DOI: 10.5061/dryad.j3tx95xkv
title: On the biodiversity of diatom communities in lakes of east China: Geochemical effects dominated after eutrophication

description: Aim: Over the last century, lakes all over the world have experienced
 significant eutrophication and become more susceptible to critical
 transitions. This has prompted a growing need to understand how community
 dynamics shift following ecological perturbations. This study aims to
 elucidate the present status, spatial patterns and determinants of
 biological diversity, and how they have changed in response to alterations
 driven by eutrophication. Location: Lakes of East China, mostly in the
 Yangtze River Basin Taxa: Bacillariophyceae (163 species in 33
 genres)  Methods: The environmental conditions of over sixty
 lakes were assessed based on parameters such as water quality, physical
 characteristics and biogeochemical constituents. Surface sediment samples
 and high-resolution sediment records were collected to quantify the
 biodiversity of diatom communities, and Principle Component Analysis (PCA)
 was used to determine the major environmental gradients. Meanwhile, linear
 regression, Canonical Correlation Analysis and Mantel tests were used to
 quantify the correlations between variables. Results: Biodiversity metrics
 showed no distinct geographic patterns, although areas near large lakes
 showed comparatively high evenness. Smaller pairwise dissimilarities were
 observed among hypereutrophic lakes in comparison to lakes with a lower
 trophic status. The past century has witnessed a decrease in both pairwise
 dissimilarity and the standard deviation of Evenness. A significant
 statistical association was found between dissimilarity and ionic
 concentration and composition in the surface sediment of lakes, rather
 than nutrient levels. Main conclusions: Following regional eutrophication
 and human disturbance, a significant reduction in biodiversity
 differentiation was observed in lakes located in East China. Currently,
 the dominant factor in determining the beta diversity of diatom
 communities is geochemical conditions rather than nutrient concentrations.
 Long-term stress caused by cultural eutrophication may also have altered
 the dominant determinant of regional biodiversity and diatom community
 dynamics.
description: The modern data in this dataset were collected in the 2016 lake
 survey. Surface sediment samples were taken using a stainless steel
 grabber. Lab analysis was conducted at Nanjing Institute of Geography and
 Limnology, Chinese Academy of Sciences. Data of the sediment cores were
 from published literature through personal communication. The age-depth
 models of the cores were attached as a supplementary document of the
 related article. The diatom species or genre when ambiguous (indicated as
 “sp.”) were identified under microscope, and at least 300 valves were
 counted in each sample. The relative abundance of diatoms was shown in
 percentage. The environmental data were all standardized so that each
 column has a mean at zero and an SD at one. Environmental variables with
 'sur_' in the name were measured from surface sediment while the
 same element might have been measured in water samples. For example,
 sur_TN means total nitrogen concentration in the surface sediment while TN
 means total nitrogen concentration in water. 
description: The data were in table delimited
 (.csv) format. Recommended programs are Microsoft Excel and R. R is
 open-source and can process these data well.
description: # DATASET: Diatom composition and environmental factors in surface
 sediment of lakes in East China *** Related article: Zhao Yanjie, Wang
 Rong, Xu Min, Zhang Enlou. On the Biodiversity of Diatom Communities in
 Lakes of East China: Geochemical Effects Dominated after Eutrophication.
 *Journal of Biogeography.* ## File list (files found within the folder)
 Zhao\_et\_al\_2023\_JBI\_1930\_compare.csv
 Zhao\_et\_al\_2023\_JBI\_2006\_compare.csv
 Zhao\_et\_al\_2023\_JBI\_env\_proxies.csv
 Zhao\_et\_al\_2023\_JBI\_rel\_abund\_diatoms.csv
 Zhao\_et\_al\_2023\_JBI\_sitesinfo.csv ## File descriptions
 **Zhao\_et\_al\_2023\_JBI\_1930\_compare.csv** \- the relative abundance
 of diatom species **(unit: % )** in Longgan, Chaohu, Liangzi, Zhangdu,
 Shitang and Wushan lake near 1930 retrieved from lake sediment cores. This
 table contains samples (6 lakes) as rownames and 70 species names as
 column names. **Zhao\_et\_al\_2023\_JBI\_2006\_compare.csv** \- the same
 format as *Zhao\_et\_al\_2023\_JBI\_1930\_compare.csv*. The first two
 columns are lake names and period(2006), and the rest of columns are Latin
 names of diatom species and their relative abundance in percentage
 **(unit: % ).** **Zhao\_et\_al\_2023\_JBI\_env\_proxies.csv** \- the
 standardized \(centered and scaled\, means at zero and standard deviation
 at one\) environmental proxies \(N = 59\) of surface sediment in 61 lakes
 \(therefore **no unit** in the table). Note: some NA existed in the table,
 which may affect the actual sample size of multivariate analyses. The
 first column "LAKECODE" shows the unique codes of samples. The
 abbreviations are used for the environmental indicators as follows: |
 Abbrev. | Meaning | Abbrev. | Meaning | | ------- | ------- | ------- |
 ------- | | WD | water depth | TN | total nitrogen | | DYR | Distance to
 Yangtze River | TP | total phosphorus | | SD | transparency(Secchi disk) |
 COD | chemical oxygen demands | | T | water temperature | DIC | Dissolved
 inorganic carbon | | Cond | conductivity | DOC | Dissolved organic carbon
 | | ORP | oxidation reduction potential | SS | Loss of Ignition | | NTU |
 turbidity measurement | SSLOI | Solid suspension Loss of Ignition | |
 Chl-a | concentration of chlorophyll a | N | nitrogen concentration in
 water | | DO | dissolved oxygen | C | carbon concentration in water | | d
 (0.1) | grain size, diameter at the smallest 0.1 quantile | sur\_TOC |
 total organic carbon in surface sediment | | d (0.5) | grain size, median
 diameter | sur\_Al,sur\_Ba,sur\_Be,sur\_K, etc | ion concentrations in
 surface sediment | | d (0.9) | grain size, diameter at the 0.9 quantile |
 Na,K,Mg,SO4, etc | ion concentrations in lake water | *\* all elements
 with prefix "sur" means the proxy was measured from lake
 sediment instead of water.*
 **Zhao\_et\_al\_2023\_JBI\_rel\_abund\_diatoms.csv** \- the relative
 abundance of diatoms in surface sediment and sediment cores of the six
 lakes\(Longgan\, Chaohu\, Liangzi\, Zhangdu\, Shitang and Wushan lake\)\.
 The unit of numbers in this table is **percentage(%)**, calculated as
 dividing the counts of frustules of one diatom species by the total counts
 of diatom frustules in this sample. Genre with *sp.* were used to show
 ambiguous species. In the upper row 2- row 62 are surficial samples
 collected in 2016 and 2017. From row 63- row 219 are subsamples from
 sediment cores in the six lakes. The diatom species in all samples in this
 study have been gathered in this file, including the information of
 *Zhao\_et\_al\_2023\_JBI\_1930\_compare.csv* and
 *Zhao\_et\_al\_2023\_JBI\_2006\_compare.csv*. The difference is that
 sediment core samples are named in "lake name + depth from the
 top(cm)", e.g., "Zhangdu29" means this sample was from
 29-cm deep in the high-resolution sediment core taken in Zhangdu lake.
 **Zhao\_et\_al\_2023\_JBI\_sitesinfo.csv** \- a list of the geographic
 location **(Latitude °N and longitude °E)** of study sites, abbreviation
 of site names and mean population density surrounding the sites (**unit:
 person per square kilometer**). The first column, i.e. LAKECODE,
 represents the unique codes of the samples, which will be used in
 *Zhao\_et\_al\_2023\_JBI\_env\_proxies.csv* and
 *Zhao\_et\_al\_2023\_JBI\_rel\_abund\_diatoms.csv* too. Lakes were
 labelled in the column "LAKECODE" of all the uploaded
 spreadsheets and kept consistent with each other. For example,
 'L2' in the diatom sheet is the same lake in the environmental
 information sheet. ## Code/Software Open in Microsoft excel/ R ##
 Collection of the data This dataset consists of modern survey data and
 sediment records of diatom communities. The modern survey data was
 obtained in 2016 by the NIGLAS (Nanjing Institute of Geography and
 Limnology, Chinese Academy of Sciences) team, including relative
 abundances of diatom species (33 genre and 163 species) from surface
 sediment(\~3cm) and environmental indicators (59 selected indices)
 examined in both surface sediment and lake water of over sixty lakes in
 East China, specifically along the Middle-Lowest Reach of Yangtze River.
 The site information was provided with GPS and surrounding population
 density. Surface sediment samples were taken using a stainless steel
 grabber. Data of the sediment cores were from published literature through
 personal communication. The age-depth models of the cores were attached as
 a supplementary document of the related article. Diatom samples were
 processed and identified following Battarbee et al.(2001).The diatom
 species were identified under microscope and at least 300 valves were
 counted in each sample. ## References \&gt; *Battarbee, R., Jones, V.,
 Flower, R., Cameron, N., Bennion, H., Carvalho, L., & Juggins, S.
 (2001). Diatoms. In J. Smol, H. J. Birks, W. Last, R. Bradley, &
 K. Alverson (Eds.), Tracking Environmental Change Using Lake Sediments
 (Vol. 3, pp. 155202). Springer Netherlands.*