Disclaimer 

The contents of this document do not necessarily reflect the views and policies of the 

National Oceanic and Atmospheric Administration (NOAA) or the United States Coral 

Reef Task Force (USCRTF), or intended to be an opinion beyond the scientific or other 

results of its authors. The mention of trade names or commercial products does not 

constitute endorsement or recommendation for their use by NOAA or USCRTF. 

About This Document

Editor’s Acknowledgements – This document was prepared and printed with support 

from NOAA through the Coral Reef Conservation Program. Layout and design were 

provided by Cheryl M. Woodley and Amanda McLenon, NOAA NOS NCCOS 

CCEHBR, and Andy Bruckner, NOAA NMFS HC. Greta Aeby, Richard Curry, Sylvia 

Galloway, Cheva Heck, Julie Higgins, Teresa Lewis, Mats Lundqvist, Margaret Miller, 

Sara Polson, Shawn Polson, Jacquie Shapo, Meir Sussman, Dana Williams and Thierry 

Work provided technical edits. We would like to acknowledge Robert Panko of the 

Everglades National Park for his guidance and editorial comments on Incident Command 

Structure (Chapter 3). 

Photo Credits – Greta Aeby, Univ. Hawaii; Andrew W. Bruckner NOAA NMFS; 

Dorothy Howard, Amanda L. McLenon, Cheryl M. Woodley, NOAA NOS NCCOS; 

Brett Seymour, National Park Service; Laurie Raymundo, University of Guam; Shawn 

Polson and James Nicholson, Medical University of South Carolina. 

About the CDHC 

The Coral Disease and Health Consortium (CDHC) is a Working Group of the U.S. Coral 

Reef Task Force charged with organizing and coordinating the scientific resources of the 

U.S. and its territories to meet the challenge presented by globally declining coral reefs. 

Its mission is to preserve and protect the health of coral reef ecosystems through an 

understanding of the effects of natural and anthropogenic stressors on reef-building 

communities. The CDHC serves to unify the coral health and disease research 

community, identify research priorities, and encourage a new generation of coral 

researchers through education and outreach. The biomedical perspective and innovative 

technologies developed from Consortium efforts is envisioned to give scientists, resource 

managers, and industry new tools to identify and alleviate hidden stresses before they 

become environmental health crises. Currently over 125 partners, including federal 

agencies, NOAA, DOI, EPA, along with academia, non-profit and industry, contribute 

their time and expertise to the CDHC, while organizational infrastructure is supported by 

the congressionally funded NOAA Coral Reef Conservation Program. 

Citation – Please cite this manual as follows: 

Woodley, C.M., Bruckner, A.W., McLenon, A.L., Higgins, J.L., Galloway, S.B. and 

Nicholson, J.H. 2008. Field Manual for Investigating Coral Disease Outbreaks. NOAA 

Technical Memorandum NOS NCCOS 80 and CRCP 6. National Oceanic and 

Atmospheric Administration, Silver Spring, MD 85pp. 
Field Manual for Investigating Coral Disease Outbreaks

CM Woodley, SB Galloway 

NOAA/NOS/NCCOS 

Center for Coastal Environmental Health and Biomolecular Research 

AW Bruckner 

NOAA/NMFS 

Habitat Conservation 

AL McLenon, JL Higgins 

Jardon and Howard Technologies, Inc.

JH Nicholson 

Medical University of South Carolina 

Department of Pathology and Laboratory Medicine 

NOAA Technical Memorandum NOS NCCOS 80 

and 

NOAA Technical Memorandum Coral Reef Conservation Program 6 

July 2008

United States Department of National Oceanic and National Ocean Service 

Commerce Atmospheric Administration 

Carlos M. Gutierrez Conrad C. Lautenbacher, Jr. John (Jack) H. Dunnigan 

Secretary Administrator Assistant 

ii 

PREFACE

Coral reefs throughout their circumtropical range are declining at an accelerating rate. 

Recent predictions indicate that 20% of the world’s reefs have been degraded, another 

24% are under imminent risk of collapse, and if current estimates hold, by 2030, 26% of 

the world’s reefs will be lost (Wilkinson 2004). Recent changes to these ecosystems 

have included losses of apex predators, reductions of important herbivorous fishes and 

invertebrates, and precipitous declines in living coral cover, with many reefs now 

dominated by macroalgae. Causes have been described in broad sweeping terms: global 

climate change, over-fishing and destructive fishing, land-based sources of pollution, 

sedimentation, hurricanes, mass bleaching events and disease. Recognition that corals 

can succumb to disease was first reported in the early 1970’s. Then it was a unique 

observation, with relatively few isolated reports until the mid 1990’s. Today disease has 

spread to over 150 species of coral, reported from 65 countries throughout all of the 

world’s tropical oceans (WCMC Global Coral Disease Database). While disease 

continues to increase in frequency and distribution throughout the world, definitive 

causes of coral diseases have remained elusive for the most part, with reef managers not 

sufficiently armed to combat it. 

Wobeser (1994) writes, “Disease management is a tactical battle in which one uses 

intelligence gathered about the disease to identify the most vulnerable point at which to 

attack”. Understanding the disease process and how it relates to ecology are the 

necessary steps when attempting to determine causation. The rationale, however, for 

studying coral disease is often challenged as an esoteric pursuit that ‘you can’t do 

anything about anyway’. This myopic point of view undermines the ‘intelligence 

gathering’ efforts. But it is this ‘intelligence’ that makes it possible to assess the nature 

and significance of the disease, and in turn identify management strategies (‘points at 

which to attack’) to restrict or curb the occurrence or effects of the disease. 

There is a recognized need, first put forth in the CDHC National Research Plan (Woodley 

et al. 2003), articulated by resource managers, and highlighted in several Local Action 

Strategy plans, to establish local response capabilities to investigate coral disease 

outbreaks. Establishing regional Outbreak Investigation Response Teams addresses this 

need by providing a network of well trained responders that can be mobilized on short 

notice to carry out formal investigations into unusual occurrences of coral disease or 

mortality. 

This document was created through the collaborative effort of members of the CDHC to 

provide standardized protocols and procedures for field investigations of coral disease 

outbreaks. The authors also gained insight and inspiration from other field manuals 

published for wildlife (Friend 2006; Friend and Franson 1999) and marine mammals 

(Geraci and Lounsbury 1993). The framework for responses is set up such that it is 

consistent with practices of veterinary and wildlife disease experts to enable 

communication with and gain support from these disciplines. Field operations provide a 
iii 

critical link in disease diagnostics. Consistent and efficient sampling and data collection 

are crucial to effective laboratory analyses and ultimately to the diagnosis of a disease. 

This manual is intended to serve as an operational guide to coordinate effective, 

informative responses by outbreak response teams to unusual incidents of coral disease or 

mortalities. As such, there are chapters intended to assist in gathering quality information 

and maintaining specimen integrity, both of which are needed to develop a reliable 

diagnosis. We have provided a summary of ecological and environmental information 

that should be collected in the field during an outbreak response to assist in developing a 

diagnosis. Outlined, in general and in specifics, are collection techniques, preservation 

methods for different analyses, and shipping procedures. Universal precaution measures 

when dealing with diseases (i.e., work from clean to dirty areas), biological containment 

and disinfection regimes have also been highlighted. We have attempted to point out 

critical control points in each of the procedures or methodologies that must be adhered to 

minimize the risk of compromising the samples or biasing further analyses. Each 

investigation will, of course, have its own unique features, requiring that some flexibility 

be incorporated into the field operation. The initial steps in a Coral Disease Outbreak 

Investigation invariably occur in the field and thus a cohesive management scheme, 

including operational pre-planning, is critical to achieve success. To provide continuity, 

structure and consistency, the Incident Command Structure (ICS) was adopted as the 

standardized emergency management strategy for Coral Disease Outbreak Investigations, 

and adapted from that used by all other U.S. agencies operating under the National 

Interagency Management System (NIMS). 

This manual was developed as an aid to provide context for outbreak investigations and 

to help train coral disease outbreak response teams so that coordinated response 

operations can be executed. Chapter 1 provides a rationale for the need to study coral 

disease and respond to disease outbreaks. Chapter 2 identifies elements critical in the 

advanced planning process and includes issues such as regulatory and permitting 

authorities, criteria for mounting a response, and logistical considerations. Chapter 3 is 

dedicated to describing ICS structure, the functional roles and responsibilities of response 

team members, and its operation as it has been adapted to Coral Disease Outbreak 

Investigations. Chapter 4 focuses on the methodologies for collecting field data, samples 

and preservation techniques to preserve sample integrity suitable for laboratory analyses. 

Since coral disease field investigations by their very nature requires underwater 

operations. Chapter 5 addresses safety precautions on the boat, by response divers and 

during field laboratory operations. 

 

 

Cheryl M. Woodley 
iv 

ACKNOWLEDGMENTS 

We would like to acknowledge the contributions of the following methods and protocols for inclusion in 

this manual: 

Microbiology Collection Protocols for the Field by Drs. Kay Marano-Briggs, Robert B. Jonas and Cheryl 

M. Woodley

Contaminant and toxicology protocols in this manual were adapted, with permission, from World Wildlife 

Fund (WWF) manual: "Sampling, Biomarker, and Contaminant Chemical Target Analyte Protocols 

Assessing the Effectiveness of Agricultural Better Management Practices in the Mesoamerican Reef"

written by Craig A. Downs, Haereticus Environmental Laboratory and Melanie McField, WWF and 

Mesoamerican Alliance of the International Coral Reef Action Network. 60p. (Downs 2005b)

Dr. Shawn McLaughlin, curator of the International Registry of Coral Pathology, and scientist at the 

NOAA NOS Oxford, MD Laboratory and Ms. Kathy Price, formally of the NOAA NOS Oxford 

Laboratory provided histology protocols, CITES information and shipping protocols. 

Dr. Esther Peters supplied protocols for fixation of corals for histological analysis. 

Accompanying instructional videos, Histology Laboratory Protocols: Coral and Collection Techniques for 

Coral Disease Outbreak Investigations were post-production edited by Ms. Dorothy Howard, ASCP of the 

NOAA NOS Oxford, MD Laboratory, who went beyond her normal laboratory duties because of the 

passion she has to contribute to our understanding of disease processes in coral and educating the next 

generation of investigators. 

 

We thank Ms. Kathy Price for hosting the Histology Laboratory Protocols: Coral video and providing the 

content and demonstration of laboratory procedures for coral histology and we thank Ms. Dorothy Howard 

as the videographer. 

For the Collection Techniques for Coral Disease Outbreak Investigations video, we appreciate the 

contributions by members of the Woodley Laboratory, Julie Higgins, Mats Lundqvist, Sara Polson, and 

Shawn Polson for their input to the storyboard for the video and their contributions to the numerous 

revisions. We are indebted to the National Park Service’s Biscayne National Park and Richard Curry for 

providing the logistics, location and divers for filming. Herve Jobert, an intern with Biscayne National 

Park from Florida Institute of Technology provided surface support. We especially thank Larry Murphy, 

Chief of the NPS’s Submerged Resources Center for making it possible for the underwater videography 

through the expertise of camera man, Brett Seymour, who gave us beautiful High Definition Video footage. 

It is with much appreciation we recognize the time, efforts and field experience of Dr. Margaret W. Miller 

of NOAA’s National Marine Fisheries Service, Southeast Fisheries Science Center, Miami Laboratory and 

Dr. Dana E. Williams of the University of Miami Rosenstiel School of Marine and Atmospheric Science, 

Cooperative Institute for Marine and Atmospheric Studies who helped to develop and refine the content of 

each of the scenes demonstrating the underwater techniques of collecting biopsies from corals and practical 

techniques to handling and containing potentially infectious materials. We appreciate the work of Dr. Mats 

Lundqvist, NOAA National Ocean Service, Charleston, SC Laboratory who demonstrated the top-side 

procedures for sampling handling, stabilization, labeling and preservation as well as culture-dependent 

microbiology procedures that are conducted in the field laboratory. We also thank Dan Diresta, University 

of Miami who demonstrated top-side support and transport activities. We would like to especially thank 

Dr. Robert Jonas for providing an informative addition to the latest edition of this video on Processing 

Coral Tissue for Microbiological Analyses. 

 
v 

TABLE OF CONTENTS 

CHAPTER 1 PERSPECTIVES ON CORAL DISEASE AND OUTBREAK INVESTIGATIONS....1 

1.1 THEISSUE.......................................................................................................1

1.2 DEFININGCORALDISEASE...................................................................................2

1.3 WHYSTUDYCORALDISEASE?..............................................................................3

1.4 WHYESTABLISHARESPONSESYSTEMFORCORALDISEASEOUTBREAK? .............................5

1.5 ANATOMYOFANOUTBREAKINVESTIGATION............................................................7

CHAPTER 2 GETTING ORGANIZED – ADVANCE PLANNING.....................................9 

2.1 CORALDISEASEINVESTIGATIVERESPONSESYSTEM:GOALS& OBJECTIVES.........................9

2.2 REGULATORYAUTHORITY..................................................................................10

2.3 ORGANIZATIONOFRESPONSESYSTEM...................................................................10

2.3.1 NATIONALCOORDINATING CENTER....................................................................11

2.3.2 NATIONAL COORDINATOR..............................................................................12

2.3.3 EXPERT WORKING GROUP.............................................................................12

2.3.4 REGIONAL COORDINATORS............................................................................12

2.3.5 MEDIA AND PUBLIC AFFAIRS OFFICIAL..............................................................13

2.4 THEDECISIONPROCESS....................................................................................14 

2.5 THEDECISIONCRITERIA....................................................................................14

2.6 THERESPONSETEAM.......................................................................................15

2.6.1 RESPONSIBILITIES.....................................................................................15 

2.6.2 TRAINING...............................................................................................16

2.7 LOGISTICALCONSIDERATIONS.............................................................................17

2.7.1 PERSONNEL SOURCES..................................................................................17

2.7.2 EQUIPMENT............................................................................................17

2.7.3 SUPPLY SOURCES......................................................................................18

2.7.4 LODGING FOR RESPONSE PERSONNEL................................................................19 

2.7.5 WORK AREAS AND WORK FLOW......................................................................19

CHAPTER 3 INCIDENT COMMAND SYSTEM..........................................................20 

3.1 WHATISICS? ..............................................................................................20

3.2 ADAPTATIONOFICSTOCORALDISEASEOUTBREAKINVESTIGATIONS.............................20

3.3 INCIDENTCOMMANDSYSTEMOPERATIONALPERIODPLAN..........................................21

3.4 ICS ROLESANDRESPONSIBILITIES.......................................................................22

3.4.1 FIVE MANAGEMENT ACTIVITIES OF ICS.............................................................22

3.4.2 INCIDENT COMMANDER..............................................................................22

3.4.3 PLANNING CHIEF.....................................................................................23

3.4.4 LOGISTICS CHIEF.....................................................................................23

3.5 ESTABLISHING...............................................................................................24

3.6 A MODELRESPONSE& DECISIONMAKINGPROCESS.................................................25

3.6.1 NOTIFICATION: LEVEL I..............................................................................25

3.6.2 DISEASE DETERMINATIONS: LEVEL II DECISIONS..................................................27

3.6.3 DECISION TO LAUNCH AN INVESTIGATION: LEVEL II...............................................29

3.6.4 LAUNCHING AN INVESTIGATION: LEVEL III ICS...................................................30
vi 

CHAPTER 4 CASE HISTORY, SAMPLE COLLECTION, PROCESSING AND SHIPMENT....32 

4.1CASEHISTORY..................................................................................................32

4.2BASICSTEPS....................................................................................................32

4.3QA/QC CONSIDERATIONS...................................................................................33

4.4SURVEYTEAMSITEIDENTIFICATIONANDASSESSMENT.................................................34

4.4.1 DUTIES OF SURVEY TEAM................................................................................34 

4.4.2 INDIVIDUAL OPERATIONS WITHIN THE SURVEY TEAM AND THEIR RESPONSIBILITIES:................34

4.4.3 SURVEY APPROACH........................................................................................35

4.4.4 DIAGNOSTIC DESCRIPTIONS OF LESIONS FROM GROSS OBSERVATIONS...............................38

4.4.5 FIELD MICROSCOPY......................................................................................40

4.5COLLECTIONTEAMSAMPLECOLLECTION..................................................................43 

4.5.1 GENERAL CONSIDERATIONS.............................................................................44

4.6COLLECTIONPROTOCOLSFORBIOLOGICALANALYSES...................................................45

4.6.1 LABELING SCHEME.......................................................................................45 

4.6.2 SEDIMENT................................................................................................46

4.6.3 DNA SWAB...............................................................................................46

4.6.4 WATER....................................................................................................46

4.6.5 MUCUS...................................................................................................47

4.6.6 TISSUE BIOSPSY.........................................................................................48

4.7SAMPLEPROCESSINGFORBIOLOGICALANALYSES.......................................................48

4.7.1 SUPPORT TEAM..........................................................................................48

4.7.2 PROCESS TIME-SENSITIVE SAMPLES FIRST............................................................49

4.8SAMPLESHIPMENT...........................................................................................51 

4.9PERMITS.......................................................................................................51

4.9.1 CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD FAUNA AND

FLORA (CITES) PERMITS...............................................................................51

4.9.2 OTHER COLLECTION PERMITS..........................................................................53

4.10TYPESOFLABORATORYANALYSES........................................................................53

4.10.1 HISTOLOGY.............................................................................................53

4.10.2 MICROBIOLOGY.........................................................................................54

4.10.3 MOLECULAR............................................................................................54

CHAPTER 5 HEALTH AND SAFETY..........................................................................56 

5.1SAFETYPLAN..................................................................................................56

5.2NOAA BOATSAFETYREGULATORYREQUIREMENTS...................................................56

5.3DIVESAFETY..................................................................................................57

5.4PRECAUTIONSINTHEFIELD.................................................................................58

5.5MATERIALSHAZARDSINFORMATION.....................................................................59

GLOSSARY OF TERMS..........................................................................................60 

REFERENCES.......................................................................................................63 

APPENDICES........................................................................................................66 

APPENDIXI.REGIONALCOORDINATORINTERVIEWCHECKLIST...........................................67

APPENDIXII.LEVELI DATACORALDISEASEEVENTREPORT..............................................68

APPENDIXIII.LEVELII DATACORALDISEASEEVENTREPORT.............................................69

APPENDIXIV.LEVELIII DATACORALDISEASEASSESSMENTFORM.......................................71

APPENDIXVI.PATHOLOGYSAMPLINGSUBMISSIONFORM................................................73

APPENDIXVII. LISTOFSAMPLINGEQUIPMENTANDSUPPLIES.............................................75

APPENDIXVIII. STEREOMICROSCOPY.........................................................................76

1 

Chapter 1

Perspectives on Coral Disease and Outbreak Investigations 

1.1 The Issue 

 

Found in seas of over 100 countries, coral reefs cover an estimated 284,300 km2 (ICRIN 

2000b). Per unit area, they are one of the World’s most valuable ecosystems in terms of 

ecological, economic and cultural resources, yet coral reefs are among the world’s failing 

ecosystems. We are losing them at an accelerating rate (Wilkinson 2002). Recent 

predictions indicate that 58–70% of coral reefs globally are directly threatened by humanassociated activities (Bryant et al. 1998; Goreau et al. 2000; Hoegh-Guldberg 1999; 

Wilkinson 1999), while over 80% of the Caribbean coral-reef cover has disappeared in 

the last 30 years (Gardner et al. 2003). According to estimates in 2004, 20% of the 

world’s coral reefs have already been degraded beyond the potential for recovery, 24% 

are under imminent risk of collapse, and another 26% are under a longer term threat of 

collapse (Wilkinson 2004). 

In both terrestrial and marine systems, wildlife disease outbreaks and mass mortality are 

recognized as important indicators of ecological disturbances. The role of diseases in 

regulating a species’ survival has escalated due to environmental changes such as 1) 

alterations in habitat (e.g., fragmentation or loss, pollution, climate change); 2) shifts in 

populations (e.g., introduction of new species; change in predator/prey relations); and 3) 

changes in disease ecology (e.g., loss of endemic stability; virulence and pathogenicity of 

agents; density of susceptible hosts) (Deem et al. 2001; Morner et al. 2002). 

Similarly, coral reef declines are viewed as sentinels for a degraded ocean condition. The 

causes have only been described in broad sweeping terms implicating coastal urban and 

industrial development, agricultural runoff, sedimentation, overfishing, marine pollution, 

climate change and disease (Bellwood et al. 2004; Bryant et al. 1998; Risk 1999; Turgeon 

et al. 2002; Walker and Ormond 1982). These threats have contributed to losses of apex 

predators, removal of key herbivorous fishes and invertebrates, precipitous declines in 

coral cover as corals become stressed and die, and ecosystem shifts to dominance by 

macroalgae on reefs and similar disruptions in other ocean systems. 

 Coral disease is manifested in a number of different forms from acute mortality leading 

to a rapid loss of diversity and abundance, to chronic partial mortality resulting in 

progressive tissue loss, with non-acute, sub-lethal effects. The outcome of various 

disease states may result in reduced growth, reduced reproductive effort and recruitment, 

increased incidence of various coral disease conditions and mortality, ultimately 

cascading into ecosystem deterioration (CRMP 2001; Hoegh-Guldberg 1999; Knowlton 

2001; Nystrom et al. 2000; Patterson et al. 2002; Porter and Tougas 2001; Richmond 

1993). Coral disease whether infectious or noninfectious in nature is a significant 

challenge to conserving and protecting coral reefs. Definitive root causes to these 
2 

Health is relative occurring along “.... a continuum between two endpoints: 

absolute health (a state in which all functions are optimal) and death, which 

occurs when functions are so severely compromised that life is impossible. 

Between the two points there is a region of relative health that blends 

imperceptibly into a region that we can define as disease.” (Wobeser 2006) 

diseases, however, remain elusive and the increasing frequency and distribution 

throughout the world pose major threats to reefs and challenges to reef managers to 

combat these threats. 

1.2 Defining Coral Disease 

It is tempting to assume that coral 

"disease" refers only to clearly 

visible signs of infection by a 

pathogen; however, disease can be 

caused by abiotic factors as well as 

a response to biotic stressors. We 

have adopted the definition of 

Wobeser (1981) that states disease 

is ‘any impairment that interferes 

with or modifies the performance of 

normal functions, including 

responses to environmental factors 

such as nutrition, toxicants, and 

climate; infectious agents; inherent 

or congenital defects, or 

combinations of these factors’ to 

characterize disease in its full 

meaning. For diseases of coral, we 

know that in addition to biological 

agents, many other risk factors 

exist, such as climate change, environment degradation, toxicants and physical damage. 

Therefore, it is more appropriate to consider coral diseases to result from a ‘web of 

causation’ with many factors and co-factors ultimately contributing to disease (Wobeser 

1994), rather than one distinct agent. To determine causation a more holistic perspective 

must be adopted that includes the host, the agent, and the environment. In the case of 

coral, this includes the animal, plant symbiont and microbial flora, collectively referred to 

as the holobiont (Wegley et al. 2004). 

Population 

density

Parasites

Interspecific 

Competition

Viruses

Pollution

Nutrition

Climatic Events

Bacteria

Impaired 

Resistance Impaired 

Reproduction

Impaired 

Growth

Altered 

behavior

Habitat 

destruction

Altered 

Environmental 

Conditions

Increased 

Sedimentation 

DISEASE

Tissue 

Damage

Toxicants

Web of Causation

After Wobeser 1994

Stress
3 

Diseases of stony corals and gorgonians can fall into several categories: 

Bleaching - loss or degradation of zooxanthellae due to biotic (bacteria) or abiotic 

(e.g., temperature, UV radiation, salinity, toxicants) causes 

Non-infectious diseases – physiological and morphological (e.g., tissue loss or 

discoloration) changes due to agents such as toxins or toxicants, sedimentation, 

pollution, and other environmental stressors 

Trauma – physical damage (e.g., groundings, fish bites, snail predation) 

Parasitic infections – infestation by protozoans (e.g., ciliates, amoeba), metazoans 

(e.g., trematodes, flatworms, flukes) or parazoans (e.g., sponges) 

Growth Anomalies - abnormal growth and development, including hypertrophy, 

hyperplasia, neoplasia, tumors 

Infectious diseases - partial and whole colony mortality caused by bacteria, fungi, 

viruses and other microorganisms

1.3 Why Study Coral Disease? 

The short answer is to determine the cause(s) in order to identify management options 

that can help control disease or mitigate its impacts to protect corals more effectively. 

Disease can cause significant effects on the ecology, structure and function of coral reef 

ecosystems. In the Caribbean, coral disease has caused extensive losses of living coral 

cover, shifts in coral community structure, and extirpations of certain key reef-building 

species. For conservation to be effective, it is imperative not only to understand 

biogeographical patterns, community structure, population dynamics and individual 

behavior (i.e., biology) of the host species (Deem et al. 2001), but also the threats 

affecting these species and the health effects (i.e., consequences of the threat). Only 

when health parameters are incorporated into conservation models and synthesized into 

knowledge, will managers have more robust management options. For stony corals, 

basic information on biogeographic distribution and community structure is known, 

baseline assessments of biodiversity, population dynamics, and cover have been 

completed in representative locations, and the broad threats impacting reef communities 

have been identified. However, specific data on the prevalence and impacts of diseases 

and relationships between coral mortality and other stressors are available for relatively 

few locations. A handful of the better known diseases have been only partially 

characterized, and effective management responses are currently unknown. Too often the 

study of coral disease is viewed more as an academic exercise rather than an avenue to 

developing successful conservation measures. In fact, local management agencies often 

view diseases and bleaching as a global problem that is “just a normal part of life that we 

can’t do anything about anyway”. As we look at the scope of disease effects----“any 
4 

impairment that interferes with or modifies the performance of normal functions, 

including responses to environmental factors such as nutrition, toxins, and climate; 

infectious agents; inherent or congenital defects, or combinations of these factors” 

(Wobeser 1981) it is the organism’s failure to resolve these ‘impairments’ (or injury), at 

the cellular physiological or tissue level that results in the dysfunction we recognize as 

disease. These dysfunctions then are driving the decline of corals (and other wildlife) by 

affecting individual responses, population dynamics, community structures and 

biogeographical patterns (Deem et al. 2001). In other words, the long-term existence of 

corals and their ability to fulfill their ecological roles are being compromised by disease. 

It is critical that health and disease are no longer allowed to be a limiting factor in coral 

conservation efforts. Therefore, every effort should be made to understand the factors 

controlling coral reef health conditions and the impact of diseases on coral reef system 

dynamics, and incorporate this information into the construction of conservation 

programs. 

The marked increase in disease incidence, the severity of the impacts being observed, and 

‘signatures’ of recently emerged coral disease were not documented before the 1990’s. 

Together, these changes mark an alarming threat to coral biodiversity, ecosystem stability 

and sustainability of reefs for the future (Daszak et al. 2001). To understand the causes 

of disease and their significance, and to identify control and management measures will 

require a broad integration of relevant disciplines that include health specialties (i.e., 

veterinary and medical sciences, pathology, medical microbiology, toxicology, 

epidemiology) together with ocean sciences (i.e., wildlife and marine ecology, marine 

biology, oceanography), basic sciences (i.e., biochemistry, cell physiology, microbiology, 

toxicology) and social and economic sciences involving those who help interface with the 

public and politicians (i.e., resource managers, sociologists, economists). 

The gaps in our understanding of many factors affecting coral health are vast. Most coral 

diseases have no known etiology nor have the diseases been rigorously classified. There 

is little in the way of diagnostics or field tests for disease surveillance. Investigations of 

coral diseases often occur without guidance from veterinary scientists, cell physiologists, 

toxicologists or epidemiologists. A valuable shift in how coral disease is studied would 

be the application of the integrated principles of epidemiology and risk analysis to coral 

health assessments. An epidemiologist is usually not trained in one specific discipline, 

but is “a master of ‘lateral thinking’, trying to see connections between what are 

probably isolated observations of completely different natural phenomena” (Halpin 1975 

as cited by; Wobeser 1994). Epidemiology is a powerful tool that can identify predictors 

(risk factors) for changes in coral health and ecosystem condition, quantify the strength of 

those associations, and focus diagnostic efforts toward identifying etiology. Since most 

disease in coral is likely to be multi-factorial, identification of risk factors and use of 

ecological risk assessment methodologies can direct and prioritize management strategies 

toward risk reduction without requiring knowledge of specific etiologies. While risk 

assessment is a process that assigns probabilities to adverse effects of human activities or 

natural damaging events, it does not address health assessment which is concerned with 

determining the occurrence and causes of impairments of nonhuman populations and 

communities, a field known as ecological epidemiology (Suter 2006). Thus, integrating 

ecological epidemiology (biological assessment and causal analyses) with risk 
5 

assessment (risk models that link alternative decisions to future conditions) provides a 

systematic means to improve an understanding of the causal chain of events, identifying 

factors on a quantitative basis for informed management decisions (Suter 2006) and a 

logical, systematic approach to understand the complexities of disease. Investigations 

require astute observations and critical thinking drawing on many disciplines and types of 

information to develop quantitative comparisons among groups and various factors. The 

synthesis of this information can then be used to solve one of three basic problems: 

causation, significance or control (Wobeser 1994). 

 Our goal in studying coral disease is conservation of our world’s reefs, but to do this we 

must be able to: 

• Describe new diseases 

• Determine causation

• Identify the source of current outbreak 

• Determine risk factors and conduct risk analysis for informed decision making 

• Implement disease-specific surveillance measures 

• Evaluate existing prevention/control measures 

• Reduce risk of future outbreaks 

Effective management of coral health will require being equipped to recognize new and 

reemerging infections, non-infectious disease conditions, and understand the factors 

involved in disease emergence, prevention, and elimination. This requires adopting a 

methodology appropriate for assimilating and synthesizing numerous and diverse data, 

such as those developed in the fields of risk analysis and ecological epidemiology. The 

broad areas that have been shown to influence emergence of disease include: 1) microbial 

adaptation and change, 2) human demographics and the consequences of that behavior, 3) 

technology and industry, 4) economic development and land-use practices, 5) 

international travel and commerce, and 6) the breakdown of health measures. In 

summary, we first need to study this major problem in a detailed, standardized manner 

and share the findings with the research and resource management communities. 

1.4 Why Establish a Response System for Coral Disease Outbreaks? 

“Stopping investigation in the here and now, will leave you vulnerable to why and how!” 

(AAZV 2008) 

An outbreak is commonly defined as an unexpected increase in disease or mortality in a 

time or place where it does not normally occur or at a frequency greater than previously 

observed. For coral, an outbreak may also be defined as disease occurring in a particular 
6 

species of interest or manifesting signs not previously described. Outbreaks are usually 

transitory and short-lived and should be treated with a matter of urgency to collect as 

much information as possible while it is available. In contrast, insidious, chronic diseases 

can have equally devastating effects on populations and communities, yet their covert 

nature make them hard to detect and difficult to garner support for an investigation. 

Nevertheless it is critically important to investigate. Developing a Response System to 

investigate coral disease outbreaks provides the opportunity to methodically collect a 

range of data to assist in determining its significance, epizootiology and causal linkages, 

to test the adequacy of wildlife disease protocols to diagnose the principal cause, and to 

evaluate the findings, develop prediction models and present options for future research 

and mitigation to resource managers in a timely manner. 

Outbreak investigations are designed to determine the extent and impact of the event, 

causative agent(s) and its reservoir or source, and transmission routes. They can also be 

used to identify knowledge gaps, help formulate hypotheses for further study and focus 

research goals, and help identify control or management strategies. Outbreak 

investigations are most important when almost nothing is known about the disease(s) (as 

is the case for most coral diseases) or when a new disease is discovered. An organized, 

systematic approach helps create both clinical and diagnostic case definitions, identify 

risk factors, and formulate hypotheses to target control and management strategies. 

When the cause of an outbreak has been clinically determined by identification of a 

known pathogen (e.g., white plague II), but the source (reservoir) or route of transmission 

remains unknown, there often remains much investigative work to be done (as was the 

case with Vibrio shiloii, the causative agent of one type of bacterial bleaching). 

Investigations can then focus on filling the knowledge gaps in the ecology of the disease 

to better guide future control and management efforts. Therefore a Response System, 

using a standardized approach helps answer the ‘big picture’ questions: 

What is it? (well recognized or emerging disease?) 

What species are being affected in the area? 

What species are NOT being affected in the area? 

Where did it come from? (reservoir) 

How is it spreading? (transmission) 

How common is it? (prevalence) 

What impact is it having on affected species and populations? (effects) 

How can you control it? (stop spread) 

What risk factors (i.e., biological, chemical or physical) are co-occurring with 

the disease? (prediction) 

What about future management? 
7 

1.5 Anatomy of an Outbreak Investigation 

(from Pavlin 2003; Reingold 1998; Wobeser 1994)

There are 10 basic steps that are common to most disease outbreak investigations: 

Establish the existence of an outbreak and develop case definitions. 

[Epidemiological Investigation] 

This is the same as starting any case description with the signalment (i.e., 

description of distinguishing features, signs, and information related to the 

organism being examined) and history of the animals and/or group of animals. This 

should include information such as their environment, proximities to potential 

contaminant sources or recent activities or weather or climatic events that may 

contribute to the outbreak. The case definition is a standard set of criteria applied to 

arrive at an initial, preliminary diagnosis and determine whether the reported 

information meets the criteria for an outbreak. 

Establish endemic level (background rate) of disease 

Determining if the disease occurrence or prevalence is higher than background 

levels, spatially (i.e., for that particular location, reef or habitat) and temporally 

(i.e., for the specific time period when the presumed outbreak is reported) is a key 

to defining ‘unusual’. This can only be accomplished through disease surveillance 

(e.g., monitoring of seasonal trends in abundance). This type of information is 

rarely available for coral disease. 

Characterize the outbreak in terms of who, what, when and where. 

The objective is to identify common factors that are associated with the disease that 

don’t occur when and where the disease is absent. Thus it is important to 

standardize collections in terms of data and types of samples because developing 

causal links may take weeks to years. 

Examine the descriptive epidemiological (or epizootiological) features of 

the case. 

Descriptive epidemiology involves determining the number of cases and mapping 

them to determine the distribution of cases in space and time and contrasting this 

with past events, including cross species comparisons with life stages and 

associated environmental factors. This information can provide valuable leads as to 

the source or nature of the agent or routes of exposure. 

Generate tentative hypotheses. 

A tentative hypothesis is developed to explain the most likely cause(s), source and 

risk of spread of the cases.

Test hypotheses 

Once the hypothesis is generated it can be evaluated against the known facts about 

the potential agent(s) (i.e., analytical epidemiology). The goal is to assess the 

relationship between a given exposure and the observed disease, determine if it is 
8 

statistically significant and biologically meaningful. Several iterations of 

hypothesis development may be required. 

Collect and test environmental and biological samples [Environmental 

Investigation] 

The findings of the ‘epidemiological investigation’ should guide the collection and 

testing of specimens and samples. The basis for these analytical tests is to compare 

affected and non-affected populations. These new data are added to previous data 

and information to accept or reject the prevailing hypothesis and develop a new one 

if rejected. This is essentially the differential diagnostic process. 

Confirm or verify the diagnosis and the cases are ‘real’.

This is not necessarily immediate. Review clinical and laboratory findings for 

consistency and confirm or reject suspected diagnosis based on these analyses. 

Prepare a written report 

It is important to summarize the investigation in a report that includes the reason for 

the investigation; general characteristics of the investigation, the clinical 

descriptions, results, conclusions on the nature of the disease, source of outbreak 

and method of transmission, and any possible recommendations for control or 

management. 

Implement control/management strategies 

Disease management strategies for coral reefs must recognize the three basic 

determinants of disease: the host, the agent and the environment. The key to 

effecting disease outcomes is through successful manipulation of disease 

determinants and management or mitigation of related human impacts. 
9 

Chapter 2 

Getting Organized – Advance Planning 

2.1 Coral Disease Investigative Response System: Goals & Objectives 

The goal of a Response System is to facilitate the investigation of coral disease outbreaks 

that are unusual in nature by providing a framework of operation that promotes a logical, 

systematic collection of information and samples, sufficient to allow the formulation of a 

hypothesis to explain why the outbreak occurred (Wobeser 1994). 

The objectives of an Outbreak Investigation System are to: 

• Provide field personnel trained in investigative techniques to ensure proficiency in 

survey, collection and processing techniques 

• Encourage Responder awareness of the need to exercise Critical Observing (i.e., 

objective rather than subjective, using validated classification schemes, being aware 

of problems associated with over-interpretation of vague signs and of bias from prior 

information) and Critical Thinking (ability and willingness to seek both contradictory 

as well as confirmatory information when collecting evidence and make objective 

judgments based on well documented information) throughout the investigation. 

• Adapt Incident Command System components to provide an incident management 

and procedural framework for conducting a coral disease outbreak investigation 

• Execute an organized, systematic approach to collect relevant epidemiological and 

environmental data, and samples for developing clinical and diagnostic case 

definitions 

• Formulate hypotheses as to the cause of the outbreak 

• Create a database of disease information for retrospective and prospective 

investigations 

• Identify knowledge gaps 

• Formulate hypotheses for further studies and focus research goals. 

• Provide information to help identify disease management and control strategies. 
10 

2.2 Regulatory Authority 

The Response System and all of its members, including the investigative response team 

must function within the legal structure of the jurisdiction overseeing the area affected by 

the outbreak. This may be federal, state, regional and/or local authorities, and in some 

cases (e.g., when working with ESA listed corals) NOAA/NMFS and U. S. Fish and 

Wildlife Service, for example, collection of coral in all U.S. jurisdictions requires 

permitting by the local governing agency(s). Permits may also be necessary for surveys, 

tagging and other activities associated with the response. It is important to identify local 

authorities, such as Sanctuary and Park managers and establish partnerships to involve 

them early in the response process. The assistance of these individuals often is critical in 

expediting permitting and providing logistical support for their specific areas. 

2.3 Organization of Response System

Every response, no matter the size, 

needs an organized protocol of 

response. The CDHC Response 

System is a tiered decision process 

coordinated through a National Center 

with input from an Expert Working 

Group and in collaboration with the 

Regional Coordinator. The initial 

phase of a response begins with an 

observation by a diver of a situation 

considered unusual and involves 

diseased coral which is reported to the 

CDHC. This is followed by 

notification though the Response 

network to the area’s Regional 

Coordinator (Chapter 3 and Level I 

Report; Appendix II). A series of 

events are then initiated that includes: 

1) evaluation of the report by experts; 2) identification of possible responses (Chapter 3 

and Level II or Level III; Appendix III & IV); 3) recommendation of possible steps to 

reduce spread (i.e., quarantine); 4) further assessment of the situation to identify 

conditions that may aggravate or mitigate the event; and if warranted; 5) mobilization of 

a Response Team to document and characterize the incident, and collect and stabilize 

samples for further analyses. These steps may be moved through more quickly, if for 

example, an experienced research diver familiar with disease is the original observer 

(e.g., a Level I report could directly trigger a Level III response). 

The implementation of the Response System is through Regional Response Coordinators 

and a network of responders. Minimally, a lead Regional Coordinator is appointed for 

each region of the U.S. (Fig. 2.3), with additional Coordinators as appropriate in specific 

Figure 2.3 Organizational Chart for U.S. Response System. 
11 

jurisdictions. Each Response Team includes an Incident Commander (who may also be 

the Regional Coordinator), a Survey Team, Collection Team and Support Team. Ideally, 

various members of the Response Team are trained in multiple tasks and can participate 

in all activities as necessary. 

The essential members of a response network include: 

An Incident Commander responsible for coordination of all field activities 

An Outbreak Investigation Response Team with a complement of scientists 

responsible for the collection of field data and samples, and on-boat processing 

of samples 

Access to veterinary consultations and scientists able to conduct specialized 

sample collection if necessary 

Local ecological and logistical experts (may be part of the Response Team) able 

to assist with coordination and knowledgeable about relevant related 

environmental and ecological parameters 

Public relations specialist 

A set of labs with a compliment of specialty diagnostic or analytical procedures 

for sample processing and analysis 

A specific outbreak investigation will be led by an Incident Commander (IC) under an 

Incident Command Structured response. The IC will make immediate recommendations 

to the coral disease outbreak network on how to proceed with response activities. 

2.3.1 National Coordinating Center

The primary responsibility of the National Coordinating Center (NCC) is to provide a 

centralized location for receiving and verifying coral disease outbreak reports and to 

coordinate the appropriate response. The NCC should also: 

Provide training to response team members and volunteers 

Provide supplies and equipment for surveys and response kits 

Serve as Liaison Office to notify and work with other federal and local 

authorities. 

Maintain current files on the capabilities of each region i.e., response team 

members, logistical support, emergency care facilities, and laboratory 

diagnostic capabilities. 

Maintain communication among all investigative team members 

Track samples sent to authorized laboratories or individuals for analyses 

Gather and archive data 
12 

Review and assist in development of reports and identification of 

recommendations 

Report findings to appropriate government agencies 

2.3.2 National Coordinator

The National Coordinator serves as a central contact for all Regional Coordinators and 

collates all reports of verified Level I observations and Level II investigations submitted 

by Regional Coordinators. The National Coordinator will convene the Expert Working 

Group to make decisions in cases that suggest the need for a Level III Response. The 

National Coordinator also works directly with the Regional Coordinator to ensure reports 

are produced in a timely manner and provides analysis and recommendations to the 

managers. (See sections 2.4 and 3.6 for description of response decision process) 

2.3.3 Expert Working Group 

The Expert Working Group includes individuals with knowledge and experience in coral 

diseases and pathology to provide guidance for (i) developing and implementing the 

contingency plan to assist in responding to unusual coral disease outbreaks; (ii) assists in 

determining whether an unusual coral disease outbreak is occurring and the need for a 

Level II or Level III response; and (iii) assists the National Coordinator in determining, 

after an unusual coral disease investigation response has begun, when response actions 

with respect to that incident should be terminated. 

2.3.4 Regional Coordinators 

The regions have been nominally designated based on the location of U.S. coral reefs, 

history of outbreaks or high prevalence of new or emerging disease and logistical 

considerations. Initially, there will be one Regional Coordinator designated for Florida 

and the Gulf of Mexico, the U.S. Atlantic (Puerto Rico and USVI), Hawaii, and the U.S. 

Pacific (American Samoa, Guam and CNMI). Regions will be added (e.g., Freely 

Associated States) and subdivided into jurisdictions as responders are available and as 

needed. 

The Regional Coordinator is responsible for the overall communication and logistics for a 

given Outbreak involving an Incident Response. This includes such activities as: 

Incident Coordination 

Logistics 

Safety and permitting issues 

Determining amount, type and quality of data appropriate to collect 
13 

Initial threat assessment 

How to implement control and prevention procedures 

Transmitting data to a centralized data analysis facility 

Communication with scientists, managers and the public. 

Preparing summary reports 

Regional Coordinators should take steps well in advance of an Incident to identify and 

train Response Team members, compile lists of support services and contacts as well as 

maintenance and replenishing sampling kits. A list of suggested equipment is provided 

(Appendix VI), recognizing equipment needs will vary based on location, species 

affected, and availability. 

The Regional Coordinator (RC) is notified when an Incident Report is received (either 

through the National Office or directly). The RC conducts interviews with those 

submitting the report to complete Level I information needs (Level I Report form, 

Appendix II) and contacts the National Coordinator (NC) to report findings and 

recommendations on whether the case is resolved or if a Level II response (Appendix III) 

is necessary. After review of the Level I report, if a Level II response is activated, the 

RC organizes and conducts the Level II response in collaboration with the designated 

Incident Commander, and reports out on findings to the NC. The RC also participates in 

the Working Group Consultation to determine the need for a Level III response 

(Appendix IV). 

Once a Level III response is activated, Regional Coordinators, in collaboration with the 

Incident Commander and Response Team, are responsible for: 1) conducting a 

preliminary assessment of the outbreak event (including sample collections, if warranted) 

and notifying management agencies and other appropriate stakeholders of the status; 2) 

evaluating the seriousness of the outbreak and classifying the threat (i.e., What impacts to 

the reef ecosystem will result from the outbreak on a local, regional, or national scale?); 

3) assessing the feasibility of containing the disease and reducing any contributing 

anthropogenic stresses (i.e. chemical and thermal inputs); 4) providing recommendations 

to decision-makers regarding potential response; and 5) providing guidance for efficient 

control methods. 

2.3.5 Media and Public Affairs Official 

Unusual outbreaks of disease among coral reefs can become a hot news topic particularly 

if diving is restricted by quarantining an affected reef. Nearly everyone is influenced by 

the media; therefore it is critical that the information given by the Response Network is 

accurate and consistent among responders, and does not extrapolate beyond the facts. 

Each Region and responding Agency should have a protocol for interacting with the 

media. It is important to become familiar with the local protocols and contacts. It is 

recommended that each Regional Coordinator identify a Public Affairs Official who is 
14 

familiar with such protocols, and who will be responsible for reporting the progress of the 

investigation to local authorities and managers, as well as interacting with the press to 

make public notification as needed. 

2.4 The Decision Process 

The response process for a coral 

disease outbreak investigation is 

essentially a triage that is 

initiated by a report from the 

field (i.e., public, research or 

recreational diver) to a Response 

Network contact. Public notices 

providing contact procedures and 

reporting forms should be widely 

distributed to commercial dive 

shops, local management 

agencies and marine patrols. 

Consultations with area experts 

verify the report and determine 

the sufficiency of information for 

decision-making. If the report is 

valid and information is 

insufficient, then additional data is obtained to determine the existence of an outbreak. If 

an outbreak is confirmed then a full response conducted under ICS guidelines is initiated 

and the Response Team is deployed to the field. 

2.5 The Decision Criteria 

Until information can be assimilated to accurately diagnose disease and sufficient 

surveillance has been conducted to determine prevalence and incidence rates it will be 

difficult to discriminate between enzootic and epizootic diseases. Therefore initially, 

several reports identifying an event, photographic documentation, and preliminary survey 

data (Levels I and II) may be needed to determine whether a Level III response is 

appropriate. The guidelines for making such decisions include: 

Does the incident represent an unexpected increase in disease or mortality in a 

time or place where it does not normally occur or at a level that cannot be 

explained? Or in a species in which it has never been reported? 

Is the frequency of occurrence or extent of mortality greater than previously 

observed? 

Is the disease affecting a particular species of interest? 

Have the manifesting disease signs been previously described? 

Figure 2.4 Response process, decision points and information flow. 
15 

Can the cause of the event be readily determined (e.g., major hurricane, oil 

spill)? 

2.6 The Response Team 

The essential elements of a response include an incident commander and an outbreak 

investigation response team with a complement of scientists capable of collecting, 

processing and analyzing samples and data. The composition of the response team will 

depend on the extent and location of any given outbreak. Different strategies will be 

required in any given situation and it is vital to distinguish between critical elements in 

the procedures and where flexibilities are acceptable. Common to all responses is the 

need to: 

Respond rapidly 

Communicate with local authorities (most often resource management offices) 

before, during and after a Response 

Evaluate the situation 

Implement the Incident Action Plan 

Ensure safety for the team 

Transport samples and data to designated labs and National Coordinating Center 

in a timely manner 

Provide relevant information to Public Affairs Officials 

Maintain Communications with the operations center and National Coordinating 

Center 

2.6.1 Responsibilities 

The core team requires a wide range of expertise. Foremost is the need for an individual 

that can organize others, delegate tasks appropriately, make informed decisions and 

manage all the tasks related to an Incident Response. All of the members should be 

trained in conducting surveys, sample collection and sample processing and capable of 

assisting as needed on each of the teams. It is important to realize that individuals differ 

in their interests, skill level, scientific biases, and endurance levels; therefore, it is 

important that the Incident Commander recognize their strengths and make team 

assignments accordingly. 

The Response Team should consist of a minimum of 6 team members (1 of the 4 divers 

may serve as Incident Commander), with two members on each of the three teams listed 

below: 

Incident Commander (IC) – The IC is responsible for overall management of 

the response. This includes developing incident objectives and managing all 
16 

incident operations. The IC sets priorities and defines the ICS organization for 

the particular response. The IC may also be one of the members of the Survey 

Team, Collection Team and/or Support Team.

Survey Team – The Survey Team is responsible for documenting the site 

(above water and underwater), collecting environmental data, mapping and 

delineating the affected area, documenting the affected corals and other biota, 

and conducting surveys. One member of the team should video and/or photodocument the scene, surrounding substrate and affected corals. Based on 

expertise, members can deploy transects, collect colony data, collect relevant 

data on affected corals, and identify corals for sampling. Their primary 

objective is to determine the extent of the affected area, the number and species 

affected (as well as those obviously not affected) and identify colonies for 

sample collection. It is preferable for this team to include coral biologists with 

at least one having some coral disease knowledge. 

Collection Team – The Collection Team is responsible for photo documenting 

colonies before and after sampling, collecting water, sediment, coral mucus and 

tissue-biopsies from reference tissues and lesions, recording relevant data on 

standardized data sheets and transporting time-sensitive samples to the surface. 

It is preferable to have one member serve as the bag handler and data recorder, 

assisting the sample collector by providing appropriate tools and pre-labeled 

sample bags in a sequential manner. 

Support Team – The Support Team is responsible for sample processing and 

data recording procedures that are conducted both on boat and land. This team 

may also shuttle samples from the collection site to the boat, and assist in 

coordinating other on-boat activities. It is preferable for one member to include 

a laboratory-trained technician capable of handling biological samples for 

microbiology and molecular procedures or contaminant chemistry, if indicated. 

2.6.2 Training 

Properly trained individuals proficient in investigative procedures, data collection, 

specimen collection and handling collection techniques are critical to the success of an 

investigation. Various formats are important to ensure properly trained teams, including 

lectures and field practicals, videos and web-based refresher training programs, each 

designed to develop and maintain essential skills. The topics should include: 

The need and purpose of conducting an outbreak investigation, and 

differentiating these procedures from a monitoring or research project 

Expected scenarios, and how to plan for varied situations 

Work standards, importance of following an Incident Command Structure and 

completing assigned tasks 
17 

Decision making, criteria and procedural guidelines 

Procedures and techniques for collection of specimens, field surveys, and 

completion of data forms: 

Handling, preservation, transport and tracking samples 

Communication and follow-up 

First Aid and Safety 

Proficiency Drills 

Proficiency drills are exercises both ‘on paper’ and in the field that give the team 

experience in reviewing each step in the response, from initial report to closing the 

investigation. The drills should consist of varying scenarios that include determining 

each member’s proficiency in conducting their assigned task, checking the condition of 

equipment, testing strategies for developing an action plan for a given situation, 

practicing collection techniques and methods as well as sample handling, processing and 

preservation techniques. This type of training is essential to identify deficiencies, correct 

a problem before an actual incident occurs requiring a coordinated response. 

2.7 Logistical Considerations 

2.7.1 Personnel sources 

Investigative teams may be composed of individuals from local, state and federal 

agencies, academic institutions, non-government organizations, and trained volunteers. It 

is critical to maintain an updated list of contact persons and their telephone numbers, 

email and surface mail addresses. (See Chapter 3 for details.) 

2.7.2 Equipment 

General Categories 

Boats: It is important to identify various agencies that can respond with small 

vessels to support dive operations. This may include state marine resource 

agencies, the National Park Service NOAA Offices such as National Marine 

Sanctuaries, National Marine Fisheries Service, National Ocean Service, or 

commercial charter companies. 

Dive gear: Most likely responders will have their own wetsuits and dive gear; 

however it is important to identify local dive shops for tanks and air and other 

equipment as necessary. 

Medical supplies: Identify local hospitals, veterinary clinics or marine labs in 

the area as these facilities can be a valuable resource for various types of 

equipment and supplies, such as liquid nitrogen, preservatives, and histological 

fixatives. (See Chapter 4 for details) 
18 

Sampling Kits: Pre-assembled kits will vary depending on the reported 

circumstances. Items often pre-assembled include data forms and pencils, tissue 

biopsy tools, markers (e.g., flagging tape, colony tags, buoys lift bags), 

preservatives and storage materials for samples, collection equipment (e.g., 

hammer, chisel, leather punch for coring or clippers for branching corals, swabs, 

sampling tubes, bags), dry shippers (aka: liquid nitrogen vapor shipper), coolers 

and cameras. (See Chapter 4 for details) 

Freezers: It is ideal to be prepared with your own dry shipper (i.e., 

cryoshipper), but in cases where this is not available, interim refrigeration 

resources are required. Often for frozen samples requiring lower than -20oC, 

dry ice can be obtained from local grocery stories and liquid nitrogen from 

specialty gas suppliers. University research facilities often have -80oC freezers 

that can provide temporary storage until shipping can be arranged. Hospitals 

often have supplies of liquid nitrogen that may provide a stop-gap in an 

emergency situation. It is prudent to identify venders in your region that offer 

either liquid nitrogen, dry ice or -80oC freezer capability. 

Safety: Adherence to institutional specific dive regulations and standards must 

be observed and enforced. All divers should be certified, trained and proficient 

in appropriate dive techniques, including dive planning, proper buoyancy, 

bottom times and safety stops, and effective communication with designated 

dive buddies. The IC should maintain a log of all divers and dive profiles, and 

review dive plans with the designated Dive Master before and during the event. 

First aid and oxygen delivery kits should be on board along with the phone 

number of local Emergency Medical Services, hospitals and location of nearest 

decompression chamber and hyperbaric medical units. 

 

2.7.3 Supply Sources 

Identify sources, addresses and telephone numbers and websites of local or closest 

sources of supplies (see Appendix VII for suggested list) that maybe need such as: 

Biopsy corers, clippers, hammers, chisels and other hardware 

Dry ice or liquid nitrogen 

Nearest shipping address for air and ground receipt of goods and supplies 

Nearest location for shipping including airlines, courier or express shipping 

Shipping containers and necessary forms, labels and documentation for shipping 
19 

2.7.4 Lodging for Response Personnel 

Identify locations for lodging response personnel. In addition to local motels, there are 

frequently marine laboratories with dormitories or housing available for scientists at 

nominal rates. 

2.7.5 Work Areas and Work Flow 

Identify working areas and establish a standard operating procedure for work flow, to 

eliminate cross contamination and attend to time-sensitive samples promptly. As part of 

any Incident Response there are generally three types of areas designated: 

Clean areas - Clean areas include the command post, meeting rooms, eating 

areas and equipment and supply receipt areas. 

Transitional areas – These areas are primarily for decontamination of personnel 

and equipment. 

Contaminated areas – Underwater these are areas with diseased corals. Topside 

or on land these areas include areas designated for sample processing or 

laboratory tests. 
20 

Chapter 3 

Incident Command System 

3.1 What is ICS? 

The Incident Command System (ICS) (US National Response Team 2000a) is a 

standardized emergency management strategy that is part of the National Interagency 

Management System (NIMS). It is used in cases that require a joint effort involving 

multiple agencies or organizations, and provides a comprehensive framework for 

managing emergency and non-emergency events. Originally created by fire departments 

to coordinate their efforts, it has expanded to be used as a more general response network 

plan. This system allows response without the boundaries that can be created by 

jurisdiction issues. ICS decreases the duplication of efforts, and coordinates different 

organizations into one operational unit. 

Federal directives mandate use of the Incident Command System (ICS) by their agencies. 

The Coral Disease and Health Consortium (CDHC) is supported by federal funds and 

operates as a consortium that includes NOAA, the EPA, and DOI, as well as academia, 

industry and NGOs, and therefore has incorporated structure and functions into their 

Coral Disease Outbreak Investigation Response Plan that are consistent with the ICS 

structure. 

ICS uses distinctive titles for each organizational level. The Incident Commander 

oversees all responsibilities associated with a response. The Command Staff includes the 

Liaison Officer, Safety Officer and Public Information Officer. The General Staff 

consists of leaders of the Operations, Planning, Finance/Administration, and Logistics 

sections. Each is titled a Section Chief, and each report directly to the Incident 

Commander. 

3.2 Adaptation of ICS to Coral Disease Outbreak Investigations 

Every response, no matter the size, has an initial response phase. For a Coral Disease 

Outbreak Investigation, this begins with an observation by a diver of a situation they 

deem as unusual that involves diseased coral that is reported to the CDHC. This is, 

followed by notification though the Response network to the area’s Regional Coordinator 

(Level I Report; Appendix II). A series of events are then initiated that includes: 1) 

evaluation of the report by experts; 2) identification of possible responses (Level II or 

Level III; Appendix III & IV); 3) recommendation of possible steps to reduce spread (i.e., 

quarantine); 4) further assessment of the situation to identify conditions that may 

aggravate or mitigate the event; and if warranted; 5) mobilization of a Response Team to 

document and characterize the incident, and collect and stabilize samples for further 

analyses. These steps may be moved through more quickly, if for example, an 
21 

experienced research diver familiar with disease is the original observer (e.g., a Level I 

report could directly trigger a Level III response). 

Once a Level III Response has been declared and the Response Team deployed, the ICS 

structure and protocols are engaged. This process should be moved as quickly as 

possible from beginning to end, although in reality it may require up to several weeks to 

accomplish. The availability of resources (both people and materials) and safe weather 

conditions will influence the timeline. 

3.3 Incident Command System Operational Period Plan 

Steps of ICS Steps of Coral Disease Outbreak Investigation 

Incident Occurs Observation by someone in the field

Notifications Level I Data Sheet

Initial Response and 

Assessment

Regional Coordinator Interviews Observer, and may conduct a Level II 

investigation to collect more detailed information. Information is discussed 

with National Coordinator and Expert Working Group

Incident Briefing 201

If the National and Regional Coordinators determine need for a Level III 

Response, an ICS 201 Incident Briefing ends the Initial Response Phase and 

launches the ICS process

Initial Unified Command 

Meeting

Use ICS 202 Form to record established jurisdictional limits, operational period 

to be used in the response, and agreed upon overall response objectives and 

priorities

Develop Tactics/ Tactics 

Meeting

Coordinators consult others as needed to determine samples to be taken and 

to train teams in protocols 

Develop priorities, 

objectives and strategies

Coordinators determine priority for list of objectives, plan sequence of events 

for safest and most accurate collection 

Planning Meeting All Command Staff and General Staff meet to write the Incident Action Plan 

Incident Action Plan 

(IAP) preparation and 

approval

Purpose of the IAP is to develop the response strategy for the next operational 

period (OP) and give specific direction to responders. The IAP only contains 

information needed by the responders to safely conduct the assigned action. 

ICS-204a form/assignment sheets

Operations Briefing Incident Commander meets with all team members to cover IAP, divide 

responsibilities and cover safety 

Execute IAP Dives to collect samples and data, input and organize data, process and ship 

samples 

Initiate planning for the 

next operational period Debriefing of teams each night leads to modifications of IAP as needed. 

Assess progress

Executive Summary Package can be prepared each OP to provide updated 

incident status report. May contain ExSum form, Situation Map, ICS-209 form, 

the General Plan, ICS-220 or others 

Unified Commands 

Objectives Meeting Coordinators meet to determine final steps, referrals, recommendations 

Figure 3.3 Incident Commander = Regional or Local Coordinator responsible for onsite response; 

IAP= Incident Action Plan
22 

3.4 ICS Roles and Responsibilities

3.4.1 Five Management Activities of ICS 

Incident Command Responsibilities 

are to set objectives and priorities with 

overall management responsibility for 

the incident. Safety, Liaison, and 

Information functions, unless assigned to 

Command Staff chiefs who report 

directly to Incident Commander are 

included in the IC responsibilities. 

Operations Responsibilities are to 

conduct tactical operations to carry out 

the action plan, develop the tactical 

objectives and organization, and direct 

all resources. 

Planning Responsibilities are to 

develop the Incident Action Plan to 

accomplish the objectives, collect and 

evaluate information, track resources 

status, and document the response effort. 

Logistics Responsibilities are to provide support to meet the incident needs, 

provide resources and all other services needed to support the incident response. 

Finance/Administration Responsibilities are to monitor costs related to the 

incident, provide accounting, procurement, time recording, and cost analysis. 

Small incidents may be managed by one person, as the Incident Commander, in charge of 

all five management activities. Larger events will require that the other four management 

activities be assigned to command staff. Span of control is maintained at 3-7 responders 

per supervisor.

3.4.2 Incident Commander 

The Incident Commander has ultimate responsibility for all five management activities of 

the IC System. In the case of coral disease outbreak investigations, it is important that 

the Response Team include a Divemaster responsible for the development and evaluation 

of the dive plan and supervision of the actual dives. Each of the Response Team 

members (Survey, Collection and Support Teams) reports to the IC. The IC must also 

ensure that the Incident Action Plan (IAP) and Site Safety Plan (SSP) are followed. The 

IC will develop the objectives and tactics to be included in the IAP. Other responsibilities 

Figure 3.4.1 Overall management structure of an Incident 

Command Operation 
23 

include keeping records of expenses to be sent to the National Coordinator, and 

maintenance of Incident History and Status Information (including weather and disease) 

records. The Incident Commander will most likely designate Planning and Logistics 

Chiefs to handle those responsibilities. Both of these individuals report to the IC, and the 

IC reports to the Regional and National Coordinators; in some cases the Regional 

Coordinator could also be the IC. 

3.4.3 Planning Chief 

The Planning Chief (PC) is responsible for collection, evaluation, dissemination, and use 

of information about the development of the incident and determines the status of 

resources. The PC is responsible for writing the Incident Action Plan (IAP). This plan 

includes tactics, or methods that will be used to complete the goals of the plan. Tactics 

should address the timing of the response, transportation of team members, and 

organization of samples, collection protocols, and a materials/equipment list. As the 

investigation progresses, the Planning Chief prepares status reports and keeps the IC 

informed of progress. Other responsibilities include: collecting weather information and 

case history (last few months- any major weather events, SST changes, new industry, 

overflow, etc.), obtaining necessary permits for dives and collection of samples, and 

making contact with laboratories to arrange for analyses of samples. 

3.4.4 Logistics Chief 

Logistics chief is responsible for: 

Facilities, services, and material support to the incident response 

Lodging accommodations for response team members 

Ordering supplies, kit materials 

Transportation arrangements for personnel, as needed 

Food arrangements, as needed 

Boat and Captain acquisition 

Evaluation of vessel operator qualifications 

Obtaining copies of training certificates and authorizations (given to the 

Incident Commander to be filed with the Safety Plan) 

Contacting shipping company and arranging shipment 

*Liaison Responsibilities 

The National Coordinator will serve as the Liaison Officer during a response. The Liaison 

Officer is responsible for addressing the concern of local agencies affected by the incident and 

communicating that information to the Incident Commander. The LO should also identify 

stakeholders and address their concerns. 
24 

3.5 Establishing a Command/Operations Center 

The Operations Center is established to continually monitor any incoming information 

regarding the response, either by phone, fax or email, and to communicate with 

Coordinators as well as federal and local authorities and involved organizations. This 

may be a research center, university office, local or federal government office (i.e., 

National Marine Sanctuary, National Park Service), or similar location, to be determined 

by the Incident Commander. Promotion and public awareness of the response may also 

be run from this office, or that of the designated Public Affairs Official. This location 

also serves to coordinate the response, check in and deploy team members, gather and 

archive data, and keep track of samples and their shipment/receipt. 

Boat Situation Land Situation 
25 

3.6 A Model Response & Decision Making Process

3.6.1 Notification: Level I 

A model response begins with an unusual observation in the field. This observation is 

most easily verified if the observer is a trained coral reef scientist, but it could come from 

anyone who describes specific coral conditions indicative of disease. The importance of 

outreach is highlighted at this crucial first step, as we need to make the reporting format 

readily available to those making the observations. The reporting form will be available 

on the CDHC website and also available at local sources such as dive shops. This Level I 

(Appendix II) information is completed and sent to a Regional Coordinator. The observer 

may be a recreational diver, dive operator, manager or researcher who observes an 

unusual disease outbreak and notifies the Regional Coordinator directly. In this situation, 

the Regional Coordinator could fill out the Level I response form during the interview. 

The Regional Coordinator (Appendix I, Regional Coordinator Check List) will contact 

the Initial Observer to conduct an interview and: 

verify the report 

determine the validity of the report 

collect sufficient information to determine the need for further response 

request additional supporting materials, if available, such as photographs 

At this point, the Regional Coordinator may elect to close the case and forward the report 

to the National Coordinator. If this is a new observation, a species at risk, or if a large 

magnitude incident is suggested, the Regional Coordinator may recommend a Level II 

response, notify the National Coordinator, and begin to organize a small-scale trip to the 

site to collect more specific information to determine whether the incident may warrant a 

Level III investigation. The Decision Tree below illustrates (Figure 3.6.1) this process. 
26 

Coral Disease Investigation Decision Tree 

Level I Response 

Interview 

Decision 

Case Closed* 

1. Already reported 

2. Lack of credibility 

3. Non-disease observation 

4. Unable to contact observer 

 

Level II Recommendation 

1. New observation 

2. Insufficient information 

3. Species at risk (multiple) 

4. Magnitude 

5. Expansion earlier observation 

6. Photograph/video details 

 

Level II Consultation 

1. Strength of observation 

2. Magnitude supported by 

surveys, photos, prevalence 

data 

3. Boat/staff in area with specific 

knowledge 

Level II Response 

Decision 

Case Closed* 

1. Observations not field supported during Level II 

response 

2. Within normal (known) background 

3. Non-diseased agent (ie., boat trauma, anchor injury, 

hurricane damage) 

4. Referral to another response team (bleaching, 

grounding, fish kills) 

5. Adequate information obtained in Level II 

Level III Consultation 

1. Strength of observation 

2. Magnitude: distribution (multiple reefs), frequency, 

multiple species, proportion colonies affected higher 

than expected, higher than expected mortality rates 

3. New/unusual condition 

4. Temporal irregularity 

5. Relative importance of species at risk 

6. Population/Community impacts 

*Final Response to Closed Cases 

1. Referral 

2. Notify Resource Managers

Level III Response 

1. Activate Rapid Response Team

2. Notify Resource Managers

Figure 3.6.1 Decision Tree for Outbreak Investigations 
27 

3.6.2 Disease Determinations: Level II Decisions 

3.6.2.1 Disease vs. Damage 

 

In corals, gross morphological signs of disease can be manifested as loss of tissue, 

damage to the underlying skeleton, alterations in color of affected tissue, or changes in 

shape, size, or texture of the corallum (Work and Aeby 2006). These signs alone can 

only be used to describe an observed lesion, not to infer causality. Additional 

morphological features (e.g., histology) and laboratory studies (molecular, microbiology, 

analytical chemistry) are needed to better characterize the etiology, and determine 

possible causes. Many lesions found on corals are not the result of an infectious agent 

but rather a result of physical damage (e.g., predation, abrasion, and storm damage), 

environmental stressors (e.g., temperature-related bleaching, sediment stress), or 

chemical damage (e.g., allographic competition, or toxicants). When a coral lesion is 

encountered in the field it is important to conduct a thorough scene investigation to 

eliminate predation, bleaching, storm damage, competition and overgrowth, algal 

interactions and other potential sources of mortality. Some investigators use a small 

magnifying hand-held lens to help discern these characters underwater, if features are still 

questionable, a portable dissecting scope, on the support vessel can help in determining 

more specific features of the lesion. If evidence suggests the lesion may be due to 

disease, and lesions are widespread and are causing extensive mortality or atypically 

affecting a certain species, recommendations should be made for an investigation with 

sample collection for laboratory analyses. 

3.6.2.2 Characteristics to Consider for Disease Determination 

Growth anomalies 

Although frequently referred to as 

‘tumors’, the abnormal growths found on 

more than 40 species of coral, result from 

several different growth processes, most of 

which do not fit the strict pathology for 

tumor definition, i.e., neoplasm 

(uncontrolled growth of abnormal cells). 

Frequently the anomalous growth forms 

are due to processes such as hypertrophy 

or hyperplasia (Domart-Coulon et al. 

2006). In general, the growth anomalies 

of coral are focal or multifocal, circular to 

irregularly shaped lesions consisting of abnormally arranged skeletal elements (corallites, 

ridges, valleys), which are larger or smaller than those of adjacent healthy tissue. They 

may protrude above the colony surface, and may or may not be covered by intact normalappearing tissue. Pigmentation may be normal, lighter (suggesting loss of 

Figure 3.6.2.2.1 Coral growth anomaly Photo courtesy of Andy 

Bruckner, NOAA
28 

zooxanthellae), or completely absent (suggesting absence of zooxanthellae). In some 

corallites reduced in number or completely absent, and the growth anomaly resembles a 

white plaque over the colony surface. In other types, corallites may be highly 

disorganized and tissue may die in irregular patches. Aberrant calyx formation, enlarged 

calices, reduced number of calices, and color changes are features that may also be 

associated with coral growth anomalies.

Tissue loss

It is easy to jump to conclusions when faced 

with corals having complete tissue loss. 

Caution should be exercised not to assume 

the lesions are a result of an infectious 

agent. Lesions can be caused from a variety 

of factors that include physical damage, 

environmental changes (e.g., temperature), 

toxicants or infectious agents. Therefore it 

is imperative that lesions be inspected 

closely for distinguishing signs. Knowledge 

of local predators and their associated 

feeding patterns is crucial in distinguishing 

predation from disease. Predators will not 

necessarily be on the affected coral colony, 

but their presence in the vicinity should be 

noted, e.g., snails often can be found hiding 

at the base of the colony or in other crevices 

nearby. Many predators are known to cause 

complete tissue loss. Crown-of-thorns 

starfish (COTs) often leave a ‘trail’ of 

damaged colonies which can lead to the 

culprit. Coral-feeding fish, on the other hand 

are usually within the vicinity, as they are 

site attached. With tissue loss it important 

to note the pattern of tissue loss, rate of 

tissue loss, and presence of loose tissue. 

Presence of loose tissue can suggest a 

"sloughing" that occurs during some 

infections. Another sign of disease is 

progressive tissue loss. The rate of tissue 

loss can often be estimated by the degree of 

algal colonization on the bare coral skeleton. 

Frequently, disease will produce a linear 

pattern of progressive tissue loss as opposed to a more amorphous pattern associated with 

certain predators. 

Figure 3.6.2.2.2 Parrotfish spot biting on star coral (Montastraea 

annularis), Photo courtesy of Andy Bruckner, NOAA. 

Figure 3.6.2.2.3 Acropora disease of unknown etiology (2003 case from 

FL Keys), Photo courtesy of Dana Williams, NOAA
29 

Color change

If there is color change, the observer should 

look for evidence of interactions with other 

organisms (coral, algae, other invertebrates). If 

the colony is white, examine the skeleton and 

differentiate between bleaching, where the 

polyps are still present, and tissue loss with a 

bare skeleton. 

Field diagnosis is only the first step in 

determining presence of coral disease. If the 

signs of disease are present, etiologic diagnosis 

will require histological and other laboratory 

analyses. Level III investigations should be 

recommended only when the accumulated facts 

in the case meet the criteria for an unusual 

disease occurrence (see section 3.6.3). 

3.6.3 Decision to Launch an Investigation: Level III 

Level II disease assessment and information is forwarded to the National Coordinator and 

the Expert Working Group (EWG) for consideration. The criteria for determining 

whether reports constitute an Unusual Coral Disease Outbreak in most instances include a 

mass mortality event and/or numerous coral colonies with gross signs of recent partial 

tissue loss and they meet one or more of the following criteria: 

Species of interest is affected (e.g., ESA-listed coral) 

Multiple species affected 

Disease appears at an abnormal time or place 

Frequency of disease (i.e., increased number of colonies affected with lesions) 

is greater than expected for that time of year or for that location 

Potential ecological effects of concern 

Signs consistent with a known or reported disease, but affected species 

previously thought to be resistant to that disease 

Possibility of new disease, i.e., disease signs are not consistent with previously 

described clinical signs 

The EWG and the National Coordinator, in consultation with the Regional Coordinator 

will use their knowledge, experience and judgment to determine whether any of the 

criteria apply in a way that warrants an organized investigation with sample and data 

collection, or Level III Response. 

Figure 3.6.2.2.4 Above Siderastrea siderea with

Dark Spots Disease with some associated tissue loss

(white skeleton) in the lower portion of the photo,

below Yellow Band Disease on Montastraea

faveolata. The colony exhibits minimal recent tissue

loss. Photo courtesy of Andy Bruckner, NOAA
30 

 3.6.4 Launching an Investigation: Level III ICS 

Once a Level III Response is initiated, the Incident Command Structure is implemented. 

An Incident Commander is appointed, and other General Staff are assigned as necessary. 

The Incident Commander is responsible for collection of a Case History, Development of 

an Incident Action Plan (IAP) and Site Safety Plan (SSP), organization of all response 

team members, acquisition of needed equipment, permits and sampling kits, and 

execution of the IAP including sample collection, processing and shipment. 

A Command Post is designated, where all team members can report and be briefed on the 

IAP and SSP. Once the field investigation begins, Survey Teams conduct the initial dives 

to collect site data, set the perimeter of the affected area, document the scene, deploy and 

assess transects, and identify colonies for sample collection. The Collection Team 

obtains samples of coral tissue and mucus and associated water and sediment. The 

Support Team aides in these dives, processes or stabilizes the samples once they arrive on 

the boat, and finalizes the processing back at the Field Lab. All samples are stabilized, 

properly processed according to the planned laboratory analyses, logged, labeled, and 

shipped to the appropriate diagnostic laboratories. The Incident Commander calls to 

verify safe arrival of samples to the appropriate contact person at each laboratory. Any 

media information is supplied by the appointed Public Affairs Official for the region. 

Throughout the Outbreak Investigation, a cycle of planning, execution, reassessment and 

adjustment to plans will assure the most effective action (See Response Cycle, Figure 

3.6.4). Debriefing at the end of each response day will help to identify areas for 

improvement in the next dive or next day’s tactics. 

Once the field investigation portion of the response is complete, and feedback is given to 

the Initial Observer and other management authorities involved in the response in the 

form of a Quick Report, which is an update that includes any preliminary findings and a 

summary of laboratory tests being conducted and any follow-up observations 

recommended. Recommendations are formulated by the Incident Commander, Regional 

Coordinator and/or National Coordinator and provided to all of the appropriate parties. 

Analysis reports from samples sent to designated laboratories are collated in the National 

Office and reviewed by the Expert Working Group and other medical experts as needed, 

to evaluate the test results and provide a diagnostic report. For example histopathology 

samples are archived at the International Registry of Coral Pathology at the NOAA 

Cooperative Oxford Laboratory, Oxford, MD and microbial pathogen screening tests may 

be conducted at NOAA NOS CCEHBR, Charleston, SC. All information associated with 

the Response is kept on file by both the regional coordinators and national office, for 

future reference. 
31 

Figure 3.6.4 Flow diagram of operations during a Level III response. Artwork by 

Thomas Bartlett. 
32 

Chapter 4 

Case History, Sample Collection, Processing and Shipment 

 4.1 Case History 

A case history is a chronological record of significant events and observations 

surrounding an outbreak of disease and should be the first entry in a case file for a given 

outbreak investigation. Detailed field observations during an outbreak and investigation 

that identify significant events that preceded the outbreak can provide valuable context 

for interpreting the analytical data. Perceptive, thorough observers are invaluable for an 

investigation and avoiding preconceptions are imperative if the investigation is to remain 

unbiased. 

Environmental Factors 

Environmental changes such as storms, heavy rains, abnormal temperature shifts, 

changes in water quality can be sources of stress that contribute to outbreaks or mass 

coral bleaching events. Satellite imagery over the previous months may reveal unusual 

situations such as large run-off or storm water inputs and should be included as data and 

information are gathered. It is also important to determine if there were recent industrial 

or agricultural spills or applications of pesticides or herbicides in the vicinity. Any 

previous disease outbreaks or die-offs in the area should also be noted. 

Estimate Onset of Disease 

The timing of disease onset and rate of progression can be estimated for some corals by 

the degree of bleached tissue or bare skeleton is associated with the lesion and the 

amount of algal colonization. Note and photo-document algal colonization of affected 

colonies. 

Species and Number Affected 

It is important to document which species are affected as well as those that remain 

unaffected as some diseases appear to infect only a narrow host range while others a 

much broader range. The incidence or proportion of sick colonies, verses the number of 

those not displaying lesions is also valuable to the diagnosis. 

4.2 Basic Steps 

General Considerations 

Field observations and data provide a critical link in disease diagnostic work and can 

significantly affect the outcome of laboratory efforts which depend on the quality of the 
33 

samples and the accuracy of the accompanying observations and measurements. The 

quality of the information depends on a number of factors which include: 

Response Team size, skill and experience 

Response Team organization, interests and biases 

Adherence to clear, detailed protocols, including time-sensitive samples 

Adequacy of planning and suitability of logistics (e.g., type of boat) 

Conducive weather conditions to support safe dive operations 

Care maintained in labeling, processing, stabilizing samples 

Care in adhering to shipping and storage guidelines 

4.3 QA/QC Considerations 

Minimizing Cross Contamination: 

Visit sites with no signs of disease first 

Sample healthy coral first, then affected/diseased coral 

Use disposable nitrile gloves that are changed between each colony visited 

Gloves will be placed in a ‘trash’ container underwater and on the surface 

placed in a second plastic bag where they can be disinfected with bleach and 

then disposed with garbage 

Use new or decontaminated equipment for each sample. 

On the boat, decontaminate collection equipment by soaking in dilute 

hypochlorite (5-10% bleach) solution for at least 10 minutes and rinsing in fresh 

water. 

Decontaminating Dive Gear 

Clean dive gear by soaking in decontaminating solution 

Rinse thoroughly in fresh water at the end of each dive. 

 **Laboratory experiments have been conducted to determine cleaning agents that are 

effective in disinfection, yet pose little threat to dive gear deterioration. The suggested 

agent to date is 5% bleach prepared fresh or 3% LysolTM (diluted according to 

sanitization strength on packaging and followed by a thorough fresh water rinse).
34 

4.4 Survey Team- Site Identification and Assessment

The Survey Team will consist of 2-3 members. The primary responsibility of this team is 

to describe the scene underwater. This includes defining the perimeter of the outbreak, 

describing the biota, including cover, diversity and presence of other stressors, describing 

the extent of the outbreak (i.e., determining prevalence: number of species and 

individuals affected in the context of unaffected individuals), characterizing the lesions, 

and marking colonies for collection. 

4.4.1 Duties of Survey Team 

To accomplish the initial site assessment all available divers* should be used to: 

Conduct a survey of the area, (if available, with tow boarding or underwater 

scooters) to determine the spatial extent of the outbreak 

Count colonies in duplicate (once by each partner) and record the condition of 

corals within replicate belt transects. Optimally a minimum of two 20 x 1 meter 

linear transects within the center of the affected area and two transects at the 

perimeter should be completed (where possible). The dimensions of these 

transects may vary depending on the size of the affected area, the abundance, 

diversity and cover of stony corals, depth of the affected area, and size of the 

team; it is important to capture the diversity of a particular area within chosen 

levels of statistical confidence. *Note that some areas are more conducive to belt 

transects and may be the preferred methodology.

Characterize affected colonies within a 20 x 1 meter belt (colony size, severity 

of lesion, genus or species). The level of detail (e.g., type of colony 

measurements) depends on the available time, size of response team, and level 

of expertise of the team. 

Assess cover of corals and other major biota 

Record all information on Survey Data Forms 

*if numbers of dives per person are restricted, this may be limited to Survey Team 

members 

4.4.2 Individual Operations within the Survey Team and Their Responsibilities: 

Videographer- Video document the site from both planar aspects (at one depth 

along transect, keeping camera a set distance from the substrate as appropriate 

for the visibility, relief, cover and size distribution of corals) and pan video to 

get documentation of general habitat. 
35 

Cartographer- Create a generalized map of the area with key landmarks and 

GPS coordinates noted to allow orientation and ability to triangulate to specific 

colonies upon follow up visits. 

Tactical Specialist- Identify affected individuals and temporarily mark them for 

sampling. The use of temporary floating chains (plastic chains) to mark 

colonies is suggested. Record Global Positioning System (GPS) location, depth, 

and other data designated on the Sample Site Documentation Form. Assign a 

unique identifier and photo-document each colony marked for sampling. 

4.4.3 Survey Approach 

Collection of epizootiological data should include, at minimum, the spatial extent of the 

outbreak; magnitude in terms of the number of colonies affected; and severity, in terms of 

the percent coral tissue affected or mortality resulting from the outbreak. A standardized 

disease response should include the following: 

Broad surveys to characterize the habitats affected, spatial distribution (e.g, 

habitats and depths affected) of affliction, and a rapid assessment of potential 

physico-chemical parameters (depth, water clarity, temperature, nutrient load, 

etc.), and anthropogenic impacts (pollution, runoff, sedimentation, etc.) that 

may be linked to the outbreak; 

Characterization of community structure in terms of cover of major benthic 

attributes (substrate, algal abundance and type, and coverage of benthic 

invertebrates by major phyla or class); 

Population information of the scleractinian corals (i.e., abundances, size 

classes, species diversity, and health status); and 

Detailed disease assessments including quantification of susceptible species 

and the diagnostic features of lesions on individual affected corals including 

photographic records of the lesions. 

The primary survey approaches are described below:

MANTA TOW SURVEY: The method can be used to estimate coral cover, 

dominant coral types, and broad patterns of disease or mortality. It is not 

possible to collect detailed diagnostic or quantitative data using this approach.

A snorkeler (or diver) is towed over the reef by a small outboard motor boat to 

characterize the major habitats, reef zones, major structural attributes, percent 

cover of major groups (e.g., stony coral, algae, soft coral, hard bottom), and 

spatial extent of the disease outbreak, noting areas with the highest prevalence. 

The snorkeler can drop marker buoys to delineate the area affected by disease. 

The precision of the manta tow surveys is limited by visibility and depth of the 
36 

site, complexity of the reef, and expertise of the observer. One advantage of the 

technique is that it enables the observer to characterize representative habitats in 

the context of the entire reef environment. 

POINT INTERCEPT SURVEY: Biotic and abiotic components are recorded 

at certain pre-defined intervals along transects to collect information on cover of 

various benthic organisms including coral as well as substrate types. 

Diver one extends a transect 20 m, parallel to depth gradients, within the 

approximate center of the affected area. The diver then slowly swims back to the 

beginning of the line recording the substrate type, and/or organisms to the highest 

taxonomic resolution possible under the tape every 0.5 m (total of 40 points per 

line; at minimum, 2 transects should be completed within the outbreak area and 

two outside of the main affected area). The cover of each component is then 

determined by dividing the number of points containing the specific category by 

the total number of points examined (and multiplying by 100). The minimum type 

of data collected for each point should include: 

o Substrate type: recorded as hard bottom, rubble, sand or dead coral 

o Specific type of algae or invertebrate to highest taxonomic resolution 

possible. The categories can include: 

Algal assemblage: recorded as fleshy macroalgae, turf algae, erect 

coralline algae (e.g., Halimeda), crustose coralline algae, and 

cyanobacteria 

Stony coral, recorded at minimum to genus 

Other invertebrate, including sponge, soft coral, gorgonian, 

anemone, bryozoan, tunicate etc. These organisms should be 

recorded by major group, and if possible, also include growth form 

and taxa to highest level possible. 

CORAL ASSESSMENT SURVEY: All corals within a predefined area (i.e., 1 x 

20 m) are counted and measured and the presence of disease is recorded. This 

approach will provide detailed data on disease prevalence based on a whole 

colony assessment, population dynamics, and health status. 

Diver two records all colonies (species, maximum diameter, and condition) within 

one meter of the transect. A 1 m bar marked in 5 cm increments is used to help 

guide estimation of transect width and to guide estimation of colony size. Only 

colonies with whose centers lie within the belt transect are recorded; large 

colonies with their centers (e.g., more than 50% of the colony) lying outside the 

transect must be ignored. 

Colony sizes are preferentially recorded to the nearest 5 cm from a planar view, 

with measurements only of corals 10 cm or larger in diameter. If the site contains 

a very large number of colonies, size classes can be lumped into six groups: 10-20 

cm; 21-40 cm; 41-80 cm; 81-160 cm; 161-320 cm; and >320 cm. Smaller 
37 

colonies should be identified (at least to genus) and counted within the 20 X 1 m 

belt, lumping them into colonies 0-5 cm and 6-9 cm. If there are large numbers of 

small colonies, these can be quantified by recording the total number within five 1 

m2

 quadrats per transect instead of surveying the entire belt. Quadrats are placed 

next to the transect tape at predetermined intervals (e.g., 0, 5, 10, 15, 20 m). 

*Note for certain areas of the Caribbean, colony sizes of 4 cm or greater may 

need to be included in the assessment.

DISEASE ASSESSMENT: All colonies with disease or other causes of mortality 

are identified and counted, and specific detailed diagnostic information is 

collected for those corals exhibiting signs of the disease under investigation. This 

approach will provide data on prevalence of all diseases as well as useful 

diagnostic descriptions for the disease of interest that can assist in determining 

when the event first occurred, how severe it is, whether it is ongoing, and if it is 

increasing or declining in severity. 

Diver three identifies every colony within the one meter belt with signs of recent 

mortality, recording the genus and the common name of the disease or other 

condition. This includes signs of predation (differentiated into gastropod, 

fireworm, COTS, or fish bites), disease, bleaching, or compromised health (e.g., 

algal or invertebrate competition, physical damage etc.). For colonies exhibiting 

signs of the disease under investigation, the observer should record the genus (or 

species), maximum diameter, and diagnostic features of the lesion (see section 

4.4.3 and Appendix IV). *If time permits accuracy may be improved by having 

the same diver(s) conduct the community structure surveys as well as the disease 

assessments. 

This same diver also identifies corals for sampling and marks them with floating 

chains and assigns temporary numbered tags. Colonies for sampling should 

include representatives from all species affected by the disease of interest, as well 

as different stages in the progression of the disease ranging along a continuum 

from colonies that appear to be newly infected (small lesions that lack algal 

colonization) to older well established infections (prominent large lesions with a 

gradation of algal colonization on exposed skeletal surface). 

Depending on the site characteristics, species diversity and abundance, and extent of the 

disease outbreak, coral assessments or disease assessments may take additional time to 

complete. As divers finish a task, they can assist the other divers by conducting coral 

assessment or disease assessment, beginning at the end of the transect and working 

towards the other divers. If the survey team consists of two divers, one diver would 

complete point intercept surveys and then begin disease assessment surveys, as the coral 

assessment may require the most time. 
38 

4.4.3.2 Possible Modifications to Consider 

Many Indo-Pacific reefs are characterized by high coral cover, a large number of species 

and colonies, and a dominance of small to intermediate sized corals, making it 

impractical to measure the size of every coral, especially if dive time is limited and the 

Response Team is small. It is best to record corals to species, but this may be impractical 

or not possible on certain high diversity Indo-Pacific reefs and depending on the expertise 

of the survey team. In this case, divers should record corals to the level of Genus, 

attempting to differentiate between growth forms when possible (e.g., massive vs. 

branching Porites). The methods described above could be further modified, based on 

the complexity and size of the affected area, size of the team, and available time. 

The minimal survey information that should be collected is an accurate list of all of the 

genera (or species) and their abundance within the sampling area, along with the numbers 

of each taxon exhibiting signs of the condition being investigated. A simple data sheet 

listing all the genera in the first column, a second column to tally the number of healthy 

corals, and subsequent columns to tally the number of colonies with each type of disease, 

predation or compromised health. This will provide information on the prevalence of 

colonies by genus (or species) that are diseased, as well as the prevalence of a particular 

disease for the entire coral community. 

A second level of information could include recording each genera observed within the 

belt transect, and the numbers of each genera that shows signs of the condition under 

investigation. The observer could record the maximum diameter of colonies, focusing on 

measuring only those taxa identified as being susceptible to the particular disease. 

A third level of information could involve recording the total numbers of each genera 

(with and without disease) within particular size classes (e.g., lump all colonies into six 

categories, <10 cm, 10-19 cm, 20-49 cm, 50-74 cm, 75-100 cm and >100 cm). This 

could be done for all genera, for a subset of the 12-15 dominant genera, or only for the 

genera affected by the disease. 

4.4.4 Diagnostic Descriptions of Lesions from Gross Observations 

For each colony exhibiting signs of the disease under consideration within the survey 

area, information should be recorded on the affected taxa, its size, and condition (see 

Appendix IV for assessment form). The lesion should be described in terms of its gross 

characteristics (tissue loss, skeletal damage, color change, or growth anomaly), the 

location, lesion pattern, lesion margin, and lesion color (See Fig. 4.4.4), including: 

Location: apical, medial or basal 

Lesion pattern or distribution: linear, annular, focal, multifocal, coalescing, or 

diffuse 

Lesion size: maximum dimensions 
39 

Lesion margin: condition of disease margin. This should include the thickness, 

lesion shape (linear, annular or diffuse), and border (smooth, jagged, tissue 

sloughing). 

Rate of Progression: extent of recent tissue loss and degree of algal 

colonization, classified as acute, sub-acute or chronic. Colonies exhibiting rapid 

(acute) disease progress have prominent exposed white skeletal areas with no or 

minimal algal colonization by turf algae. Moderate (sub-acute) lesions are 

characterized by large patches of exposed white skeleton along with initial signs 

of turf and macroalgal colonization on older tissue-denuded skeletal surfaces. 

Chronic lesions often have a narrow (<1 cm) border of white exposed skeleton 

adjacent to living tissue, or an absence of recently exposed skeleton; previously 

denuded skeletal areas are colonized to various degree by turf, macroalgae and 

crustose corallines. 

 

Figure 4.4.4 Diagnostic descriptors for lesions on stony 

corals. Modified from (Work and Aeby 2006). 
40 

4.4.5 Field Microscopy 

4.4.5.1 Introduction 

Magnification is the ability to visibly scale up specimens to be able 

to see more detail than with the naked eye alone. It can be 

accomplished using a variety of techniques which increases 

resolution which is the smallest distance between two objects at 

which they can just be seen as two separate and distinct objects. 

Magnification of specimens in the field can be accomplished by using simple hand lenses 

(e.g., 5X magnification) while diving or at the surface or using a simple dissecting 

microscopes (also called stereomicroscopes) on the boat. Using these simple tools to 

provide a closer look at field specimens, lesions and disease margins can provide 

valuable visual details that are not apparent to the naked eye and contribute significantly 

to the diagnostic process. For example, when observing a brown banding pattern on a 

coral, it is relatively easy to distinguish between tissue discoloration and a band of 

ciliates, when 5X magnification is used, whereas visual inspection with the naked eye 

alone can lead to an erroneous conclusion of tissue discoloration (Figure 4.4.5.2). 

4.4.5.2 Relative Sizes 

Although visual inspections are imperative during field investigations, closer 

examinations with a magnifying lens or stereomicroscope is important to consider as a 

regular part of lesion characterization in order to see its unique physical characteristics 

(size, shape, motility, color). It is also important to recognize the relative sizes of cells or 

organisms and to put them in proper perspective and to avoid erroneous descriptions. For 

example, bacteria are too small to be observed with simple magnifying lenses or even a 

stereomicroscope since neither instrument has the ability to resolve objects in this size 

class. Figure 4.4.5.2 illustrates the relative sizes of specimens related to coral reefs and 

the instruments required to view them. 

Figure 4.4.5.1.1 

Resolution is the shortest 

distance between objects 

that allow each to be seen. 

Figure 4.4.5.1.2 Acropora surculosa, infected by the Brown band ciliate in a laboratory aquarium tank. 

A= low power stereoscope B= high power stereoscope Photo courtesy of Dr. Laurie Raymundo, Univ of 

Guam.

A B 
41 

Figure 4.4.5.2 The scale of coral reefs and the instruments used to view them. 

Artwork by James Nicholson 
42 

4.4.5.3 Use of Stereo Microscope 

The American Optical Cycloptic 

microscope (Figure 4.4.5.3) is a 

sturdy, easy to use microscope that 

is available for field investigations. 

To FOCUS the microscope, 

use the focus knob starting 

above the good focus level and 

rack down until the specimen 

is in sharp focus. This 

particular microscope is 

collimated (parallel beams of 

light) to assure parfocality 

(stays in focus when 

magnification is changed) at all 

magnifications. 

To CORRECT for individual 

eye differences, first focus the 

microscope with the right eye. 

Turn the left eyepiece focusing 

sleeve counterclockwise until 

the left image is out of focus, 

then turn clockwise until the 

image is in sharp focus with 

the left eye. 

To adjust INTER-PUPILLARY DISTANCE, grasp the eyepiece housing and adjust 

the spacing by moving the two until able to view a full single field with both eyes. 

To Change MAGNIFICATION, rotate magnification knob to desired magnification. 

Magnification values can be read at the indicating dot. 

4.4.5.4 Care and Maintenance of a Stereo Microscope 

A well-designed stereo microscope requires surprisingly little maintenance. Most 

problems can be prevented by some simple, common sense, proactive preventative steps. 

Bear in mind that cleaning optics is inherently destructive over a long period of time so 

preventing optical contamination is better than cleaning it off. One of the most useful 

microscope accessories, often unused is the simple dust cover. A microscope should 

always be covered when not in use. Special consideration should be given to the type of 

cover where ever there is the possibility of water, chemicals or blowing sand affecting the 

scope. 

Eyepieces

Figure 4.4.5.3 Illustration of an American Optical dissecting scope. Illustration 

by Athena Avadanei

Magnification 

Eyepiece 

Focus 

Microscope Body

Microscope Base

Specimen Stage

Housing
43 

Common dust is usually not of concern and if excessive enough to be bothersome is 

easily removed with a source of air, either commercial canned air, or an ear syringe. The 

most common type of contamination that requires prompt and thorough cleaning is finger 

prints. The oils in a finger print can actually etch the optical coatings on the lens. Eye 

makeup such as mascara can be a chronic problem in the contamination of the eyepieces. 

The best solution is to discourage the use of eye makeup by personnel using microscopes. 

Salt spray needs to be removed by the careful use of fresh water cleaning using damp 

clothes, never liquids that could get into the scope. 

Tips for proper cleaning of optics: 

1. Have proper materials on hand including good quality lens paper, a source of air and 

lens cleaner. 

2. Always first use air to blow off the optical surface to remove any grit that could 

scratch the optics during cleaning. 

3. Never touch an optical surface with any dry material. Always moisten the cleaning 

cloth or tissue with lens cleaner or use your breath to fog the lens. 

4. Suitable cleaning materials include lens tissue, microcloth, or a well laundered clean 

handkerchief. 

5. Clean in a circular motion without applying excessive force. Make several passes 

using a clean surface each time. 

6. The use of solvents should be carefully restricted to lens contamination such as oil or 

mounting media that actually requires it. Never apply any solvent directly to a lens 

but always apply it to lens paper or a cotton swab. Shake off excess liquid before 

applying to the lens. Materials like oil will require the use of multiple swabs or papers 

as they must be discarded after each pass. Check all safety instructions for any 

solvent and make sure you have adequate ventilation, and personal protection as 

required. 

4.5 Collection Team- Sample Collection 

The Collection Team may consist of 3 members: the Sampler, Sample Handler, and the 

Records Diver. However, the tasks can be accomplished by 2 divers, with assistance 

from a snorkeler on the surface to ferry samples to the boat between each colony. The

Sampler will physically collect the prescribed samples from coral colonies and 

photograph the pre- and post- biopsy condition of the affected areas. The Sample 

Handler will assist the sampler in keeping track of the collection bags or tubes, verifying 

the labeling, securing the samples once taken, and seeing that time intervals are 

maintained for time-critical samples such that the samples are transported to the surface 

in the prescribed time. The Records Diver is responsible for the Diseased Colony 
44 

Collection Form, and will ferry time-sensitive samples to the surface. The Sample 

Handler may also perform the duties of the Records Diver on the occasion of a twoperson collection team. 

4.5.1 General Considerations 

Specimens are material representative of the problem and suitable for further laboratory 

analyses. The specimen may be tissues, mucus, environmental samples (e.g., water or 

sediment) or other flora or fauna that associate with the diseased corals. Photographing 

lesions and surrounding area provides a record of color, location and appearance of 

lesions. Both actual size and macro shots should be taken before and after removal of 

tissue biopsies. It is also important to include a color scale and metric to size and color 

correct photos. 

The primary consideration when collecting diseased tissue is personal safety; universal 

precautions for potential health hazards should be observed. To avoid transmission of 

possible disease agents, disposable gloves should be used, and disinfection with a 

commercial disinfectant or 

a 5-10% bleach solution 

(prepared w/in 12 hrs of use 

and kept out of direct 

sunlight) should be used to 

decontaminate collection 

tools, work areas and dive 

gear. Observations of these 

guidelines will minimize 

transmission and protect 

team members. 

“Collection and analysis of 

samples is the basis of 

investigation, and the 

validity of the results and 

conclusions of any study is 

totally dependent on the 

quality of the samples 

collected” (Wobeser 1994). 

Properly trained individuals 

proficient in collection 

techniques are critical to the proper collection and preservation of samples. Improperly 

collected or preserved specimens can look the same as a good sample, but if handled 

improperly or contaminated, it will preclude further analyses and compromise the 

integrity of an investigation. 

 

Figure 4.6.1.1 Diagram illustrating disease margin, unaffected areas and possible sampling 

design. Illustration by Shawn W. Polson.(Polson et al. 2006).
45 

4.6 Collection Protocols for Biological Analyses 

4.6.1 Labeling Scheme Guideline 

Letter or number designation of the collection site 

Four letter abbreviation for coral species (first letter of genus, first three of 

species) 

Colony number within site 

Two letter sample type abbreviation 

 

Colony Type Analyses/Collection Method Example

Reference Water Protein R-P 

Healthy Sediment Fixative H-F 

Unaffected Mucus Bacteria U-M 

Diseased Applicator (Swab) D-S 

ex. Reference Site A= A.Dstr.1.R-P 

 Diseased Site B= B.Apal.4.D-F and B.Apal.2.U-M

Definitions 

“Reference” - uninfected or ‘healthy-looking’ colonies from areas where no 

corals exhibit signs of the disease 

“Healthy” - apparently healthy corals in affected sites 

“Unaffected” - areas of diseased colonies with normal appearance, distant from 

the lesion 

“Diseased" - margin of the lesion 

Figure 4.6.1.2 Example of components that may be used in for specimen collections during an outbreak 

investigation 
46 

Due to time sensitivity of some samples, such as the tissue for protein analyses, sampling 

should adhere to a specific order. 

Within each site, samples should include: 

Water 

Sediment 

Applicator/Swab 

Syringe/Mucus 

Core or Clipped Tissue Samples for each analysis planned

4.6.2 Sediment 

Scoop sediment with sterile pre-labeled 

15mL conical or similar container 

This type of sample is used solely for 

microbiological sample analyses as a reference for 

microbes situated in the sediments that may be 

mobilized from disturbances such as storms. 

4.6.3 DNA Swab 

Wipe across the area to be sampled three 

times. 

This is currently experimental and may provide 

less invasive sampling. The swab samples are 

limited to DNA analyses of surface tissue and 

mucus. 

4.6.4 Water 

Collect one reference volume for each 

colony 

Should be equal in volume to mucus 

sample 

Collect in a 3cc or larger syringe 

 

This sample is used as a reference for 

microbiological analyses to allow analyst to 

account for possible water contamination of 

mucus and tissue samples as well as a comparison 

for microbes that may be found in surrounding 

waters, but not primary colonizers of corals. 

Figure 4.6.2 15cc Falcon tube for microbiology 

sediment collection 

Figure 4.6.3 Epicenter DNA swabs 

Figure 4.6.4 Syringes for water and mucus collections 
47 

4.6.5 Mucus 

A sterile syringe without the needle is used to aspirate (draw in) mucus from the surface 

of the coral. For diseased samples, mucus is collected along the disease margins and 

unaffected samples across the surface of unaffected areas. If swab samples are collected, 

this should be done first which should provide the irritation required to obtain mucus. It is 

important to collect mucus already present on the colony. The diver should avoid initially 

irritating the colony, as mucus subsequently released by the coral will have a depauperate 

microbial flora community. 

Mucus samples have been one of the primary types of specimens used in culture 

dependent and independent microbiological analyses. It seems to provide consistency 

across temporal and spatial sampling for microbial diversity studies. Recent work 

however has shown different microbial profiles are obtained depending on whether liveground tissue or mucus is being analyzed. It appears that these two micro-environments 

contain different microbial communities, with tissue samples having a more diverse and 

robust community than mucus. 

 

4.6.6 Tissue biopsy 

Fragment/Tissue 

Coring technique- 1- 2.2cm diameter uniform disk samples of tissue + skeleton 

for larger colonies, using two punch sizes. *clay should be inserted after coring 

to minimize further damage (Roma Plastalina, no 2-from Rex Art, Miami, FL)

Clippers/Pliers/Garden Shears- can be used for clipping from branching 

specimens 

Tissue samples are collected for a variety of clinical analyses. Currently available 

analyses include histology/histopathology, microbiology, cellular diagnostics (primarily 

Figure 4.6.6.1 Clippers 

used for sampling 

branching corals 

Figure 4.6.6.2 Tools used for bolder corals. Stainless steel coring tube for histology (A) is 2.5 cm, while 

leather punch (B) biopsy is 1.5 cm. 
48 

protein chemistry based and includes a suite of various biochemical and cell-based 

parameters that can be measured for building a diagnosis) and genetic or functional 

genomic assays. 

4.7 Sample Processing for Biological Analyses 

Each sample has a predetermined experimental or analytical role, which determines how each 

will be processed on the boat and back on land. The Sample Technician of the Support Team will 

do most processing.

4.7.1 SUPPORT TEAM 

This team will consist of at least 2 members who will provide topside and field-lab 

support. The primary job of the Sample Technician is to ensure the proper handling, 

documentation and stabilization of each sample collected. The Logistics Chief is 

responsible for all dive gear and collection equipment and assists the Sample Technician. 

4.7.2 PROCESS TIME SENSITIVE 

SAMPLES FIRST 

Tissue for Protein (H-P, U-P, D-P) samples 

should come to the surface in dark bags or covered 

(e.g., glove) to protect them from light for light 

sensitive assays. They are time sensitive and need to 

be processed in a dark or shaded area. Mucus 

should be rinsed by swishing in seawater, dabbing 

on BountyTM paper towel (or lint-free paper towel), 

and placing in a new, prelabeled WhirlpakTM. Since 

WhirlpakTM bags are prone to shattering at liquid 

nitrogen vapor temperatures, the bags are wrapped 

in aluminum foil with an identifying label on the 

outside and placed immediately into a dry shipper. 

Do not write on aluminum foil as it is not 

permanent, use labeling tape or cryotags and 

waterproof marker. The time interval between 

collection and freezing should be approximately 15 

minutes, longer than this will exclude certain 

cellular diagnostic assays due to creating artifact by 

changes in the sample. 

Figure 4.7.2.1 Collection bags for healthy coral 

samples for H-F=fixative (histology), H-P=protein 

H-B=bacteria (microbiology) 

Figure 4.7.2.2 Collection bags for diseased coral 

samples. D-P=protein, D-F=fixative (histology), 

D-B=bacteria (microbiology) 
49 

Tissue for Histology - The tissue biopsies collected from Healthy, Unaffected 

portion of diseased colony and the Disease margin (H-F, U-F, D-F) are placed in 

bags or tubes underwater and on reaching the boat, if transport of fixative is 

logistically sound, the samples are immediately placed in a 50cc polypropylene tube 

containing approximately 25 mL of an appropriate fixative for a 2cm punch biopsy 

or an approximately 2-3 cm branch (if larger, the fixative volume should be 

increased in proportion). When fixative transport is precluded, histological samples 

should be stored in bags or a container containing seawater and securely stored to 

minimize stress until a destination for fixation is reached. We routinely use Z-fix 

(Anatech Ltd.) diluted 1:4 in sterile artificial sea water (ASW; 35ppt) and held at 

~25°C, because of the ability to retrieve intact DNA from the samples for 

subsequent molecular and immuno-staining. The ratio of tissue to fixative should be 

at minimum 1:10 (1:20, preferred). DO NOT FREEZE THESE SAMPLES. 

Alternatively seawater-buffered formalin can be used for fixation of corals for light 

microscopy and formalin is generally available at marine labs, hospitals and 

veterinary clinics. This is prepared by filtering either natural or artificial seawater 

and diluting formalin stock (37.5% formaldehyde) 1 part formalin to 9 parts filtered 

seawater. The samples are fixed from 4 hrs to overnight then rinsed in tapwater and 

stored in 70% ethanol or alternatively can be stored in the 3.75% formalin-seawater. 

For shipping Kim-wipesTM or other lint-free paper is saturated with the preservative 

(e.g., 70% ethanol) and stuffed into the tube. This stabilizes the samples and keeps 

them moist, while avoiding shipping tubes filled with a hazardous material.

These samples are planned for light microscopy analyses. Electron microscopy requires different 

stabilization and processing and is not covered here. 

 

Figure 4.7.2.3 Summary of samples to be frozen showing the packaging used for freezing. 
50 

Tissue for Microbiology (H-B, UB, D-B) should be kept in a 

WhirlpakTM with sterile 35 ppt 

artificial sea water added if needed, 

keep at ambient temperature in a 

cooler with local seawater. Upon 

return to shore, homogenize tissue 

and skeleton with sterile mortar 

and pestle (with its own mucus), 

flash freeze half of homogenate, 

and culture bacteria on marine agar 

or other desired media, with other 

half of homogenate. 

Swabs or Applicators (H-A, U-A, 

D-A), if they are Whatman FTATM

type swabs, should be wiped on the 

card, and then the tip should be 

broken off and stored in a 15 cc tube or cryovial. Other types of swabs (Epicenter, 

Madison WI) simply need to be broken off and the tip stored. Cards can be stored in 

a reclosable food storage bag (e.g., ziplocTM) and shipped at ambient temperature; 

swab tips should go in the cryovial. **Alternative storage to freezing is being 

investigated using sodium chloride saturated dimethylsulfoxide (DMSO). 

Mucus samples which were collected in a syringe without needle need to be split: 

Half should be placed in a cryogenic vial and immediately flash frozen in a liquid 

nitrogen dry shipper for molecular analyses. The other half should be kept in screw 

top vials at ambient seawater temperature and cultured on marine agar media as soon 

as possible for microbiology. (See Support Team Processing Guidelines Form in 

Appendix V). 

Surface sediment (H-S, D-S) - loosen cap and attempt to remove as much water as 

possible. Leave about a 2 cm gap between sample and cap, cap tightly and freeze in 

dry shipper. 

Water (H-W, D-W) should be split into two samples. Half can be transferred from 

the syringe to a 2.0 mL cryogenic vial and placed in the dry shipper. The other half 

should also go in a 2.0 mL vial, but be kept at ambient temperature for culturedependent methods. 

The other roles of the Support Team at this point are to catalog these samples, track and 

label all samples, label and link digital photos to samples, download GPS coordinates and 

upload to GIS (if available), and prepare to ship time-sensitive samples.

Figure 4.7.2.4 Equipment used in processing tissue samples for microbiology.

These include a mortar and pestle for grinding fresh tissue, device to flame

sterilize spreading rods, agar plate for culturing bacteria and cryovial for freezing

ground tissue sample.
51 

4.8 Sample Shipment

The Planning Chief or Incident Commander, in 

collaboration with the Regional Coordinator and 

National Coordinator should make prior 

arrangements with the appropriate diagnostic 

laboratories to conduct the analyses, and provide 

advanced notification with likely dates of sample 

arrival before conducting the response. These 

dates should be confirmed before shipping 

samples. The Incident Commander should also 

follow up with the lab to ensure arrival of samples 

to the lab and to the appropriate person. 

Samples should be placed in appropriate packaging to ensure safe delivery, avoid leaks, 

and fines. Each shipment should be labeled as non-regulated material to avoid concerns 

by the currier or inspection agents (e.g., customs). Dry ice and dry shipper labels should 

be used where appropriate. 

4.9 Permits 

It is imperative that all biological samples are collected and shipped under appropriate 

permits, and relevant documentation is included with samples. 

4.9.1 Convention on International Trade in Endangered Species of Wild Fauna 

and Flora (CITES) Permits 

CITES is an international agreement between 166 governments to ensure that 

international trade in specimens of wild animals and plants does not threaten their 

survival. Under CITES, a species is listed at one of three levels of protection, each of 

which has specific restrictions on trade: no commercial trade is allowed in Appendix I 

species, while trade is allowed for Appendix II species when accompanied by an export 

permit that indicates the species was legally acquired and trade is non-detrimental. Coral 

reef species currently listed in CITES on Appendix II are 1) all corals including 

scleractinian (stony) corals, hydrozoan corals (Millepora and Stylaster), organ pipe coral 

(Tubipora), and blue coral (Heliopora), 2) all antipatharian (black) coral species, 3) giant 

clams (Tridacna and Hippopus spp.), 4) queen conch (Strombus gigas), 5) all seahorses 

(Hippocampus), and 6) humphead wrasse. For stony corals, permits are required for live 

corals (whole colonies and pieces with recognizable corallites), skeletons, 

eggs/sperm/planula, live rock, reef substrate and eroded skeletal fragments greater than 3 

cm in diameter. A CITES permit is also required for coral samples less than 3 cm in 

diameter if the corallites are discernable and allow identification of the coral to genus (or 

species). 

Figure 4.8 Dry shipper. Note lid and canister alignment 

are critical to ensuring proper seal. 
52 

When shipping coral samples from outside of the U.S. and U.S. territories to laboratories 

located in the U.S., shipments must include a valid export permit issued by the exporting 

countries Management Authority in the country of origin (or an approved equivalent form 

issued by equivalent national authority in the case of countries not party to CITES). The 

U.S. does not require import permits. CITES permits are not required for shipments 

between the U.S. and our territories (Puerto Rico, U.S. Virgin Islands, Guam,

Commonwealth of the Northern Mariana Islands (CNMI) and American Samoa). 

When shipping coral samples from the U.S. to international destinations a valid export 

permit issued by the CITES Management Authority in the U.S. [Division of Management 

Authority (DMA), U.S. Fish and Wildlife Service] must be included with each shipment; 

depending on the destination country (e.g., the European Union), a CITES Import Permit 

is also required. 

Importation of fish and wildlife, including corals, must be imported at one of the 14 

Designated Ports and must be declared using USFWS Form 3-177. It is important that 

shipments are clearly labeled as CITES material. 

When using international mail or an overnight type courier (e.g., Federal Express or 

UPS), shipments sometimes bypass USFWS and are delivered directly to the importer. It 

remains the responsibility of the importer to file the appropriate declaration form; failure 

to file when required is a violation of the Endangered Species Act of 1973. USFWS has 

simplified the declaration process by allowing the 3-177 Form to be submitted 

electronically (eDec) followed by mailing the original CITES permits along with a copy 

of the eDec confirmation page (https://edecs.fws.gov). If Certificates of Scientific 

Exchange are used (see below), no original CITES permits need to be sent to USFWS. 

As an alternative, the CITES Secretariat has endeavored to streamline the permitting 

process for scientific samples by encouraging scientific institutions to register for 

Certificates of Scientific Exchange (COSE). The International Registry of Coral 

Pathology (IRCP) in Oxford, MD, administered by Dr. Shawn McLaughlin 

(shawn.mclaughlin@noaa.gov) and the Coral Disease and Health Consortium, 

administered by Dr. Cheryl M. Woodley (cheryl.woodley@noaa.gov) in Charleston, SC 

hold COSE permits for exchange of histological materials. To facilitate such exchanges, 

investigators are urged to work with their local scientific institutions to register for a 

COSE with the CITES Management Authority of their country (or approved for this 

purpose by an equivalent national authority in the case of countries not party to CITES). 

A one-time application and minimal fee (or waived in certain cases) permits exchange of 

specimens among registered institutions in lieu of filing CITES export or import permits 

for each shipment. COSE authorizes non-commercial loan, donation, and exchange of 

legally acquired scientific specimens between any institutions registered for this purpose. 

In the U.S., application is made by submitting USFWS Form 3-200-39 to the Division of 

Management Authority (http://www.fws.gov/). Upon approval, the institution is assigned 

a registration number and added to the list of registered institutions. Fixed and embedded 

specimens and micro-slides prepared from legally obtained corals may then be shipped 

from a registered institution to a registered institution without application for additional 
53 

CITES permits. Legally obtained Appendix II specimens may be imported into the U.S. 

by simply entering the registration number of the importer and exporter on the USFWS 

claim form. This significantly reduces the time, effort, and potential cost spent on 

obtaining export or import permits for individual shipments (Mc Laughlin et al. 

Unpublished) however, both the exporting institution and the importing institution must 

be registered. 

4.9.2 Other Collection Permits 

Each state, territory and jurisdiction has their own regulations regarding scientific 

collection permits. In some locations multiple jurisdictions exist, for example the Florida 

Keys National Marine Sanctuary’s boundaries are within the State of Florida’s waters and 

both the State and Sanctuary permits are required for the collection of coral, in others one 

entity issues permits. To date blanket permits have not been approved for Coral Disease 

Outbreak Responses, but managers acknowledge the urgency of these cases and have 

recommended an expedited or emergency permit process. It is important for Response 

Coordinators to develop a dialogue with permit offices in their region that explains the 

Response process and oversight provided in determining when sampling is warranted. 

The coordinators should also include a minimal sampling plan, rationale and projected 

analyses for samples that are taken during an investigation. 

4.10 Types of Laboratory Analyses 

4.10.1 Histology 

Histological analyses are used to characterize the microscopic morphology of tissue and 

may help guide further investigations. They provide systematic evaluation of cellular 

changes that occur in tissues under normal, stressed or diseased conditions. The 

microscopic evaluation determines which cells or tissues are affected and whether foreign 

organisms (i.e., bacteria, fungi, metazoa, protistans, viruses) are present. Most 

evaluations begin with light-level microscopy; however transmission electron microscopy 

can provide evidence of sub-cellular changes that are informative in understanding 

functional changes associated with a particular pathology. 

Figure 4.10.1 Histological specimens and slides (left), micrograph of coral tissue (right) (Photos courtesy of Shawn 

McLaughlin) 
54 

4.10.2 Microbiology 

Microbiology is one of the fundamental disciplines used in clinical diagnostics when an 

infectious agent has not been excluded. Coral disease research focuses heavily on 

microbiology ideally combining culture-dependent methods, with DNA-based 

technologies. While culture dependent methods are useful in identifying specific 

dominant cultivable microorganisms, culture-independent methods allow examination of 

the diversity of microbial communities associated with corals and coral mucus and shifts 

in these communities between hosts, species, seasons, geographic location and when 

exposed to different stressors. This facilitates investigations in microbial ecology, 

functional studies of microbial communities and differential analyses of these 

communities between various health conditions of corals. 

4.10.3 Molecular 

Molecular analyses address the formation, structure, and function of macromolecules 

essential to life, such as nucleic acids and proteins. Biochemical and cellular endpoints 

are often used in clinical diagnostic assays. Several of these have been adapted to coral 

and referred to as cellular diagnostics (Downs 2005a). The concept of cellular 

diagnostics is based on using a systematic approach to defining biomarkers of exposure, 

effect, and susceptibility and integrating levels of these cellular parameters into a profile 

that is diagnostic for certain cellular functions and disease states, and provide indicators 

of overall performance. The selection of cellular parameters is based on known 

functionality within a cell and knowledge or inference of how alterations in single or sets 

of cellular parameters affect cellular physiological processes. Many of these processes 

are involved in key metabolic pathways or cellular structural components that are 

Figure 4.10.2.1 Culture dependent microbiology. Shown are samples

plated on selective media (TCBS) and general media (glycerol

seawater agar) Figure 4.10.2.2 Culture independent microbiology. 

Example shown is microbial community profile using 

denaturing gradient gel electrophoresis. 
55 

essential for cellular function and homeostasis. The behavior of these processes defines 

the cell’s physiological condition. Thus the identification and quantification of pattern 

changes in the cellular endpoints provides a basis for defining health status (i.e., 

diagnosis) and providing a prognosis. 

Molecular biology and coral functional genomics projects focus on nucleic acid, RNA 

and DNA. These studies are also vital to improving our understanding of the function 

and control of coral genes. One of the most urgent applications is to begin identifying 

more coral genes, understanding their expression patterns and control mechanisms. This 

will assist in improving our understanding of coral cellular physiology and form a 

stronger basis for pathology and the development of new diagnostic assays for studying 

and diagnosing coral disease. 

Figure 4.10.3 ELISA assay for measuring cellular diagnostic parameters. (Photo 

courtesy of CA Downs)
56 

Chapter 5 

Health and Safety 

5.1 Safety Plan 

The Incident Commander is responsible for completing the Site Safety Plan (SSP), which 

is part of the Incident Action Plan (IAP). This plan must consider personal needs, 

physical condition of personnel, adequacy of transportation, and potential dangers of 

response activities. The incorporation of diving into the investigations increases the 

safety concerns significantly. Boat use has its own set of regulations and requirements 

for safety, also. The processing of samples requires chemicals, which will need to be 

addressed in the SSP. The final concern is that of coral and human health when disease 

agents may be present. 

5.2 NOAA Boat Safety Regulatory Requirements 

http://www.ndc.noaa.gov/gi.html 

The Operator in Charge (OIC), Vessel Operator, or Crewmember must conduct a 

thorough safety briefing with all embarked personnel prior to getting underway. The 

briefing shall include general vessel familiarity and the locations of all safety systems 

and equipment carried aboard (fire extinguishers, life rafts, life rings, personal 

floatation devices, immersion suits, Emergency Position Indicating Radio Beacon 

(EPIRB), etc.). The embarked personnel shall be apprised of the procedures to follow 

during fire, abandon ship, man overboard, and other emergencies. The use of a 

formal, written checklist detailing all of the topics to be covered during each safety 

briefing is strongly encouraged. 

NOAA’s National Ocean Service VESSEL POLICY FOR SMALL BOATS can be 

used for further guidance, references, directives, and details in applicable Program 

Operational Risk Assessments, a boat’s Vessel Operations Manual (VOM), Original 

Equipment Manuals (OEM), or applicable United States Coast Guard (USCG) and 

federal regulations. 

Personal Floatation Devices (PFD’s), signaling devices, and standard survival 

equipment and rescue devices must be available and in serviceable condition on the 

boat. In addition, the Safety Plan must include emergency communications 

procedures, man overboard rescue and in-water survival techniques, and fire fighting 

procedures. 

 

Ideally, all Operators in Charge, Vessel Operators, and Crewmembers will have 

current Red Cross or equivalent certification in cardiopulmonary resuscitation (CPR), 

including the use of Automated External Defibrillators (AED), Oxygen 
57 

Administration, and First Aid. Inspection records for the vessel should be copied and 

examined for any deficiencies. 

The OIC is responsible for reviewing and being familiar with both prevailing and 

anticipated weather conditions for the area in which the mission is planned. The OIC 

shall obtain a briefing by a qualified meteorological forecast service (i.e. NOAA 

weather radio, National Weather Service website, calling local Coast Guard for 

conditions, etc.). The briefing information shall consist of, at a minimum, current 

weather, sea state, trends, and forecasts for the departure location, proposed route, 

destination, and any alternate working areas. 

Based on weather and sea state forecasts, the OIC will determine if conditions are 

suitable for operations. The OIC has the authority to cancel operations if he/she 

determines that personnel safety or the safety of the vessel will be subject to 

unnecessary risk. A float plan must be submitted and will include contact information 

for all members of the response. 

5.3 Dive Safety 

An Emergency Dive Plan should be written to include the following: 

Name, phone number and relationship of person to be contacted for each diver 

Name, phone number, and transport plans to the nearest operational 

recompression chamber 

Nearest accessible hospital 

Available means of transport 

Number, depth, and duration of proposed dives 

Location of proposed dives 

Estimated depth and bottom times anticipated 

Decompression status and repetitive dive plans 

Any hazardous conditions anticipated 

Divers must have appropriate dive certifications and letters of reciprocity determined by 

the organization in charge of the response in order to participate in a response dive. A 

dive master will plan and supervise dives according to the rules of the organizing 

institution and capabilities of the participating divers. Participating divers will adhere to 

all aspects of the plan, (provided it does not violate the rules of the divers’ institution). 

The buddy system that requires at least two divers in constant communication on a 

simultaneous dive is a requirement of all response divers. 

 
58 

5.4 Precautions in the Field 

Coral Health & Safety Recommendations from the CDHC 

In recognition of the increased prevalence of coral disease occurring worldwide, the 

Coral Disease and Health Consortium (CDHC) has proposed guidelines for scientists and 

researchers going into the field to collect specimens where infectious agents may be 

present. Medical and veterinary containment measures may be easily applied to 

potentially infectious disease outbreaks in the aquatic environment and should be 

included in each response activity. The guidelines, listed below, were developed by 

veterinary pathologists who specialize in disease investigation and epizootics to outline 

preventative measures and limit the possible spread of infectious agents. 

 

A first general response to an epizootic and epidemic is to quarantine. Limited access to 

an area can help prevent potential spread of disease agents to unaffected areas. 

1. When multiple sites are to be visited, ALWAYS visit the healthy (or apparently 

healthy) sites before entering an area with known disease to prevent potential spread 

of infectious agents. Do not visit the reference site (a site with no signs of disease) 

after diving a diseased site without first decontaminating dive gear. 

Remember: Movement should always be from "clean" to "dirty 

2. Sterilize equipment/instruments between sampling (or use separate equipment/ 

instruments for each sample collected). Change gloves between samplings. 

Sanitization may be achieved by using a simple bleach solution soak (5% solution for 

5-10 minutes) followed by a freshwater rinse. 

3. When collecting samples, take care to prevent small pieces from falling or floating 

away from the sample site. Each sample should be placed into a separate clearly 

labeled container. Never open a sample container from one site in another area. Be 

sure to document the specifics of the collection site. Information should include 

location, morphology of the change observed (e.g. severity, area of involvement, 

color change, texture, patter of change, skeletal damage). Identify the specific area of 

tissue collected (i.e. along the margin between affected and unaffected tissue; 

apparently healthy tissue). 

4. The responders (divers) should consider themselves and their equipment as potential 

vectors of disease to other locations. To minimize this risk, ALL equipment should 

undergo a simple sterilization process subsequent to entering an infected area or 

before moving to a new location. As with any disease agent, the responder should 

also take care to thoroughly shower with disinfectant soap prior to moving to a new 

location. 
59 

5. Biocontainment procedures are to be used for handling any live material taken from 

affected areas 

5.5 Materials Hazards Information 

A Material Safety Data Sheet (MSDS) shall be available for all hazardous materials 

carried aboard. Each vessel that is proposed to carry hazardous material must first meet 

all storage requirements, must have spill response kits on board, and must adhere to all 

NOAA hazardous material regulations prior to leaving the pier. 

Chemicals used during an investigation will be documented and accompanied by 

appropriate MSDS forms. The crew will be properly trained in handling practices for 

hazardous materials (i.e. z-fix, gluteraldehyde, liquid nitrogen, dry ice). The OIC should 

be informed of potential hazards in order to plan effectively for any emergencies. 
60 

Glossary of Terms 

Bleaching: Loss or degradation of zooxanthellae due to biotic (bacteria) or abiotic (e.g., 

temperature, UV radiation, salinity, toxicants) causes.

Coral Disease Outbreak Investigation: An unusual disease occurrence has been 

reported. Regional Coordinator is notified and implements a level of investigation he 

sees fit. Sampling procedures in an investigation are standardized, and effort is made to 

determine the severity and causality of the outbreak. 

Disease: Any impairment that interferes with or modifies the performance of normal 

functions, including responses to environmental factors such as nutrition, toxicants, and 

climate; infectious agents; inherent or congenital defects, or combinations of these 

factors. (Wobeser 1981). 

 

Enzootic: Disease that occurs in a population at a regular, predictable or expected rate, 

usually low frequency, affecting only a few animals at any one time; similar to endemic, 

used for human populations 

Epizootic: Disease that appears at a time or place where it does not normally occur or 

with an abnormally greater frequency for a specified time; similar to epidemic, used for 

human populations

Expert Working Group: Complied by the National Coordinator, this group of coral 

disease experts assists the National Coordinator in decisions during an outbreak 

investigation, i.e., when to close the case/ implement a response plan. 

Growth Anomalies: Abnormal growth and development, including hypertrophy, 

hyperplasia, neoplasia, tumors 

Health: A continuum between “... absolute health (a state in which all functions are 

optimal) and death, which occurs when functions are so severely compromised that life is 

impossible. Between the two points there is a region of relative health that blends 

imperceptibly into a region that we can define as disease.” (Wobeser 2006). 

Holobiont: (coral) A collective term referring to the totality of a coral animal, its 

endosymbiotic zooxanthellae, and the associated community of microorganisms. 

Hyperplasia: an increase in the number of normal cells in normal arrangement in a tissue 

or organism, increasing its size. 

Hypertrophy: Occurs in tissues or organs due to an increase in the size of cells, while 

the number stays the same. 

Incidence: Frequency with which the disease has increased from base line (new 

occurrence) 
61 

Incident Command System: Management tool used by Federal (and State) emergency 

responders in response to a planned event, natural disaster, or terrorist attack. It can be 

used to investigate the causes/ prevention measures for an emergency, and can be applied 

to an Outbreak Investigation (http://www.nrt.org/(2000a)). 

Incident Commander: In a Level III response, oversees response teams in order to take 

samples for detailed analyses, makes arrangements for logistics, lodging, boats, support 

staff, shipping of samples, laboratory use, permits, etc. and is designated by the Regional 

Coordinator. 

Infectious diseases: Partial and whole colony mortality caused by bacteria, fungi, 

viruses and other microorganisms.

Level I Response: An unusual observation is made in the field. Regional Coordinator 

interviews the observer. 

Level I case closed: Regional Coordinator determines the case is closed after the 

interview for reasons such as, but not limited to, the case already being reported, lack of 

credibility given to the initial observer, determination that it was a non-disease 

observation, or if the Regional Coordinator is never able to contact observer.

Level II Consultation: Used to determine the need for a Level II data collection trip and 

requires the following be considered: strength of observation; magnitude supported by 

surveys, photos, and prevalence data; and availability of boats and staff in the area with 

specific knowledge. 

Level II Recommendation: May be made if the report constitutes a new observation, if 

more information is needed, if the species affected is one at particular risk, if the 

magnitude appears to be large, if there is a change from earlier reports, or if there are 

pictures needed to validate the report. 

Level II Response: Reconnaissance team of knowledgeable divers observes the incident 

to investigate its severity and report findings to the Regional Coordinator. 

Level II Case Closed: After a Level II response, the Regional Coordinator determines 

that the case is closed for the following reasons: observations were not supported during 

Level II response; the disease is within normal (known) background levels; non-diseased 

agent (i.e., boat trauma, hurricane damage) caused the issue; the decision to refer the case 

to another response team (bleaching, grounding, fish kills); or adequate information was 

obtained in Level II. 

Level III Consultation: Aids the National Coordinator and expert working group in 

their decision to launch a level III response, and includes considerations such as: the 

strength of the Level II observations; the magnitude (distribution (multiple reefs), 

frequency, multiple species, higher than expected proportion of colonies affected or 
62 

mortality rates); the apparent occurrence of a new/unusual condition; temporal 

irregularity; the relative importance of species at risk; or potential population and/or 

community impacts. 

Level III Response: Full scale investigation to determine causality and clarify severity; 

launched upon the recommendation from the Regional Coordinator and confirmed by the 

National Coordinator. 

Monitoring of Coral Disease: A routine, local effort to sample or observe coral. 

Disease may or may not be present, but it is not considered a direct threat. Sampling 

techniques may vary. A severe disease outbreak has not been reported 

National Coordinator: Versed in coral disease; Serves as central contact for all Regional 

Coordinators, collates all reports of verified Level I and II investigations submitted by 

Regional Coordinators, and convenes the Expert Working Group to make decisions for a 

Level III response 

Non-infectious diseases: Physiological and morphological (e.g., tissue loss or 

discoloration) changes due to agents such as toxins or toxicants, sedimentation, pollution, 

and other environmental stressors 

Parasitic infections: Infestation by protozoans (e.g., ciliates, amoeba), metazoans (e.g., 

trematodes, flatworms, flukes) or parazoans (e.g., sponges) 

Prevalence: Current number of the population affected by the disease (old and new) 

Proficiency Drills: In class and field exercises to review each response step and consist 

of varying scenarios aimed to determining a team member’s ability to conduct their 

assigned tasks 

Regional Coordinator: Knowledgeable about coral disease and its occurrence in his/her 

region; Coordinates communication between scientists, managers and the public in order 

to assess the threat of an incident, implement control and prevention procedures, 

determines the amount and type of data needed to recommend further action. Regional 

Coordinators conduct interviews with initial observers after a Level I observation, and 

evaluate the need for a Level II response. Following this, Regional Coordinators 

recommend to National Coordinators a need for a Level III investigation, or to close the 

case. Current regions include the Southeast United States, Gulf of Mexico and Florida 

coast; the Caribbean; and the Pacific. 

Surveillance: Systematic collection, analysis, and interpretation of health data 

Trauma: Physical damage (e.g., groundings, fish bites) 

 
63 

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66 

Appendices 

 
67 

Appendix I. Regional Coordinator Interview Checklist

Interviewer Contact Information 

Name ____________________________ 

 Address ____________________________ 

 ____________________________ 

 ____________________________ 

 Tele ____________________________ 

 Email ____________________________ 

 Affiliation __________________________ 

 Date of Interview (mm/dd/yy)___________ 

Was Case Number Assigned? Yes_____ No______; Case Number _____________________ 

Contacted ‘Observer’? Yes______ No ______ date (mm/dd/yy)_____________ 

 Comments____________________________________________________________ 

Verified Level I Report? Yes______ No ______ 

 Comments____________________________________________________________ 

Asked if there were unusual observations? Yes______ No ______ 

 Comments ____________________________________________________________ 

 _____________________________________________________________________ 

Verified where Observer obtained Level I form? Yes______ No _____ 

 Comments _____________________________________________________________ 

 Was Level II information acquired? Yes ____: Complete ___, Partial ____; NO ___ 

 Comments______________________________________________________________ 

 Level II Form attached? Yes______ No ______ 

Was Level II Case Worker Assigned? 

Name ________________________________________________ 

E-mail ________________________________________________ 

Contacted Level II Observer? Yes______ No ______ 

Comments ______________________________________ date (mm/dd/yy)_____________ 

Contacted Advisory Team? Yes______ No ______ 

Comments ______________________________________ date (mm/dd/yy)_____________ 

Type(s) of Feed back: telephone call ____; E-mail ______; letter______; webpage info_____ 

 Comments ____________________________________________________________ 

 ______________________________________________________________________ 

Case Identification Number Generation 

 SSCC## - mmddyy – XXX,#### 

 (Group ID) - (Date) - (species, sample #) 

Group ID 

 SS – two letter State Designation 

 (e.g. FL, PR, VI, HI) 

 CC - two letter City Designation (to be generated) 

Species, Sample Number 

XXX - use first letter of the genus and first 

two of the species, e.g., Porites lobata, Plo 

### – #### designates event # 
68 

Appendix II. Level I Data – Coral Disease Event Report

Case ID # __________________________ (Administrative Use Only) 

*Required Information 

*Observer Information 

 Name ____________________________ 

 Address ____________________________ 

 ____________________________ 

 ____________________________ 

 Tele ____________________________ 

 Email ____________________________ 

 Affiliation __________________________ 

 Date of Observation (mm/dd/yy) 

 ____________________________ 

Location of Suspected Disease Event 

*Geographic locality (site, city, county, state) 

________________________________________ 

Name of Reef ____________________________ 

Reef Type if known _______________________ 

GPS coordinates __________________________ 

 __________________________ 

How many times have you dived on this reef? 

 __________________________ 

Occurrence Details 

 Single location Yes___ No___ Unk___ 

 Throughout Reef Yes___ No___ Unk___ 

 Multiple Reefs Yes___ No___ Unk___ 

 How many coral colonies? ______________ 

 Coral types affected (circle) 1 2 >3 

 *Recent Change Yes___ No___ Unk___ 

 *Previously observed? Yes___ No___ Unk___ 

Species Affected 

 Genus _________________ 

 Species _________________ 

 Common name ________________ 

 *Describe types _________________________ 

 (e.g., branching, boulder) 

 

*Description of Affected Coral 

 Color change Yes___ No___ Unk___ 

 Tissue loss Yes___ No___ Unk___ 

 Skeletal damage Yes___ No___ Unk___ 

 Growth anomaly Yes___ No___ Unk___ 

 Describe ___________________________

 (any specific information you may have) 

Data Collected 

 Sea state ____________________________ 

 Water temperature ___________________ 

 Water clarity ________________________ 

 Photographs ________________________ 

 Depth ____________________________ 

*General Description of what you saw:

______________________________________________________________ 

______________________________________________________________ 

______________________________________________________________ 

Thank you for filling in this form, your information will be used to assist in the study of coral disease. 

For additional information please see the webpage: http//:www.coral.noaa.gov/coral_disease/cdhc.shtml 

It would be helpful to know where you obtained this form: 

__________________________________________________________________ 

(e.g., Web, Dive Shop, Nat. Park Serv., Nat. Mar. Sanc., Other-describe) 
69 

Appendix III. Level II Data – Coral Disease Event Report 

Field Identification Number __________________ (see instructions below) 

Level II Observer (or...Interviewer) 

Information: 

 Name ____________________________ 

 Address ____________________________ 

 ____________________________ 

 ____________________________ 

 Tele ____________________________ 

 Email ____________________________ 

 Affiliation __________________________ 

 Date of Observation (mm/dd/yy) 

 ____________________________

Reef Descriptors: 

Reef Name _____________________________ 

Reef Type _____________________________ 

Depth _________________________________ 

GPS coordinates 

 ___________________________________ 

Semi-quantitative extent of the affected areas 

_______________________________ 

Adjacent Reef Information 

_______________________________ 

 _______________________________ 

 Location relative to affected reef: 

_______________________________ 

Background Information: 

Case ID # _________________________ 

 (provided by Regional Coordinator) 

Level I Data Sheet attached Yes ____ No ____ 

 (provided by Regional Coordinator) 

Date of Level I Observation 

 (mm/dd/yy) _______________ 

Data Collected on Boat: 

GPS coordinates ________________________ 

Weather _______________________________ 

Water temperature _______________________ 

Sea state _______________________________

Characteristics of Affected Reefs: 

1. Are corallivores present (give species)? 

___________________; if absent go to 2. 

2. Is there overgrowth (competition)? 

 yes ________; if no go to 3. 

3. Suspect disease present? 

 no ___; if yes, answer following questions: 

a. Reef type (circle appropriate descriptors): 

inshore, offshore, bank, patch, barrier, 

emergent, submergent 

b. Provide any missing information in Level I 

Report __________________________ 

c. Dominant or other coral species affected? 

Yes (identify) ______________; No___ 

d. Other marine species affected? 

 Yes (identify) ______________; No___ 

e. Are key indicator species present? 

 Yes (identify) ______________; No___ 

f. Reef relief – high ______; low ______ 

g.Rugosity – high ______; low ______ 

h.Cover – percentage 

______________________. 

i. Species associations 

_____________________. 

j. Macroalgae? present _______; absent 

_______. 

k. Distribution of affected corals 

_____________________________ 

l. Prevalence of affected corals 

 _____________________________ 

m. Recently dead colonies – if yes _____ is 

there algal cover? If yes ____then what is 

the estimate of days of algae growth (7-10 

days?); No ______. 

 
70 

Level II Data: Coral Disease Event Report - Continued

 

Coral Species Affected: 

 Genus _______________________ 

 Species _______________________ 

 Common name ____________________ 

 Describe types (e.g., branching, boulder) 

 _______________________________ 

 _______________________________ 

 

Coral Species Not Affected: 

 Describe __________________________ 

___________________________________ 

___________________________________ 

Data Collected at Reef Site: 

Water clarity ___________________________ 

Map drawing of site _____________________ 

Quantitative transects/survey of reef area 

 ___________________________________ 

Signs of recent reef disturbance ______________ 

Photographs ______________________________ 

Videos __________________________________ 

Samples (circle appropriate selections) 

a. diseased coral tissue 

b. healthy coral tissue near to diseased tissue 

c. healthy coral tissue from another coral 

d. other species 

e. water 

f. nearby sediment/soil/sand 

Depth ______________________ 

Description of Affected Coral 

Tier 1: 

 Color change Yes___ No___ Unk___ 

 Tissue loss Yes___ No___ Unk___ 

 Skeletal damage Yes___ No___ Unk___ 

 Growth anomaly Yes___ No___ Unk___ 

 Describe ___________________________

 (any specific information you may have)

Description of Diseased Tissue on Affected Coral 

Tier 2: 

 Shape ______________________________ 

 Color ______________________________ 

 Size ______________________________ 

 Distribution __________________________ 

 Number _____________________________ 

 Polyps ______________________________ 

 

Additional Information - Provide Narrative Description of Diseased Coral ___________________ 

___________________________________________________________________________________ 

___________________________________________________________________________________ 

Indicate whether you used Http://usgs.madison.gov/coral_disease_characterization to develop a 

preliminary diagnosis of the disease: Yes_____ No _____ 

Thank you for participating in the Level II response to a recent report of coral disease and collecting 

information/ samples in support of the CDHC Rapid Response to Coral Disease. Your information 

will be used to further the study of coral disease. For additional information please see the webpage: 

http://www.coral.noaa.gov/coral_disease/cdhc.shtml 

Field Identification Number Generation 

SSCC## - mmddyy –XXX,###XX 

(Group ID) - (Date) - (species, sample #) 

Group ID 

 SS – two letter State Designation (e.g. FL, PR, 

VI, HI) 

CC - two letter City Designation (to be 

generated) 

Species, Sample Number 

 XXX - use first letter of the genus and first two 

letters of species, e.g., Porites lobata, Plo 

###XX – ### designates event # and XX is 

sample designation by letters, e.g., AA, AB 
71 

Appendix IV. LEVEL III - Coral Disease Assessment Form 

Date: _______ Site: ___________ Recorder: _____________ Transect: _____ Depth:____ Heading:______ Comments:_______________ 

Spp. Diam. 

(cm) 

Lesion 

Type 

Distribution 

F, M,C, D, L 

Location 

B, M, A 

Lesion

Size 

Lesion

color 

Lesion 

margin 

Lesion 

Severity

Duration 

A, S, C 

Comments 

 Lesion Location Lesion Distribution

Lesion Margin: Smooth (S), Irregular (I) Lesion Severity: Mild (<10%), Moderate (10-24%) Severe (25-49%), 

Extreme (50-100%) 

Lesion Duration: Acute (no algal colonization Subacute (filamentous 

algae) Chronic (gradation of algal types) 
Appendix V.

72 

Support Team Processing Guidelines Form 

Analysis Processing Preparation to Ship

H-P Tissue U-P Tissue D-P Tissue 

Molecular (protein/DNA) 

Time sensitive- IN SHADED OR DARK AREA: Rinse mucus by swishing in seawater, dab on Bounty, place in new pre-labeled Whirlpak

TM

Wrap in aluminum foil, label with waterproof marker or pre-printed cryotags, place in dry shipper 

H- F Tissue U-F Tissue D-F Tissue 

Histology (fixative) 

Immediately preserve by transfer to a 50 cc polypropylene tube with approximately 25 mL of an appropriate fixative, such as Z-fix (Anatech Ltd.) diluted 4:1 with sterile ASW (35ppt) * 1:10 tissue: fixative ratio 

Hold at ~25°C (Store in cooler) DO NOT FREEZE 

H-B Tissue U-B Tissue D-B Tissue 

Microbiology Keep in WhirlpakTMadd sterile artificial sea water if 

needed, keep at ambient temperature in cooler filled with local seawater 

Upon return to shore, homogenize tissue and skeleton with sterile mortar and pestle 

– Flash freeze half of homogenate – Culture bacteria with other half of homogenate 

H-S Swab U-S Swab D-S Swab 

Molecular and Microbiology 

Epicenter type swab- break off tip and put in cryovial, FTA type swab wipe on card, then break tip and store in 15 cc tube or cryovial 

Put cryovials in dry shipper, store card at ambient temp. in Ziploc or other container 

H-M Mucus U-M Mucus D-M Mucus 

1⁄2 Molecular Should be placed in a container, such as a cryogenic vial Immediately flash freeze in a liquid nitrogen dry shipper1⁄2 Microbiology Should be kept at ambient seawater temperature, possibly 

in screw top vials 

Culture on media as soon as possible (2-3 hours)

H-Sediment D- Sediment 

Microbiology & Molecular 

Top-side- Invert tube- shake- loosen cap and decant water into 2 mL cryovial Leave gap ~2 cm between sediment sample and cap 

Cap sediment tightly and freeze in dry shipper Store liquid at ambient temperature and plate in lab 

H-Water D- Water 

1⁄2 Molecular Transfer from syringe to 2.0 mL cryogenic vial Place in dry shipper 1⁄2 Microbiology Transfer from syringe to 2.0 mL cryogenic vial Keep at ambient temperature for culture dependent methods 
73 

Appendix VI. Pathology Sample Submission Form 

 
74 

 
75 

Appendix VII. List of Sampling Equipment and Supplies 

Documents Histology Sample Processing 

Collection Permits Seawater buffered formalin (Z-Fix, 1X 

aliquoted) 

Travel Documents 50 cc Falcon tubes & 4ml cryotubes 

4% glutaraldehyde-2% formalin in seawater 

(TEM) 

Surveillance & Ecological Data Collection Sterile seawater (for fixative dilution) 

Underwater digital camera still and video Cooler & ice packs for glutaraldehyde fix 

Datasheets, pencil and clip board 

Floating chains weighted Contaminant Chemistry Sampling 

GPS Nitrile gloves, assorted sizes 

Scale bar and identifier board for photos Sediment jars (250-500cc) pre-cleaned EPA 

standard 

Scooter and batteries Teflon bags w/ sealing clips 

Slates Aluminum foil acetone-pre-cleaned 

Tape measures Stainless steel coring tube, acetone cleaned 

Tags e.g. cattle tags 

Biological Sampling On Board General Supplies 

Dive slates Utility knife 

Data sheets and pencil Scissors 

Camera Permanent marking pens & pencils 

Mesh dive bags Rubber bands 

 Tissue Collection String 

Film canisters or 50cc tubes for tissue Clipboards 

Nitrile gloves (S-XL) Batteries for cameras and GPS 

Stainless steel coring tubes (for boulder corals) Whirl-PakTM or ZiplockTM bags qt and gallon 

sizes 

Clay- Roma Plastalina #2 Rex Art Miami, FL Plastic cable ties, assorted sizes 

Clippers, curved blade (for branching corals) Clear tape 

Hammer Labeling tape 

Chisel (small) Waterproof paper 

Mucus Collection Fishing weights 

Syringes with caps – 3cc, 5cc or 10cc KimwipesTM large and small 

15cc Falcon tubes for sediment as background BountyTM paper towels (or other lint free brand) 

15cc Falcon tubes for water column Plastic garbage bags 

DNA swabs - Epicenter Bleach 

On board Sample Preservation & 

Processing 

Equipment for Refurbishing Collection 

Tools 

Cryoshippers Angle grinder – 4.5 inch e.g. Dewalt 402K 

Marine coolers & ice packs Grinding wheels – assorted 

2ml and 4 ml cryovials Cutoff wheels (min. 6) and adapter for attaching 

Aluminum foil (tissue packaging) Safety goggles 

Labels – waterproof and cryogenic Leather gloves for sharpening cores 

 Angle file 

Sample Processing Equipment Round file 

Portable vacuum pump 

Tubing, stoppers, side-arm flask (trap) 

Disposable sterile vacuum filter units w/bottle 
76 

Appendix VIII. Stereo Microscopy 

Introduction 

The stereo microscope, also known as a dissecting microscope or operating scope is an 

entirely separate design from the more familiar 

compound microscope, and serves a different 

purpose. It produces a three-dimensional

visualization of the sample being examined 

through the use of two separate optical paths so 

that the left and right eyes receive slightly 

different viewing angles which the brain 

interprets as a three dimensional image. The 

stereo microscope should not be confused with 

the compound microscope which is also 

equipped with binocular eyepieces. Both eyes 

see the same image in the compound 

microscope so the visual image is no different 

from that obtained with a single monocular 

eyepiece. In this type of microscope the 

binocular eyepieces provide greater viewing 

comfort rather than three dimensional imaging. 

The design of the stereo microscope provides 

great working distance and depth of field which 

are essential qualities for this type of 

microscope. Working distance and depth of field are inversely correlated with resolution. 

The greater the depth of field and working distance the lower the resolution (the distance 

at which two adjacent points can be visually resolved as separate). The stereo 

microscope’s useful magnification is 

up to 100X which is approximately 

the same magnification of the 10X 

scanning objective in a compound 

microscope. In practice, the majority 

of stereo microscope observations 

are made between 4X and 40X. 

Optical Design and Magnification 

Total magnification in the stereo 

microscope is achieved by a primary 

magnification which is further 

increased by a secondary 

magnification. The primary 

magnification of the microscope is 

determined by a primary objective 

lens which can be either a single lens 
77 

called a Common Main Objective (CMO) or a paired set of objective lenses often called a 

Greenough design. The main advantage of the CMO design is the infinity focus which 

produces two collimated light paths with parallel axes between the objective and the 

eyepieces that allow the easy insertion of various optical and accessory components such 

as camera ports and drawing tubes. This gives the greatest versatility and makes it the 

preferred choice for research applications. Some models have interchangeable primary 

lenses giving a choice of several different ranges of magnifications. The Greenough 

design is often smaller, less expensive, rugged, and simple to use and maintain. They are 

a popular choice for simpler workhorse applications which don’t require a large variety 

of accessories. 

The secondary magnification is achieved in one of three ways depending on the optical 

components. The simplest is fixed magnification which has a single set secondary 

magnification. This means that the microscope is limited to one final magnification. This 

is most often seen in small and highly portable scopes intended for field use; some of 

which can fit in a pocket. The next type is a system of selectable set magnifications 

controlled by a rotating drum or ring. The most complex system is zoom magnification, 

capable of a continuously variable magnification across a set range. Zoom systems can 

also have interchangeable primary lenses or use auxiliary objectives that increase total 

magnification by a set factor. Also, total magnification in both fixed and zoom systems 

can be varied by changing eyepieces. 

Illumination 

The most common form of illumination for a stereo microscope is reflected illumination 

rather than transmitted illumination. That means the light is reflected from the surface of 

an object rather than transmitted through an object like a compound microscope. This 

allows the examination of specimens that are opaque or too thick to allow light to pass 

through them. Stereo microscopes can use transmitted light illumination as well if 

equipped with a light source beneath a transparent stage or inset in the base; however the 

transmitted illumination is not focused through a condenser like a compound microscope. 

Optional illuminators are also available for reflected or transmitted dark field 

microscopy. 

Primary Applications of the Stereo Microscope 

The stereo microscope is most often used to study solid specimens or to carry out tasks 

such as dissection, or sorting that require a close-up view. The long working distance and 

the fact that specimens can be examined without any preparation or processing makes 

this a uniquely versatile instrument for field use. Aquatic organisms can be easily 

examined live in a suitable container of water. 

Different models are available ranging from large sophisticated research models often 

equipped with cameras to small pocket size models for on-site field examination. A 

recent innovation has been a new class of research stereo microscopes designed 

especially for fluorescent imaging requiring special light sources and exceptionally high 
78 

light gathering ability. A digital camera is used which combines high image quality with 

the ability to image weak light signals. These microscopes are very large and extremely 

expensive but they have opened a whole new way of studying the often weak fluorescent 

material with a much larger field size and on opaque materials that would be impossible 

on a compound fluorescent microscope. 

Choosing a Stereo Microscope 

The choice of the best model for a particular application is determined by the following 

criteria: 

The physical environment in which it will be used. Larger research grade microscopes are 

best used in a laboratory or on larger research vessels with electrical power for cameras 

and light sources, and climate control to protect more delicate optics and electronics. 

Smaller simpler and more robust models are suitable for use where environmental factors 

are less ideal. Pocket sized and preferably water proof models are best for small boats and 

on-foot research. 

Whether imaging is required. Stereo microscopes for imaging require higher quality 

optics and a separate trinocular port for the camera. Ultra high resolution and low light 

level cameras are best used in a laboratory. The new relatively inexpensive CMOS 

cameras with a USB2 interface are ideal for portable use because they can be plugged 

into any notebook computer with basic software installed. 

The primary intended use. Microscopes intended to cover a wide and varying 

combination of research applications should have the greatest range of magnifications 

and light sources. Here the CMO design should be considered first. Microscopes intended 

for surveying or sorting specimens can have a more modest range or in many cases a 

fixed magnification. The simpler Greennough design might be a better choice for this 

work. 

The type of stand required. The standard short desk stand can accommodate specimen 

and container sizes over typically a 6” to 12” range. Optional taller stands are often 

available where a greater range is required. Most versatile is a stand and arm combination 

which allows a large range of vertical and horizontal movement which can be used for 

applications such as close-up examination of marine animals too large to place and move 

under a standard stand. 

Budget and appropriate quality for the intended use. Stereo microscopes can cost 

anywhere from up to $20,000 for the most sophisticated research models to a few 

hundred dollars for the most basic models. Besides budget restrictions, it is inappropriate 

to get a very expensive microscope for a destructive environment such as exposure to salt 

spray since any microscope will have a short service life. The very least expensive 

microscope adequate to perform the required work is a better choice with frequent 

replacement as required. 
79 

 

With reasonable care stereo microscopes have long service lives and highly serviceable 

older models can be found at bargain prices by a careful shopper. A search on the internet 

will located microscope dealers that carry used equipment inventories. The AO 

Cycloptic, the first modern commercial stereo scope, is a robust instrument, ideal for a 

field station or research vessel use and can be found at very modest prices. A quick 

survey on EBay produced 536 stereo microscopes for sale. The majorities were new 

student grade scopes of questionable quality but there were also older models, some of 

which were top of the line in their day and now offer sophisticated performance at 

bargain basement prices. 
80 

Care and Maintenance of a Stereo Microscope 

A well designed stereo microscope requires surprisingly little maintenance. Most 

problems can be prevented by some simple, common sense, proactive preventative steps. 

Bear in mind that cleaning optics is inherently destructive over a long period of time so 

preventing optical contamination is better than cleaning it off. One of the most useful 

microscope accessories that is too often unused is the simple dust cover. A microscope 

should always be covered when not in use. Special consideration should be given to the 

type of cover where ever there is the possibility of water, chemical or blowing sand 

affecting the scope. 

Common dust is usually not of concern and if excessive enough to be bothersome is 

easily removed with a source of air, either commercial canned air, or an ear syringe. The 

most common type of contamination that requires prompt and thorough cleaning is finger 

prints. The oils in a finger print can actually etch the optical coatings on the lens. Eye 

makeup such as mascara can be a chronic problem in the contamination of the eyepieces. 

The best solution is to discourage the use of eye makeup by personnel using microscopes. 

Salt spray needs to be removed by the careful use of fresh water cleaning using damp 

clothes, never liquids that could get into the scope. 

Proper cleaning of optics 

1. Have proper materials on hand including good quality lens paper, a source of air and 

lens cleaner. 

2. Always first use air to blow off the optical surface to remove any grit that could 

scratch the optics during cleaning. 

3. Never touch an optical surface with any dry material. Always moisten the cleaning 

cloth or tissue with lens cleaner or use your breath to fog the lens. 

4. Suitable cleaning materials include lens tissue, microcloth, or a well laundered clean 

handkerchief. 

5. Clean in a circular motion without applying excessive force. Make several passes 

using a clean surface each time. 

6. The use of solvents should be carefully restricted to lens contamination such as oil or 

mounting media that actually requires it. Never apply any solvent directly to a lens 

but always apply it to lens paper of a cotton swab. Shake off excess liquid before 

applying to the lens. Materials like oil will require the use of multiple swabs or papers 

as they must be discarded after each pass. Check all safety instructions for any 

solvent and make sure you have adequate ventilation, and personal protection as 

required. 
81 

United States Department of Commerce 

Carlos M. Gutierrez 

Secretary 

National Oceanic and Atmospheric Administration 

Vice Admiral Conrad C. Lautenbacher, Jr. USN (Ret.) 

Under Secretary of Commerce for Oceans and Atmospheres 

National Ocean Service 

John (Jack) H. Dunnigan 

 Assistant Administrator for Ocean Service and Coastal Zone Management