 Analysis After the Calibration Set is Complete...................................................................6 

 9.3.1 Passively Plotting on the Calibration Set....................................................................6 

 9.3.2 Dissimilarity Measure.................................................................................................7 

 9.3.3 Environmental Reconstructions..................................................................................7 

9.4 Analyses for Lakes with Downcore Diatom Data ...............................................................7 

9.5 Literature Cited ....................................................................................................................7 

Tables 

 Page 

Table 1. Sequence of steps used in diatom data analysis. ...............................................................2 

Table 2. Summary and classification of ordination methods. .........................................................5 

Figures 

 Page 

Figure 1. PCA of environmental data (ecoregion excluded) from the 145-lake MN 

 calibration set....................................................................................................................9 

Figure 2. CA biplots of the 145- lake MN calibration set with a) sites displayed and b) species 

displayed. ........................................................................................................................10 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page iii

Figure 3. DCA biplots of the 145-lake MN calibration set with a) sites displayed and b) species 

displayed. ........................................................................................................................11 

Figure 4. CCA of the 145-lake MN calibration set, with all of the environmental variables 

included (sites plotted)....................................................................................................12 

Figure 5. CCA of the 145-lake MN calibration set with the forward selected variables...............13 

Figure 6. Subset of the MN calibration set (89 lakes) showing a modern and downcore 

assemblage from a Twin Cities metro lake passively plotted.........................................14 

Figure 7. CA of downcore samples from Shell Lake (Sleeping Bear Dunes National Lakeshore) 

based on species assemblages, from sections dating from 1727 to 2003. ......................15 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page iv

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page v

Acknowledgements 

In writing this SOP we relied heavily on the lecture notes and course materials from Steve 

Juggins’ Analysis of Environmental Data course that he taught at Iowa Lakeside Laboratory in 

July 2006. Many thanks to Steve for all he has taught us about multivariate data analysis and all 

of the questions he has answered for us over the years. Gavin Simpson was extremely helpful in 

providing information on chord distance. Thanks to Avery Cook Shinneman for helpful 

discussions and reviews of this SOP. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 1

9.0 Introduction 

Diatoms are being analyzed in surficial lake sediments to address the following questions: 

• What is the current ecosystem status of a particular lake in relation to other regional 

lakes? 

• Are similar ecological trends occurring among regional lakes? 

• What is the ecosystem status of this lake in relation to historical environmental change 

noted in regional sediment cores? 

• Has this lake changed since the last time it was sampled? If so, what is the magnitude 

and direction of that change? 

This SOP describes how the diatom species data will be analyzed to answer the above questions. 

Multivariate statistical analyses will be used to compare diatom species assemblages with water 

chemistry measurements to derive an understanding of diatom response to physical/chemical 

variables. In addition, changes in the community composition of diatoms will be analyzed in 

relation to other lakes as well as within the context of the range of natural variability, as 

determined by diatoms present in cores dating back to the time of European settlement. 

Approximately 50-60 surface sediment samples will have been collected from Great Lakes 

Network (GLKN) parks between 2005 and 2009 as part of a project to analyze diatoms to 

understand historical and current water quality conditions (contract # J21050428). The diatom 

assemblages from these samples will be appended to a diatom calibration set that exists for 

Minnesota lakes (henceforth referred to as “the MN calibration set”; Ramstack et al. 2003; 

Edlund and Kingston 2004; Edlund 2005). After this amendment to the calibration set, analyses 

of diatom samples will no longer be appended to the calibration set, but will be plotted passively 

on this set to look for changes in the lakes. It is important to note that before any statistical 

analyses are done, the diatom taxonomy should be harmonized with the MN calibration set. 

Table 1 outlines the sequence of steps that will be used in the diatom data analysis; each of these 

steps is described in detail in this SOP. 

The majority of examples used throughout this SOP refer to a diatom calibration set with data 

from 145 MN lakes. This full calibration set is used to illustrate the various statistical analyses 

described in this SOP; however, once data from the 50-60 GLKN lakes are available, it may 

prove more effective to append these to a smaller subset of the MN calibration set. For example, 

it might make sense to remove shallow lakes from the calibration set, or lakes from certain 

ecoregions (e.g., prairie/agricultural). This decision will have to be made after merging the 

datasets and determining if the full suite of MN lakes, or some subset of the calibration set is 

most useful for reconstructing variables of interest in the Great Lakes Network lakes. 

9.0.1 Recommended Reading 

Jongman et al. (1995), Leps and Šmilauer (2003), McCune and Grace (2002), and Shaw (2003) 

provide detailed discussions of the multivariate statistical methods covered in this SOP. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 2

Table 1. Sequence of steps used in diatom data analysis. 

Analyses to be conducted when the NPS calibration set is complete 

• Passively plot new species data on the calibration set 

• Use the calibration set to predict environmental variables from diatom species 

assemblage 

Analyses to be conducted for any lakes with downcore diatom data 

• Exploratory detrended correspondence analysis (DCA) of combined downcore and 

surface diatom species data 

• If gradients are short in DCA, use principal components analysis (PCA) of 

species data 

• If gradients are long in DCA, use correspondence analysis (CA) or DCA of 

species data 

9.0.2 Software Suggestions 

Currently, several statistical packages are available for these analyses; the most common are 

CANOCO (ter Braak and Šmilauer 1998), R (R Development Core Team 2006), and PC-ORD 

(McCune and Mefford 1999). CANOCO and PC-ORD offer a Microsoft Windows-type menudriven approach, while R requires the user to write small programs (referred to as scripts) in the 

S computing language. Although R is not as immediately user-friendly as the other alternatives, 

some advantages are that the software is available as a free download, it is supported by 

comprehensive help windows and a large community of users, it is easy to replicate analyses, 

and it produces high quality graphics that the user can customize (e.g., all of the graphs in this 

SOP were produced in R). Download of the free text editor, Tinn-R (Faria et al. 2007), is highly 

recommended when using R; Tinn-R is designed to interface with R and allows users to save all 

of the scripts they have written. 

9.1 The GLKN Diatom Calibration Set 

9.1.1 Species Data 

Diatom species are listed by their 8-character taxon codes; (see SOP #7 Analysis of Slides, 

Appendix 1, for a list of all codes used in the 145 lake Minnesota calibration set). These codes 

follow the format used by the Great Lakes Environmental Indicators (GLEI) project (E. Reavie, 

Natural Resources Research Institute, University of MN, Duluth); the GLEI list will be used as a 

starting point, however many taxa and codes will need to be added as the project progresses. A 

complete and up-to-date list of codes for this project will be maintained in a database at the St. 

Croix Watershed Research Station (SCWRS). (Note: if a different contractor is conducting the 

work, replace each reference to SCWRS with that of the contractor’s name.) 

Taxa that occurred in at least two samples with a maximum abundance greater than or equal to 

1% of the diatom sum for that sample are included in the analysis for construction of the 

calibration set. In addition, if a species occurred in only one sample, but at more than 5% of that 

lake’s diatom assemblage, it is included. Note that these criteria only apply to building the 

calibration set. For analyses after the calibration set is complete, data for all species will be used. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 3

When performing any multivariate analyses (building the calibration set, or analyses afterward) 

diatom species data will be entered as the percent abundance of that species relative to the total 

diatom counts in the sample (not the raw counts). 

9.1.2 Environmental Data 

The top 1 cm of surface sediment that is used for diatom analysis represents the diatoms that 

have settled out of the water column over the previous 3-5 years. Therefore, it is appropriate to 

compare the diatom counts to the average water chemistry conditions for the ice-free season 

during the year that the sediment sample is collected. When the calibration set is built, water 

quality data from each of the season’s samplings will have been averaged, and those averages 

will have been used for comparison with the diatom counts. 

For the statistical analyses, it is important that the environmental data are normally distributed 

and have similar scaling. Therefore, many of the environmental parameters in the calibration set 

are transformed (e.g., log10, square root) to achieve a normal distribution of data. 

9.2 Multivariate Analyses 

The following section is an overview of commonly used multivariate analyses, using the MN 

diatom calibration set as an example. The purpose of this section is to describe the analyses that 

were used in constructing the MN diatom calibration set, and is not intended to be an exhaustive 

review of all available multivariate analyses. For example, nonmetric multidimensional scaling 

(NMS) is an indirect (unconstrained) ordination method that could be used to examine species 

data in place of correspondence analysis, which is discussed below (see McCune and Grace 

(2002) for a detailed discussion of NMS). However, the main focus of this SOP is on the diatom 

calibration set; the calibration set approach requires a direct (constrained) method of ordination 

such as canonical correspondence analysis (CCA). In addition, as the project progresses, 

additional statistical methods may be necessary to explain trends and make management 

decisions (e.g., Sgro et al. 2007). 

9.2.1 Principal Components Analysis 

Principal components analysis (PCA) is an indirect ordination method. One of the uses of PCA is 

to show variation in the lakes in terms of environmental variables alone, not being constrained by 

a secondary dataset (see Table 2 for a classification of ordination methods). A linear method of 

indirect ordination is used in this case because environmental data generally exhibit linear 

relationships with each other and the underlying gradients, as opposed to diatom species data 

which often have a unimodal response to an underlying gradient (with an optimum and tolerance 

range for each species along that gradient). Figure 1 is an example PCA of MN lakes based on 

environmental variables. Axis 1 represents the maximum variation in the dataset; this is a 

theoretical variable, not necessarily something that was measured. Axis 2 represents the second 

most explanatory gradient in the dataset. The vectors represent the environmental variables that 

were included in the analysis, with the value of the variable increasing in the direction of the 

arrow, and decreasing in the opposite direction (the origin represents the average value for each 

variable). The absolute length of the vector is not meaningful, but the relative length of the 

vector in relation to the other vectors is important (the longer the vector the greater the increase). 

The vectors that are most correlated with Axis 1 are those that best explain the maximum 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 4

variation in the dataset, and the vectors most closely correlated with Axis 2 best explain the 

secondary gradient in the dataset. 

9.2.2 Correspondence Analysis and Detrended Correspondence Analysis 

The species data can also be examined with an indirect model; this will show the patterns in the 

lakes based on species assemblage alone. First, the analyst must determine, using gradient 

lengths, if it is appropriate to use a linear or unimodal model with a given set of species data. If 

the gradients are short (generally less than 2 standard deviation units is used as a cutoff; 

however, both methods are effective for standard deviations in the range of 1.5-3), then many of 

the species responses to the underlying gradients will be linear and it is appropriate to use a PCA 

(if this is the case, it would be appropriate to use the same approach that was used with the 

environmental data in Section 9.2.1). If the gradients are long (greater than 2 standard deviation 

units), then the gradients are generally long enough to have captured most of the tolerance range 

of a given species and many or most of the species responses to the underlying gradients will be 

unimodal. In this case, it is appropriate to use correspondence analysis (CA) or detrended 

correspondence analysis (DCA). 

To determine the gradient lengths for a given model, DCA is used as a means to compute axis 

lengths in standard deviation units. If the gradients are long then CA is used to examine the 

variation in the lakes based on the species assemblages. The sites, species, or both can be plotted. 

Occasionally after running a CA, the data have a distinct arch when plotted. The arch is present 

when the first ecological gradient is much longer than the second gradient; an arch artifact occurs 

because CA constructs the second gradient as a non-linear function of the first. If this is the case, 

DCA can be used because it removes this arch effect by detrending and rescaling the data. Since 

the arch results in shrinking at the ends of the ordination, removing the arch is desirable for 

accurate interpretation of distances among points. 

In the MN dataset, a DCA shows that the gradients in the species data are long (greater than 2 

standard deviation units), so a unimodal model is appropriate. There is a strong arch in the data 

when a CA is run; this is evident in both the plot of sites (Figure 2a) and the plot of species 

(Figure 2b). Figure 3 demonstrates that running a DCA removes this arch effect in the data. 

9.2.3 Canonical Correspondence Analysis 

Biological datasets often contain a large amount of variation, some of which can be attributed to 

‘noise,’ or to other gradients that were not measured. In order to examine the patterns in the 

dataset that can be attributed to the variables that were measured, a constrained ordination is 

used. In the MN dataset, the gradients in the species data are long (see Section 9.2.2 for how this 

is determined), so it is appropriate to use canonical correspondence analysis (CCA), which is a 

unimodal direct ordination method (if the gradients were short, then a linear model such as 

redundancy analysis [RDA] would be appropriate [Table 2]). It is important to note that CCA 

generally removes the arch that is sometimes present in a CA, because now the axes are being 

constrained by the measured environmental variables. However, if the data have a long primary 

gradient it is possible that there will still be an arch in the CCA; if this is the case, detrended 

CCA (DCCA), which is available in CANOCO, can be used to remove the arch. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 5

Often, many of the environmental variables measured are highly correlated. Therefore, the next 

step is to determine the best subset of environmental variables that independently explain the 

variation in the species data. Some statistical packages (for example, CANOCO) will perform 

this forward selection of variables automatically, or this can be done manually by performing a 

series of partial CCAs to determine the best subset of variables to use. The result of this forward 

selection step is a subset of variables that independently explain almost as much variation as the 

full set of variables. Refer to Ramstack et al. (2003), Edlund and Kingston (2004) and Reavie et 

al. (2006) for examples of how calibration sets are developed using forward selection. 

Figure 4 is a CCA biplot of the 145 lakes MN calibration set, with all of the environmental 

variables included. In this plot, the sites (lakes) are displayed, but as with CA, the species could 

be displayed. As in PCA, the variable increases in the direction of the vector, and decreases in 

the opposite direction. Again, the absolute length of the vector is not important, but its relative 

length and position compared to the other vectors is meaningful; the variables with the longer 

vectors are more important in determining that gradient, and variables for which the vectors are 

situated close together are more closely related to one another. 

Figure 5 shows a CCA biplot of the 145 lakes MN calibration set with only the forward selected 

variables included in the analysis, and gives an example of different ways that results can be 

displayed. For example, in this plot the environmental vectors have been plotted as a separate 

biplot to make things easier to read. Also, the ecogregions have been plotted as centroids, both in 

a separate biplot and as large symbols in the main biplot. Notice that in Figure 5 some of the 

highly correlated variables have been removed. For example, total phosphorus (TP), total 

nitrogen (TN), and chlorophyll-a (Chla) were highly correlated (Figure 4) and forward selection 

determined that Chla was the best of the three variables to independently explain a significant 

amount of variation. 

Table 2. Summary and classification of ordination methods (modified from Juggins 2006). 

 Response Model 

Role of explanatory variables 

in analysis 

Linear Unimodal 

Indirect 

(variation is not constrained 

by a secondary dataset) 

Principal Components 

Analysis (PCA) 

Correspondence Analysis 

(CA) & Detrended 

Correspondence Analysis 

(DCA) 

Direct 

(variation is constrained by a 

secondary dataset) 

Redundancy Analysis (RDA) Canonical Correspondence 

Analysis (CCA) & Detrended 

Canonical Correspondence 

Analysis (DCCA) 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 6

9.3 Analysis After the Calibration Set is Complete

Diatom samples collected during routine monitoring can be passively plotted on the existing 

calibration set, and the calibration set can be used to determine the environmental conditions in 

the lake based on the diatom species assemblage. Before beginning these analyses, diatom 

taxonomy should be harmonized with the MN/GLKN calibration set. Diatom species should be 

coded with the same 8-character taxon codes used in the calibration set (see Section 9.1.1). When 

performing the following analyses, the diatom species data should be entered as the percent of 

that species occurrence relative to the total diatom count for that sample (not the raw counts). 

9.3.1 Passively Plotting on the Calibration Set 

After the calibration set has been established, subsequent diatom data from surface sediment 

samples will be passively plotted onto the calibration set to see which lakes they are most similar 

to, and to see where they plot along the environmental axes. As lakes are revisited, analyses will 

show whether a given lake’s diatom assemblage has changed since the lake was last sampled, 

and if it has changed, with which environmental axis (or axes) the change is correlated. 

For example, Figure 6 is a CCA biplot of a subset of the MN calibration set containing 89 lakes. 

A modern surface sample from a Twin Cities metro area lake and a downcore sample from that 

same lake are passively plotted on this calibration set. The plot shows that over time the lake’s 

diatom assemblage has changed (if it had remained stable, both samples would have plotted on 

top of each other), and this change follows the trajectory of the pH and chloride (Cl) axes. From 

this plot one can infer that over time this lake likely had an increase in pH and Cl levels. This 

same method can be applied to GLKN lakes. 

9.3.2 Dissimilarity Measure 

To determine the amount of floristic change in the diatom community between subsequent 

sampling events, the chord distance dissimilarity measure will be used. The chord distance 

provides a quantitative measure of the amount of change in the diatom species assemblage 

between two samples. So, beginning with the second round of sampling, the chord distance can 

be used to quantify the change in the diatom community for a given lake since the previous 

sampling event. The chord distance ranges from 0 (samples are exactly the same) to 1.41 

(samples are completely different). Meaningful change can be assessed using percentile cutoffs 

according to the approach used in Bennion et al. (2004). In addition, lakes which have been 

cored can be used to determine how large of a chord distance is meaningful; changes in 

downcore chord distance can put current measurements into context (see Section 9.4). 

 

9.3.3 Environmental Reconstructions 

After establishing the calibration set, the environmental variables that were selected in the 

forward selection step can be predicted for a new species assemblage. This is generally referred 

to as ‘reconstructing’ environmental conditions from fossil diatoms in a sediment core, but this 

same technique can be applied to new surface sediment samples after the calibration set has been 

established. If, for example, TP was one of the variables found to be significant after forward 

selection with the new calibration set (or if independent, constrained testing of TP demonstrated 

an important relationship to the diatom gradient), then a TP value can be determined from a 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 7

subsequent diatom surface sediment sample in one of the GLKN lakes. The statistical program 

C2 (Juggins 2003) is widely used for this step. 

9.4 Analyses for Lakes with Downcore Diatom Data 

As part of the 2004 - 2009 GLKN diatom project (Task Agreement #J2105040028), a select 

subset of GLKN lakes was cored for diatom and geochemical analysis to determine the timing 

and magnitude of historical environmental change. For the lakes where these data are available, 

an indirect ordination of the diatom species assemblage can be plotted and any subsequent 

diatom surface sediment samples can be added to this plot to see how the species assemblage is 

changing (see Section 9.2.2 for instructions on how to decide between a linear or a unimodal 

model for indirect analysis). Figure 7 is an example of a CA from Shell Lake (Sleeping Bear 

Dunes National Lakeshore) based on diatom species assemblage. This shows that the diatom 

community began to change in the late 1800s/early 1900s, and has also been changing along a 

new trajectory in the past decade or so. When this lake is re-sampled for diatoms in the future, 

the new sample can be added to this plot and it can be determined if the diatom species 

assemblage in this lake is continuing to change along the trajectory established in the last decade, 

if the community is remaining stable, or if it is returning to what it looked like at some point in 

the past, etc. This can provide an early warning sign of change in the GLKN lakes based on 

biological communities. To determine which environmental variables are causing the change, the 

core samples can be passively plotted on the calibration set (follow the method used in Section 

9.3.1 and Figure 6). 

To determine the amount of floristic change throughout the core, the chord distance can be 

calculated between each core section. The chord distances throughout the core can be used to put 

modern distances into context. For example, the chord distance between two samples dating 

before European settlement could be used as a measure of low floristic change, which could then 

be compared to the chord distance between two modern samples. 

9.5 Literature Cited

Edlund, M. B. 2005. Using diatom-based analysis of sediment records from central Minnesota 

lakes for TMDL and nutrient criteria development. Final report to the Minnesota 

Pollution Control Agency. 

Edlund, M. B., and J. C. Kingston. 2004. Expanding sediment diatom reconstruction model to 

eutrophic southern Minnesota lakes. Final report to the Minnesota Pollution Control 

Agency. 

Faria, J. C., P. Grosjean, and E. Jelihovschi. 2007. Tinn-R - GUI/Editor for R language and 

environment statistical computing. URL http://sourceforge.net/projects/tinn-r. 

Jongman, R. H., C. J. F. terBraak, and O. F. R. Van Tongeren. 1995. Data Analysis in 

Community and Landscape Ecology. Cambridge University Press, Cambridge. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 8

Juggins, S. 2003. C2 version 1.3, Software for ecological and palaeoecological data analysis and 

visualization. University of Newcastle, Newcastle upon Tyne, NE17RU, United 

Kingdom. 

Juggins, S. 2006. Lecture notes and course-pack from Analysis of Environmental Data course. 

Iowa Lakeside Laboratory. 

Leps, J., and P. Šmilauer. 2003. Multivariate Analysis of Ecological Data using CANOCO. 

Cambridge University Press, Cambridge, United Kingdom. 

McCune, B., and J. Grace. 2002. Analysis of Ecological Communities. MjM Software Design, 

Gleneden Beach, Oregon. 

McCune, B., and M. J. Mefford. 1999. PC-ORD. Multivariate Analysis of Ecological Data. 

Version 4.0. MjM Software, Gleneden Beach, Oregon, USA. 

R Development Core Team. 2006. R: A language and environment for statistical computing, 

version 2.4.1. The R foundation for Statistical Computing, ISBN 3-900051-07-0. 

<http://www.r-project.org>. 

Ramstack, J. M., S. C. Fritz, D. R. Engstrom, and S. A. Heiskary. 2003. The application of a 

diatom-based transfer function to evaluate regional water-quality trends in Minnesota 

since 1970. Journal of Paleolimnology 29:79-94. 

Reavie, E. D., R. P. Axler, G. V. Sgro, N. P. Danz, J. C. Kingston, A. R. Kireta, T. N. Brown, T. 

P. Hollenhorst, and M. J. Ferguson. 2006. Diatom-based weighted-averaging transfer 

functions for Great Lakes coastal water quality: Relationships to watershed 

characteristics. Journal of Great Lakes Research 32:321-347. 

Sgro, G. V., E. D. Reavie, J. C. Kingston, A. R. Kireta, M. J. Ferguson, N. P. Danz, and J. R. 

Johansen. 2007. A diatom quality index from a diatom-based total phosphorus inference 

model. Environmental Bioindicators 2:15-34. 

Shaw, J. 2003. Multivariate Statistics for the Environmental Sciences. Arnold, London. 

ter Braak, C. J. F., and P. Šmilauer. 1998. CANOCO reference manual and user's guide to 

Canoco for Windows: Software for Canonical community ordination (version 4). 

Microcomputer Power, Ithaca. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 9

-1.5 -1.0 -0.5 0.0 0.5 1.0

-1.0 -0.5 0.0 0.5 1.0

PC1

PC2

ANC

Chla

Cl

Color

Cond

LakeArea

pH

Secchi

TN

TP

WshdArea

DepthMax

DepthAvg

Figure 1. PCA of environmental data (ecoregion excluded) from the 145-lake MN 

calibration set; the dots represent sites (lakes). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 10

-3 -2 -1 0 1 2 3

-3 -2 -1 0 1 2

CA1

CA2

a) Sites displayed

-3 -2 -1 0 1 2 3

-3 -2 -1 0 1 2

CA1

CA2

b) Species displayed

Figure 2. CA biplots of the 145-lake MN calibration set with 

a ) sites displayed and b) species displayed. Note that there is 

an arch in the data. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 11

-2 -1 0 1 2

-1 0 1 2

DCA1

DCA2

a) Sites displayed

-4 -3 -2 -1 0 1 2

-2 -1 0 1 2 3 4

DCA1

DCA2

b) Species displayed

Figure 3. DCA biplots of the 145-lake MN calibration set 

with a) sites displayed and b) species displayed. Note that the 

DCA removes the arch effect that was present in the data in 

the CA (Fig. 2). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 12

-2 -1 0 1 2

-2 -1 0 1 2

CCA1

CCA2

ANC

Chla

Cl

Color

Cond

LakeArea

pH

Secchi

TN

TP

WshdArea

DepthMax

DepthAvg

Figure 4. CCA of the 145-lake MN calibration set, with all of the environmental 

variables included (sites plotted). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 13

-1 0 1 2

-2 -1 0 1

CCA1

CCA2

NLF

CHF

Metro

WCP

NGP

Color

Cond

Cl ANC

pH

Chla

DepthMax

-0.5 0.0 0.5 1.0

-1.0 -0.5 0.0 0.5

NLF

CHF

Metro

WCP

NGP

Figure 5. CCA of the 145-lake MN calibration set with the forward selected variables. 

The environmental vectors have been plotted as a separate biplot to make the plot easier 

to read. The ecoregions have been plotted as centroids, both in a separate biplot and as 

large symbols in the main plot. Ecoregion codes: NLF=Northern Lakes and Forests, 

CHF=Central Hardwood Forests, Metro=Twin Cities Metropolitan Area, 

WCP=Western Corn Belt Plains, NGP=Northern Glaciated Plains. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 14

-2 -1 0 1 2

-1 0 1 2

CCA1

CCA2

NLF

CHF

Metro

WCP

NGP

MCWD

logTP

logZmax

pH

logColor

logx1Cl

Cond

modern sample

X

X

downcore sample

Figure 6. Subset of the MN calibration set (89 lakes), showing a modern and 

downcore assemblage from a Twin Cities metro lake passively plotted. This plot 

demonstrates that over time this lake has likely experienced an increase in pH and Cl, 

and a slight increase in TP and conductivity. Ecoregion codes: NLF=Northern Lakes 

and Forests, CHF=Central Hardwood Forests, Metro=Twin Cities Metropolitan Area, 

WCP=Western Corn Belt Plains, NGP=Northern Glaciated Plains, 

MCWD=Minnehaha Creek Watershed District. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #9, page 15

-3 -2 -1 0 1

-2 -1 0 1 2

CA1

CA2

X2003 X1997

X1991

X1980 X1968

X1953

X1941

X1925

X1912

X1889

X1870

X1841

X1810

X1771

X1727

Figure 7. CA of downcore samples from Shell Lake (Sleeping Bear Dunes 

National Lakeshore) based on species assemblages from sections dating from 

1727 to 2003. 
Standard Operating Procedure #10: Reporting 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation:

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #10, 

Reporting. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, and J. E. Elias. 

2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort Collins, 

Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #10, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

10.0 Introduction..........................................................................................................................1 

10.1 Annual Reports ....................................................................................................................1 

10.2 Scientific Journal Articles....................................................................................................1 

10.3 Other Communications ........................................................................................................2 

10.4 Literature Cited ....................................................................................................................2 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #10, page iii

Revision History Log 

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #10, page iv

Acknowledgements 

This standard operating procedure is based on SOP #10, Reporting, by Sanders and Elias (2008), 

from the Water quality monitoring protocol for inland lakes (Elias et al. 2008).
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #10, page 1

10.0 Introduction

A primary goal of the NPS Inventory and Monitoring (I&M) Program is to ensure that the results 

and knowledge gleaned from monitoring are shared with all appropriate parties, especially the 

parks and their natural resource managers. Because the Great Lake Network’s (GLKN) main 

focus is to assist parks with monitoring needs, we will strive to provide park managers with 

clear, meaningful products to convey our findings. 

While GLKN primarily addresses concerns of the parks, its monitoring program has the potential 

to serve a much broader community. For example, monitoring projects can provide a starting 

point for external scientific research (especially to establish cause-effect relationships) and can 

provide insights for adaptive management on other public lands. The GLKN is also accountable 

to multiple organizations within the federal government, including the NPS I&M Program and 

the U.S. Congress. To ensure accountability and to meet the requests of all parties, we will 

provide the types of reports and communications detailed below. 

10.1 Annual Report

The contractors will write annual reports in collaboration with GLKN’s aquatic ecologist. The 

reports will be written using a typical scientific format and will contain: 

• a brief introduction that describes why we are using diatoms for monitoring 

• an outline of the sampling strategy, including the number and location of sites sampled 

• multivariate statistical summaries of the diatom and water quality data, including tables 

and figures to enhance visual presentation, as well as a text explanation of the findings 

• any other relevant or significant findings 

• a discussion section in which important results are interpreted 

• literature cited 

The analyses and synthesis reports will become progressively more in-depth as lakes in the 

National Park units are monitored repeatedly. The reports will place the observed results in both 

a regional and historical context by relating them to other published literature. The significance 

of the results will be discussed in terms of environmental change, and management 

recommendations will be provided based on the findings. 

The target audience of these reports will be the parks (primarily the natural resource managers), 

GLKN staff, and both regional and Servicewide I&M. Outside of the NPS, the target audience 

includes the four state departments of natural resources (Indiana, Michigan, Minnesota, 

Wisconsin), the St. Croix River Interagency Basin Team, the Twin Cities Metropolitan Council, 

and the broader scientific community. 

10.2 Scientific Journal Articles

Diatom monitoring results are expected to be highly defensible and meet the standards of the 

peer-review process. The publication of diatom monitoring results in scientific journals will 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #10, page 2

allow GLKN to reach the scientific community in a way that internal NPS reports cannot. 

Further, peer-reviewed publications can promote collaborative investigation by members of the 

scientific community, either independently or in cooperation with GLKN. Ultimately, this 

process should foster a greater understanding of ecosystem components and processes. 

For these reasons, the Great Lakes I&M Network will strive to publish analysis and synthesis 

reports in peer-reviewed scientific journals. The preparation of manuscripts will be encouraged, 

and reviewers of analysis and syntheses reports will be asked to recommend whether publication 

is warranted and suggest appropriate journals. 

10.3 Other Communications

While reports are a definitive method of documenting the progress of each program, other means 

of communication can further disseminate information to a broader audience. To this end, the 

following additional types of communications will be provided: 

Briefings to park biologists 

The NPS project manager will present the findings from the water quality monitoring program to 

the biologists from the parks in which monitoring was conducted the previous year. These 

presentations, which will likely occur at the annual technical committee meeting in March, will 

provide a concise synopsis of monitoring results as well as management considerations. 

Conference presentations 

When possible, the researchers and the NPS project manager will present monitoring results at 

regional and national scientific conferences. Such presentations will allow GLKN to reach the 

broader scientific community, as well as land managers and conservation practitioners. Potential 

conferences include those sponsored by the Ecological Society of America, Society for 

Conservation Biology, The Wildlife Society, the Natural Areas Association, the NPS Water 

Professionals Meeting, and the George Wright Society. At a more local scale, the Western Great 

Lakes Research Conference, which is sponsored in part by GLKN, is a valuable venue for 

information exchange. 

10.4 Literature Cited

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol narrative for 

inland lakes, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. 

National Park Service, Fort Collins, Colorado. 

Sanders, S., and J. E. Elias. 2008. Standard operating procedure #10, Reporting. In Elias, J. E., R. 

Axler, and E. Ruzycki. 2008. Water quality monitoring protocol for inland lakes, Version 

1.0. National Park Service, Great Lakes Network, Ashland, Wisconsin. Natural 

Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. National Park 

Service, Fort Collins, Colorado. 
Standard Operating Procedure #11: 

Post-Season Procedures 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #11, 

Post-season procedures. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. Lafrancois, 

and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park Service, Great 

Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National Park Service, Fort 

Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #11, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

11.0 Introduction..........................................................................................................................1 

11.1 End of Season Procedures....................................................................................................1 

 11.1.1 Field Equipment........................................................................................................1 

 11.1.2 Laboratory Equipment ..............................................................................................1 

11.2 Data Management ................................................................................................................1 

11.3 Quality Assurance/Quality Control......................................................................................1 

11.4 Literature Cited ....................................................................................................................1 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #11, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #11, page iv

Acknowledgements 

This standard operating procedure is based on SOP #11, Post-season procedures, by Axler et al. 

(2008), from the Water Quality Monitoring Protocol for Inland Lakes (Elias et al. 2008).
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #11, page 1

11.0 Introduction

The proper maintenance and storage of field and laboratory equipment will prolong the life of 

the gear as well as simplify start-up procedures for the next field sampling season. 

11.1 End of Season Procedures

11.1.1 Field Equipment 

Clean and dry the surface corer and return removable parts to the storage case before storage. 

Inventory all supplies (such as specimen cups) and replace supplies as needed as soon as 

possible. 

11.1.2 Laboratory Equipment 

Inventory all supplies (microscope slides, coverslips, chemicals, etc.) and replace, if necessary, 

as soon as possible. 

11.2 Data Management

Complete and accurate record keeping of field-derived data is extremely important. At the end of 

each field season, all field notes should be either scanned or photocopied. Field technicians, crew 

leaders, and project leaders share responsibility for collecting, verifying, and documenting data 

according to the guidelines in this monitoring protocol and all applicable standard operating 

procedures. Refer to the GLKN Data Management Plan for overall guidance (Hart and Gafvert 

2005). 

11.3 Quality Assurance/Quality Control

Proper care of all field and lab instrumentation and sampling gear is a fundamental part of any 

QA/QC program. 

11.4 Literature Cited

Axler, R., E. Ruzycki, and J. E. Elias. 2008. Standard operating procedure #11, Post-season 

procedures. In Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring 

protocol for inland lakes, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—

2008/109. National Park Service, Fort Collins, Colorado. 

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol narrative for 

inland lakes, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. 

National Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #11, page 2

Hart, M., and U. Gafvert. 2005. Data management plan: Great Lakes Inventory & Monitoring 

Network (draft). National Park Service Great Lakes Inventory and Monitoring Network 

GLKN/2005/20.
Standard Operating Procedure #12: 

Quality Assurance and Quality Control 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008 

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #12, 

Quality assurance and quality control. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page ii

Contents

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

12.0 Introduction..........................................................................................................................1 

12.1 QA/QC Specific to Other SOPs...........................................................................................1 

 12.1.1 Field Methods ...........................................................................................................1 

 12.1.2 Cleaning Samples and Preparing Slides ...................................................................2 

 12.1.3 Couning Slides..........................................................................................................2 

 12.1.4 Archiving ..................................................................................................................3 

 

12.2 Literature Cited ....................................................................................................................3 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to Revising the Protocol, SOP #13. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page iv

Acknowledgements 

Thanks to Kalina Manoylov, Euan Reavie, Sarah Spaulding, and Don Charles for discussions of 

QA/QC procedures. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page 1

12.0 Introduction

Long-term monitoring is only valuable if users have confidence in the data. Efforts to detect 

trends and patterns in ecosystem processes require high-quality, well-documented data that 

minimize error and bias. Data of inconsistent or poor quality can result in loss of sensitivity and 

lead to incorrect interpretations and conclusions. 

NPS Director’s Order #11B: Ensuring Quality of Information Disseminated by the National Park 

Service (www.nps.gov/policy/DOrders/11B-final.htm) specifies that information produced by 

the NPS must be of the highest quality and based on reliable data sources that are accurate, 

timely, and representative of the most current information available. Therefore, GLKN will 

establish and document procedures for quality assurance (QA) and quality control (QC) to 

identify and reduce the frequency and significance of errors at all stages in the data life cycle. 

Under these procedures, the progression from collection of samples in the field to verified data to 

validated data implies increasing confidence in the quality of those data. Quality assurance and 

quality control procedures will document review processes and include guidance for addressing 

problems with data quality. 

Examples of general QA/QC practices include: 

• Standardized field data collection forms 

• Proper maintenance of equipment 

• Training of field crew and laboratory technicians 

• Duplicate sampling 

12.1 QA/QC Specific to Other SOPs 

12.1.1 Field Methods

The Wiegner corer, used to collect surface sediment samples, is not a complicated instrument, 

though collection of a good sediment sample depends on its proper use. Ensure field personnel 

are adequately trained in the proper use of the corer and have ample opportunity to practice 

taking samples prior to taking an actual sample. To ensure cross-contamination of samples does 

not occur, thoroughly clean corer and all parts between sampling sites. 

 

Collect the sample during the final round of water quality sampling at the proper location. 

Examine the core in the field to ensure it is a good sample (e.g., depositional sediment rather 

than sand, and an undisturbed sediment-water interface). Use new disposable pipettes for 

dispensing each sample into sample cups to avoid cross-contamination. Record the sampling 

location on the field form and ensure all other information is recorded completely and accurately. 

Send a copy of the field form to the contractor and keep the original on file in the GLKN office. 

Store the sample in the dark on ice. 

Only one field sample will be collected. In lake environments, the deep-water sediments provide 

a highly integrated sample of diatom community structure for the lake as a whole. Sedimentary 

processes collect and mix diatoms from all habitats within the lake (plankton, periphyton, 

epilithic, epipelic) and deposit them in a uniformly mixed assemblage across the deeper regions 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page 2

of the lake. This means that only a single sample of surface sediment is needed to characterize 

the entire lake (Anderson 1990) – as compared to the numerous samples required to overcome 

spatial heterogeneity for other bioindicators (e.g., benthic invertebrates). The uniformity of 

sedimentary diatom samples has been repeatedly verified from multiple cores and transects of 

surface samples taken from individual lakes (e.g., Anderson 1990). Although there is a tendency 

for benthic species to be better represented in near-littoral areas, this does not present a problem 

for surface sediments if roughly the same locations are resampled (which is easily accomplished 

with GPS). Resampling will be done within meters of a station's fixed location to minimize 

variability across the depositional basin. At this sampling resolution, difference in cores and 

surface samples will be minimal (Charles et al. 1991, Petterson et al. 1993). 

 

12.1.2 Cleaning Samples and Preparing Slides 

Process the samples within two weeks of collection to ensure samples are representative of the 

diatom assemblage at the time of sampling. Avoid cross-contamination of samples during every 

step of handling by maintaining clean work surfaces and using new disposable pipettes for each 

sample. 

All slides will be prepared in duplicate: set ‘a’ will be counted, set ‘b’ will be archived and 

available for loan to other laboratories. To ensure duplicates are as similar to each other as 

possible, mix each sample thoroughly prior to preparing the slides. Follow procedures detailed 

in SOP #8 for the archival of duplicate slides. 

12.1.3 Counting Slides 

Any new technicians introduced into the program will need to be trained by an experienced 

diatom taxonomist. To ensure internal taxonomic consistency, photographic databases will be 

constructed for all predominant diatom taxa; this collection of photographs will be maintained at 

the St. Croix Watershed Research Station (SCWRS). 

Each year, 10% of the samples collected will be recounted by another analyst in the program. 

The primary analyst will etch a line in the slide to mark the transect counted, and will etch circles 

at the start and end points of the area counted along the transect. The QC analyst will then use 

the etchings to count the exact same portion of the slide. The percent difference between the two 

counts will be calculated as follows: 

 %Difference = (1 – Σ min(a,b)) * 100 

Where a and b are the relative proportions recorded for a given taxon by the primary taxonomist 

(a) and the QC taxonomist (b). 

The two counts should have a percent difference of less than or equal to 30% (this is the criteria 

being used by the EPA National Lakes Assessment program; K. Manoylov, pers. comm.). If the 

percent difference exceeds 30%, the two taxonomists will discuss the discrepancies between the 

samples. If significant differences are found to exist in how the two analysts have been 

identifying diatoms, samples may have to be recounted by the primary taxonomist. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #12, page 3

Duplicate counts will be used only for taxonomic control; only the original counts will be used in 

data analysis. 

12.1.4 Archiving 

Archived slides and samples will be checked periodically to be sure that they have not been 

damaged while in storage. 

12.2 Literature Cited 

Anderson, N. J. 1990. Variability of diatom concentrations and accumulation rates in sediments 

of a small lake basin. Limnology and Oceanography 35:497-508. 

Charles, D. F., S. S. Dixit, J. P. Smol and B. F. Cumming. 1991. Variability in diatom and 

chrysophyte assemblages and inferred pH: paleolimnological studies of Big Moose Lake, 

N.Y. Journal of Paleolimnology 5:267-284. 

Petterson, G., I. Renberg, P. Geladi, A. Lindberg, and F. Lindgren. 1993. Spatial uniformity of 

sediment accumulation in varved lake sediments in northern Sweden. Journal of 

Paleolimnology 9:195-208. 

Standard Operating Procedure #13: 

Procedure for Revising the Protocol 

Version 1.0 

In Diatom Monitoring Protocol

Prepared by 

Joy Ramstack, Mark Edlund, and Daniel Engstrom 

St. Croix Watershed Research Station 

Science Museum of Minnesota 

16910 152nd Street North 

Marine on St. Croix, Minnesota 55047 

August 2008

Suggested citation: 

Ramstack, J. M., M. B. Edlund, and D. R. Engstrom. 2008. Standard operating procedure #13, 

Procedure for revising the protocol. In Ramstack, J. M., M. B. Edlund, D. R. Engstrom, B. M. 

Lafrancois, and J. E. Elias. 2008. Diatom monitoring protocol, Version 1.0. National Park 

Service, Great Lakes Network, Ashland, Wisconsin. NPS/GLKN/NRR—2008/068. National 

Park Service, Fort Collins, Colorado. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #13, page ii

Contents 

 Page 

Revision History Log..................................................................................................................... iii 

Acknowledgements........................................................................................................................ iv 

13.0 Introduction..........................................................................................................................1 

13.1 Steps for Revising the Protocol............................................................................................1 

13.2 Literature Cited ....................................................................................................................2 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #13, page iii

Revision History Log

The following table lists all edits and amendments to this document since the original publication 

date. Information entered in the log must be complete and concise. Users of this standard 

operating procedure will promptly notify the project manager and/or the Great Lakes Network 

(GLKN) data manager about recommended and required changes. The project leader must 

review and incorporate all changes, complete the revision history log, and change the date and 

version number on the title page and in the footer of the document file. For complete 

instructions, please refer to the information in this protocol, below. 

Revision History Log:

Previous 

Version # 

Revision 

Date 

Author (with 

title and 

affiliation) 

Location in Document 

and Concise 

Description of Revision 

Reason for Change New 

Version # 

 

Add rows as needed for each change or set of changes tied to an updated version number 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #13, page iv

Acknowledgements 

This standard operating procedure is based on SOP #12, Procedure for revising the protocol, by 

Sanders and Elias (2008), from the Water quality monitoring protocol for inland lakes (Elias et 

al. 2008). 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #13, page 1

13.0 Introduction

Long term monitoring programs like that of the National Park Service must be able to 

accommodate change. Refined field methods, advances in analytical techniques, and feedback 

from field crews and project managers can all contribute to the improvement of the monitoring 

protocols. The purpose of the current SOP is to define a systematic and routine process for 

incorporating these changes into the protocol. 

13.1 Steps for Revising the Protocol

Participants in this diatom monitoring project who see a need for change should: 

1. Attempt to incorporate the changes by first modifying only the SOP(s), without making 

changes to the protocol narrative. However, if it is clear that changes are needed in the narrative, 

it should be revised as well. 

2. Make all revisions using the Track Changes feature of Microsoft Word. For minor changes, at 

least one other person must review the revision. If the change is more extensive, a discussion by 

Network staff is warranted before acceptance of the revision. For major changes, review from 

outside of the Network should be sought. Examples of major changes include modifications of 

the sampling design, significantly altered field methods, and revised analysis techniques. 

3. Record the changes in the revision history log of the SOP and/or in the narrative, as 

appropriate. Include the date of revision, full name(s) and affiliation(s) of author(s), description 

of and reasons for the changes, and section of SOP or narrative where changes were made. 

4. Rename the version of the SOP and/or narrative. For minor changes, only revise the version 

number after the decimal point (e.g., change V. 1.1 to V. 1.2). For major changes, revise the 

number before the decimal point (e.g., V. 2.3 to 3.0). Also change the version number of the SOP 

or protocol in the header or footer, as appropriate. 

5. Notify the data manager of the change(s) so that the metadata of the project database will be 

updated. 

6. Distribute the revised version to all appropriate parties, including the members of the field 

crew and appropriate GLKN staff. The revised version must also be posted on the Network’s 

website. 

7. Maintain a library of previous versions. Such historical information may be crucial for 

understanding, interpreting, and analyzing data. 
Great Lakes Network Diatom Monitoring Protocol, Version 1.0 August 2008

SOP #13, page 2

13.2 Literature Cited 

Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring protocol narrative for 

inland lakes, Version 1.0. National Park Service, Great Lakes Network, Ashland, 

Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—2008/109. 

National Park Service, Fort Collins, Colorado. 

Sanders, S., and J. E. Elias. 2008. Standard operating procedure #12, Procedure for revising the 

protocol. In Elias, J. E., R. Axler, and E. Ruzycki. 2008. Water quality monitoring 

protocol for inland lakes, Version 1.0. National Park Service, Great Lakes Network, 

Ashland, Wisconsin. Natural Resources Technical Report NPS/MWR/GLKN/NRTR—

2008/109. National Park Service, Fort Collins, Colorado. 
The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and 

other information about those resources; and honors its special responsibilities to American Indians, Alaska Natives, and 

affiliated Island Communities. 

NPS D-85, August 2008
National Park Service 

U.S. Department of the Interior 

 

Natural Resource Program Center 

1201 Oak Ridge Drive, Suite 150 

Fort Collins, CO 80525 

www.nature.nps.gov 

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