On the biodiversity of diatom communities in lakes of east China: Geochemical effects dominated after eutrophication
Data files
Sep 17, 2023 version files 324.26 KB
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README.md
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Zhao_et_al_2023_JBI_1930_compare.csv
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Zhao_et_al_2023_JBI_2006_compare.csv
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Zhao_et_al_2023_JBI_env_proxies.csv
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Zhao_et_al_2023_JBI_rel_abund_diatoms.csv
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Zhao_et_al_2023_JBI_sitesinfo.csv
Abstract
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.
README: 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 |
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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
> 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.
Methods
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.
Usage notes
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.