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Zhang Z, Li J, Li H, Wang L, Zhou Y, Li S, Zhang Z, Feng K, Deng Y. Environmental DNA metabarcoding reveals the influence of human activities on microeukaryotic plankton along the Chinese coastline. WATER RESEARCH 2023; 233:119730. [PMID: 36801577 DOI: 10.1016/j.watres.2023.119730] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Microeukaryotic plankton, with its extremely diverse taxa, is a key component in both the marine food web and biogeochemical cycling. Coastal seas, which are home to the numerous microeukaryotic plankton that underpin the functions of these aquatic ecosystems, are often impacted by human activities. However, understanding the biogeographical patterns of diversity and community structure of microeukaryotic plankton and the role that major shaping factors play at the continent scale is still a challenge in coastal ecology. Here, the biogeographic patterns of biodiversity, community structure, and co-occurrence patterns were investigated by environmental DNA (eDNA) based approaches. Unlike most eDNA studies, we combined several methods (in silico PCR, mock and environmental communities) to systematically evaluate the specificity and coverage of primers to overcome the limitation of marker selection on biodiversity recovery. The 1380F/1510R primer set showed the best performance for the amplification of coastal plankton with the highest coverage, sensitivity, and resolution. We showed a unimodal pattern for planktonic alpha diversity with latitude (P < 0.001), and nutrient-related factors (NO3N, NO2N, and NH4N) were the leading predictors for spatial patterning. Significant regional biogeographic patterns and potential drivers for planktonic communities were found across coastal regions. All communities generally fitted the regional distance-decay relationship (DDR) model with the strongest spatial turnover rate was found in the Yalujiang (YLJ) estuary (P < 0.001). The environmental factors, especially inorganic nitrogen and heavy metals (HMs), had the greatest impact on planktonic community similarity in the Beibu Bay (BB) and East China Sea (ECS). Furthermore, we observed spatial plankton co-occurrence patterns, and the networked topology and structure were strongly driven by potential anthropogenic activity factors (nutrients and HMs). Overall, our study provided a systematic approach for metabarcode primer selection in eDNA-based biodiversity monitoring and revealed that the spatial pattern of the microeukaryotic plankton community was mainly controlled by regional human activity-related factors.
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Affiliation(s)
- Zheng Zhang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jiang Li
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources; Key Laboratory of Ecological Environment Science and Technology, Ministry of Natural Resources, Qingdao, China, 266061.
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Linlin Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science College of Environmental and Natural Resource Sciences, Zhejiang University, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
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Isabwe A, Yao H, Zhang S, Jiang Y, Breed MF, Sun X. Spatial assortment of soil organisms supports the size-plasticity hypothesis. ISME COMMUNICATIONS 2022; 2:102. [PMID: 37938741 PMCID: PMC9723746 DOI: 10.1038/s43705-022-00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2023]
Abstract
The size-plasticity hypothesis posits that larger size organisms are less plastic in their metabolic rates and, therefore, are more strongly environmental-filtered than smaller organisms. Many studies have supported this hypothesis by evaluating the relative roles of environmental filtration and dispersal for different taxonomic groups of soil organisms. Most observations are made at large spatial scales, which are assumed to have a wide array of varying habitats. However, since urbanization causes habitat fragmentation at smaller regional scales, testing the size-plasticity hypothesis at this scale would help better understand the spatial assortment of urban soil organisms which, in turn, would help to develop improved management and conservation strategies for urban soil health. Here, we used DNA metabarcoding on five groups of soil biota (bacteria, fungi, protists, nematodes, and invertebrates) to assess the relative importance of dispersal and environmental filters to examine the size-plasticity hypothesis at this spatial scale in an urban environment. We observed strong distance-decay of community similarities associated with higher levels of stochastic changes in bacteria, nematode, and protist communities but not fungal or invertebrate communities. Bacterial communities occupied the widest niche followed by protists and nematodes, potentially because of their higher dispersal abilities compared to the larger soil organisms. Null deviation of communities varied with taxonomic groups where bacteria and nematodes were mainly driven by homogenizing dispersal, protists and fungi by drift, and soil invertebrates by environmental selection. We further identified a small percentage of locally-adapted taxa (2.1%) that could be focal taxa for conservation and restoration efforts by, for example, restoring their habitats and enhancing their regional connectivity. These results support the size-plasticity hypothesis at the relatively unexplored regional scale in an urbanization context, and provide new information for improving urban soil health and sustainable city models.
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Affiliation(s)
- Alain Isabwe
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China
| | - Haifeng Yao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Shixiu Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, 315830, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ma G, Logares R, Xue Y, Yang J. Does filter pore size introduce bias in DNA sequence-based plankton community studies? Front Microbiol 2022; 13:969799. [PMID: 36225356 PMCID: PMC9549009 DOI: 10.3389/fmicb.2022.969799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.
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Affiliation(s)
- Guolin Ma
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- *Correspondence: Yuanyuan Xue,
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- Jun Yang,
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Miya M, Sado T, Oka SI, Fukuchi T. The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.80444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To test the feasibility of a citizen science program for fish eDNA metabarcoding in coastal marine environments, we recruited six groups of voluntary citizens for a science education course at a natural history museum. We held a seminar on eDNA and a workshop for seawater sampling and on-site filtration using syringes and filter cartridges for the participants. After that, they selected single survey sites following the guidelines for conducting a safe field trip. They performed seawater sampling and on-site filtration at these sites during their summer holidays. The six selected sites unexpectedly included diverse coastal habitats within a 40 km radius, located at temperate latitudes in central Japan (~35°N). After the field trips, they returned filtered cartridges to the museum, and we extracted eDNA from the filters. We performed fish eDNA metabarcoding, along with data analysis. Consequently, we identified 140 fish species across 66 families and 118 genera from the six samples, with species richness ranging from 14 to 66. Despite its limited sample size, such a diverse taxonomic range of fish species exhibited spatial biodiversity patterns within the region, which are consistent with species distribution. These include north-south and urbanization gradients of species richness, geographic structure of the fish communities, and varying salinity preferences of the component species. This case study demonstrates the potential of fish eDNA metabarcoding as an educational and scientific tool to raise public awareness and perform large-scale citizen science initiatives encompassing regional, national, or global fauna.
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