1
|
Zhang H, Wang N, Zhang D, Wang F, Xu S, Ding X, Xie Y, Tian J, Li B, Cui Z, Jiang T. Composition and temporal dynamics of the phytoplankton community in Laizhou Bay revealed by microscopic observation and rbcL gene sequencing. MARINE ENVIRONMENTAL RESEARCH 2024; 202:106734. [PMID: 39244953 DOI: 10.1016/j.marenvres.2024.106734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/15/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
Laizhou Bay, a major breeding ground for economic marine organisms in the northern waters of China, is facing rapid environmental degradation. In this study, field surveys in this area were conducted in the spring, summer, and autumn of 2020. Microscopic observation and RuBisCO large subunit (rbcL) gene analysis were employed to understand the community structure and temporal dynamics of phytoplankton. The phytoplankton community structures detected by the two methods showed significant differences. Microscopic observation revealed the dominance of dinoflagellates in spring that shifted to the dominance of diatoms in summer and autumn. However, rbcL gene sequencing consistently identified diatoms as dominant throughout all three seasons, with their relative abundance showing an increasing trend. Conversely, the relative abundance of the second- and third-most abundant taxa, namely, haptophytes and ochrophytes, decreased as the seasons transitioned. rbcL gene sequencing annotated more species than microscopy. It could detect haptophytes and cryptophytes, which were overlooked by microscopy. In addition, rbcL gene sequencing detected a remarkable amount of Thalassiosira profunda, which was previously unidentified in this sea area. However, it appeared to underestimate the contribution of dinoflagellates considerably, with most taxa being only identified through microscopic identification. The two methods jointly identified 28 harmful algal bloom taxa with similar detection quantities but substantial differences in species composition. Phytoplankton communities were influenced by temperature, salinity, and nutrients. The results of this work suggest that a combination of multiple techniques is necessary for a comprehensive understanding of phytoplankton.
Collapse
Affiliation(s)
- Huihui Zhang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Nan Wang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Di Zhang
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Fei Wang
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Shiji Xu
- Yantai Ocean Center, Ministry of Natural Resources, Yantai, 264006, China
| | - Xiaokun Ding
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Yixuan Xie
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Jinghuan Tian
- School of Oceanography, Yantai University, Yantai, 264005, China
| | - Bin Li
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, China
| | - Zhengguo Cui
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Tao Jiang
- School of Oceanography, Yantai University, Yantai, 264005, China.
| |
Collapse
|
2
|
Kaleli A, Gozde Ozbayram E, Akcaalan R. Environmental DNA metabarcoding reveals diverse phytoplankton assemblages and potentially harmful algal distribution along the urban coasts of Türkiye. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106623. [PMID: 38917660 DOI: 10.1016/j.marenvres.2024.106623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024]
Abstract
Marine phytoplankton are widely used to monitor the state of the water column due to their rapid changes in response to environmental conditions. In this study, we aimed to investigate the coastal phytoplankton assemblages, including bloom-forming species using high-throughput sequencing of 18S rRNA genes targeting the V4 region and their relationship with environmental variables along the Istanbul coasts of the Sea of Marmara. A total of 118 genera belonging to six phyla were detected. Among them, Dinoflagellata (36) and Bacillariophyta (26) were represented with the highest number of genera. According to the relative abundance of DNA reads, the most abundant taxa were Dinoflagellata_phylum (18.1%), Emiliania (8.4%), Biecheleria (8.4), and Noctiluca (8.1%). The ANOSIM test showed that there was a significant temporal difference in the assemblages, while the driving environmental factors were pH, water temperature, and salinity. According to the TRIX index, the trophic state of the coasts was highly mesotrophic and eutrophic. In addition, 45 bloom-forming and HAB taxa were detected and two species of Noctiluca and Emiliania, which frequently cause blooms in the area, were recorded in high abundance. Our results provide insight into the phytoplankton assemblages along the urbanized coastlines by analysing the V4 region of 18S rRNA. This data can support future studies that use both traditional methods and metabarcoding, employing various primers and targeting different genes and regions.
Collapse
Affiliation(s)
- Aydın Kaleli
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| | - Emine Gozde Ozbayram
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| | - Reyhan Akcaalan
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, 34134, Istanbul, Türkiye.
| |
Collapse
|
3
|
Strauss J, Choi CJ, Grone J, Wittmers F, Jimenez V, Makareviciute-Fichtner K, Bachy C, Jaeger GS, Poirier C, Eckmann C, Spezzano R, Löscher CR, Sarma VVSS, Mahadevan A, Worden AZ. The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients. Environ Microbiol 2023; 25:2118-2141. [PMID: 37311449 DOI: 10.1111/1462-2920.16431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/13/2023] [Indexed: 06/15/2023]
Abstract
The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104 cells ml-1 , predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104 cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104 cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.
Collapse
Affiliation(s)
- Jan Strauss
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Chang Jae Choi
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jonathan Grone
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Valeria Jimenez
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université - CNRS, Roscoff Culture Collection, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Gualtiero Spiro Jaeger
- Physical Oceanography Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Charlotte Eckmann
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Rachele Spezzano
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Carolin R Löscher
- Nordcee, DIAS, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - V V S S Sarma
- Regional Centre, CSIR-National Institute of Oceanography, Visakhapatnam, India
| | - Amala Mahadevan
- Physical Oceanography Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Faculty of Mathematics and Natural Sciences, Christian-Albrecht University of Kiel, Kiel, Germany
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| |
Collapse
|
4
|
Shuwang X, Zhang G, Li D, Wen Y, Zhang G, Sun J. Spatial and temporal changes in the assembly mechanism and co-occurrence network of the chromophytic phytoplankton communities in coastal ecosystems under anthropogenic influences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162831. [PMID: 36924961 DOI: 10.1016/j.scitotenv.2023.162831] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 05/06/2023]
Abstract
As a typical semiclosed coastal sea area in China, the ecological environment of Bohai Bay has been significantly disturbed by human activities. As primary producers, the chromophytic phytoplankton are the basis of ecosystems, especially in coastal ecosystems, and changes in the chromophytic phytoplankton community can affect the stability of the entire ecosystem. In this study, we investigated the effects of the human activity-induced spatial and temporal environmental heterogeneity on the community composition, diversity, assembly mechanisms, and co-occurrence networks of chromophytic phytoplankton in Bohai Bay during the wet season and the dry season. The results showed that in both seasons, there was obvious environmental heterogeneity between the nearshore area and the offshore area, and the nearshore areas were more affected by human disturbance. Although higher diversity was supported by the abundance of nutrients in nearshore areas, co-occurrence network analysis revealed that the chromophytic phytoplankton were less closely connected to each other in nearshore areas than in offshore areas due to chemical oxygen demand (COD), eutrophication index (EI), and dissolved inorganic nitrogen (DIN). The nearshore network was less stable than the offshore co-occurrence network in both seasons, which was related to the concentration of dissolved oxygen and COD. Both stochastic and deterministic processes dominated the assembly of the chromophytic phytoplankton communities, with different importance rankings of stochastic and deterministic processes in the nearshore and offshore areas. Drift dominated the assembly of the communities in nearshore areas, while variable selection dominated the assembly of the communities in offshore areas. DIN, EI, and COD, rather than geographic distance, were the main environmental factors affecting the phylogenetic turnover of the chromophytic phytoplankton. Our study showed that environmental heterogeneity caused by human disturbance had a greater impact on the chromophytic phytoplankton communities in Bohai Bay than natural factors such as temperature and salinity.
Collapse
Affiliation(s)
- Xinze Shuwang
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China; College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Guodong Zhang
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Danyang Li
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yujian Wen
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guicheng Zhang
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou 511462, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan 430074, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China.
| |
Collapse
|
5
|
Akcaalan R, Ozbayram EG, Kaleli A, Cam AO, Koker L, Albay M. Does environmental DNA reflect the actual phytoplankton diversity in the aquatic environment? Case study of marine mucilage in the Sea of Marmara. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27528-7. [PMID: 37178301 DOI: 10.1007/s11356-023-27528-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
The present study was designed to assess the effectiveness of the eDNA metabarcoding approach to determine the phytoplankton composition in the marine environment with a special focus on mucilage episodes in the Sea of Marmara. For this purpose, the samples were collected from 5 different sites located in the Sea of Marmara and the northern Aegean Sea during the mucilage episode in June 2021. The phytoplankton diversity was analyzed morphologically and by 18S rRNA gene amplicon sequencing, and the dataset of both methods was compared, accordingly. The results showed significant differences between methods in terms of composition and the abundance of the phytoplankton groups. While Miozoa was the most abundant group by metabarcoding, light microscopy (LM) indicated a dominance of Bacillariophyta. Katablepharidophyta was found at lower abundances by the metabarcoding (representing < 1% of the community); the members of this phylum were not observed by a microscope. At the lower taxonomic levels, Chaetoceros was the only genus detected in all samples by both methods. Additionally, while mucilage-forming Gonyaulax fragilis, Cylindrotheca closterium, and Thalassiosira rotula were detected to species-level by LM, metabarcoding was able to determine these organisms at the genus level. On the other hand, the genus Arcocellulus was found in all metabarcoding datasets and not detected by microscopy. The results indicated that metabarcoding can detect a greater number of genera and reveal taxa that were overlooked by light microscopy but to develop a complete picture of phytoplankton diversity in the sample, microscopical observations still are in need.
Collapse
Affiliation(s)
- Reyhan Akcaalan
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey.
| | - Emine Gozde Ozbayram
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Aydın Kaleli
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Ayca Oguz Cam
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Latife Koker
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| | - Meric Albay
- Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134, Istanbul, Turkey
| |
Collapse
|
6
|
Pujari L, Kan J, Xin Y, Zhang G, Noman MA, Nilajkar S, Sun J. Deciphering the diversity and distribution of chromophytic phytoplankton in the Bohai Sea and the Yellow Sea via RuBisCO genes (rbcL). MARINE POLLUTION BULLETIN 2022; 184:114193. [PMID: 36209535 DOI: 10.1016/j.marpolbul.2022.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Present study investigated composition and distribution of chromophytic phytoplankton in the Bohai Sea (BS) and the Yellow Sea (YS) by using rbcL genes. Bacillariophyceae, Haptophyceae and Pelagophyceae were the most abundant phytoplankton groups. Distinct phytoplankton communities were observed in the BS and the YS: offshore stations were dominated by bloom forming genera Thalassiosira and Skeletonema, while brown tide-forming species including Chrysochromulina spp. and Aureococcus anophagefferens were commonly found in the nearshore areas. Redundancy analysis showed that phosphate, temperature and silicic acid play key roles in structuring chromophytic phytoplankton, such as phytoplankton at nearshore stations were affected by nutrient runoff from adjacent rivers (Yellow River). Anthropogenic activities in the Bohai Sea and seasonal circulation of ocean currents may also contribute to shaping chromophytic phytoplankton communities. This study provides data support and foundational observations of chromophytic phytoplankton in the BS and the YS, and their responses to environmental gradients and human activities.
Collapse
Affiliation(s)
- Laxman Pujari
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Business Development Group, National Institute of Oceanography, Goa, India; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, USA
| | - Yehong Xin
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Md Abu Noman
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Sujata Nilajkar
- Biological Oceanography Division, National Institute of Oceanography, Goa, India
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
| |
Collapse
|
7
|
Chen X, Zhao H, Jiang G, Tang J, Xu Q, Li X, Huang Y, Zou S, Dong K, Hou W, Pan L, Wang P, Huang L, Li N. Trophic states regulate assembly processes and network structures of small chromophytic phytoplankton communities in estuarine and coastal ecosystem. MARINE POLLUTION BULLETIN 2022; 175:113327. [PMID: 35077925 DOI: 10.1016/j.marpolbul.2022.113327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Small chromophytic phytoplankton (SCP) are anticipated to be more important for a significant proportion of primary production in estuarine-coastal ecosystems. However, responses of SCP community to coastal eutrophication are still unclear. In this study, we investigated diversity, co-occurrence and assembly features of SCP communities, as well as relationship with environmental factors in subtropical Beibu Gulf. The results exhibited that the alpha diversity and beta diversity of SCP communities were significantly different among eutrophic states. Co-occurrence network revealed a complex interaction that most amplicon sequence variants (ASVs) in modules of the network were specific to trophic states. Further, phylogenetic based β-nearest taxon distance analyses revealed that stochastic processes mainly provided 69.26% contribution to SCP community assembly, whereas deterministic processes dominated community assembly in heavy eutrophic state. Overall, our findings elucidate the mechanism of diversity and assembly in SCP community and promote the understanding of SCP ecology related to subtropical coastal eutrophication.
Collapse
Affiliation(s)
- Xing Chen
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China; College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Huaxian Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China
| | - Gonglingxia Jiang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China
| | - Jinli Tang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China
| | - Qiangsheng Xu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China
| | - Xiaoli Li
- School of Agriculture, Ludong University, Yantai 264025, China
| | - Yuqing Huang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China
| | - Shuqi Zou
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Weiguo Hou
- State Key Laboratory of Biogeosciences and Environmental Geology and Institute of Earth Sciences, China University of Geosciences, Beijing 100083, China
| | - Lianghao Pan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, 92 Changqing Road, Beihai, Guangxi 536000, China
| | - Pengbin Wang
- Fourth Institute of Oceanography, Ministry of Natural Resources, 26 New Century Avenue, Beihai 536000, China; Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, 36 Baochubei Road, Hangzhou 310012, China
| | - Liangliang Huang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (Nanning Normal University), 175 Mingxiu East Road, Nanning 530001, China.
| |
Collapse
|
8
|
Keck F, Blackman RC, Bossart R, Brantschen J, Couton M, Hürlemann S, Kirschner D, Locher N, Zhang H, Altermatt F. Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Mol Ecol 2022; 31:1820-1835. [PMID: 35075700 PMCID: PMC9303474 DOI: 10.1111/mec.16364] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
Collapse
Affiliation(s)
- François Keck
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Rosetta C Blackman
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Raphael Bossart
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Marjorie Couton
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Dominik Kirschner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, Universitätstr. 16, 8092, Zürich, Switzerland.,Landscape Ecology, Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nadine Locher
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Heng Zhang
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| |
Collapse
|
9
|
Wu C, Kan J, Narale DD, Liu K, Sun J. Dynamics of bacterial communities during a seasonal hypoxia at the Bohai Sea: Coupling and response between abundant and rare populations. J Environ Sci (China) 2022; 111:324-339. [PMID: 34949362 DOI: 10.1016/j.jes.2021.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 06/14/2023]
Abstract
Marine bacterial community plays a vital role in the formation of the hypoxia zone in coastal oceans. Yet, their dynamics in the seasonal hypoxia zone of the Bohai Sea (BHS) are barely studied. Here, the 16S rRNA gene-based high-throughput sequencing was used to explore the dynamics of their diversity, structure, and function as well as driving factors during the gradual deoxygenation process in the BHS. Our results evinced that the bacterial community was dominated by Proteobacteria, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Cyanobacteria, etc. The abundant subcommunity dominated in the number of sequences (49%) while the rare subcommunity dominated in the number of species (99.61%). Although abundant subcommunity accounted for most sequences, rare subcommunity possessed higher diversity, richness and their population dramatically changed (higher turnover) during the hypoxia transition. Further, co-occurrence network analysis proved the vital role of rare subcommunity in the process of community assembly. Additionally, beta diversity partition revealed that both subcommunities possessed a higher turnover component than nestedness and/or richness component, implying species replacement could explain a considerable percentage of community variation. This variation might be governed by both environmental selection and stochastic processes, and further, it influenced the nitrogen cycle (PICRUSt-based prediction) of the hypoxia zone. Overall, this study provides insight into the spatial-temporal heterogeneity of bacterial and their vital role in biogeochemical cycles in the hypoxia zone of the BHS. These findings will extend our horizons about the stabilization mechanism, feedback regulation, and interactive model inside the bacterial community under oxygen-depleted ecosystems.
Collapse
Affiliation(s)
- Chao Wu
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin 300457, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinjun Kan
- Department of Microbiology, Stroud Water Research Center, Avondale, PA 19311, USA
| | - Dhiraj Dhondiram Narale
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin 300457, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Kun Liu
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jun Sun
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin 300457, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan 430074, China.
| |
Collapse
|
10
|
Armbrecht L, Eisenhofer R, Utge J, Sibert EC, Rocha F, Ward R, Pierella Karlusich JJ, Tirichine L, Norris R, Summers M, Bowler C. Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME COMMUNICATIONS 2021; 1:66. [PMID: 36755065 PMCID: PMC9723766 DOI: 10.1038/s43705-021-00070-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022]
Abstract
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
Collapse
Affiliation(s)
- Linda Armbrecht
- Institute for Marine and Antarctic Studies (IMAS), Ecology & Biodiversity Centre, University of Tasmania, Battery Point, TAS, 7004, Australia.
- Australian Centre for Ancient DNA, School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Raphael Eisenhofer
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - José Utge
- UMR 7206, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, 75016, Paris, France
| | - Elizabeth C Sibert
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, 06511, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA
| | - Fabio Rocha
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Ryan Ward
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Richard Norris
- GRD, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92093-0244, USA
| | - Mindi Summers
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| |
Collapse
|
11
|
Fawley MW, Fawley KP, Cahoon AB. Finding needles in a haystack-Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbcL gene using lineage-directed primers. JOURNAL OF PHYCOLOGY 2021; 57:1636-1647. [PMID: 34218435 PMCID: PMC8530920 DOI: 10.1111/jpy.13196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 05/02/2023]
Abstract
Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastid rbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184 rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA-based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species-level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.
Collapse
Affiliation(s)
- Marvin W. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - Karen P. Fawley
- Division of Natural Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas, 72830, USA
| | - A. Bruce Cahoon
- Department of Natural Sciences, University of Virginia’s College at Wise, Wise, VA 24293, USA
| |
Collapse
|
12
|
Li L, Pujari L, Wu C, Huang D, Wei Y, Guo C, Zhang G, Xu W, Liu H, Wang X, Wang M, Sun J. Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean. Front Microbiol 2021; 12:616956. [PMID: 34456881 PMCID: PMC8385211 DOI: 10.3389/fmicb.2021.616956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.
Collapse
Affiliation(s)
- Liuyang Li
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Laxman Pujari
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Chao Wu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Danyue Huang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqiu Wei
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Congcong Guo
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
| |
Collapse
|
13
|
Deng X, Zhang GL, Xin M, Liu CY, Cai WJ. Carbonate chemistry variability in the southern Yellow Sea and East China Sea during spring of 2017 and summer of 2018. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146376. [PMID: 33752023 DOI: 10.1016/j.scitotenv.2021.146376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Marginal seas are highly productive and disproportionately large contributors to global air-sea CO2 fluxes. Due to complex physical and biogeochemical conditions, the southern Yellow-East China Sea is an ideal site for studying carbonate chemistry variability. The carbonate system was investigated in the area in spring of 2017 and summer of 2018. Dissolved inorganic carbon (DIC) and total alkalinity (TA) concentrations were higher in the SYS than the ECS due to material from carbonate weathering and erosion carried by the Yellow River. High pH and low DIC and TA were observed in the Zhe-Min Coastal Current in spring due to high primary productivity caused by Changjiang River input and the Taiwan Warm Current. Temperature and biological activity were the primary drivers controlling the partial pressure of CO2 (pCO2) in the SYS, pCO2 was controlled by primary productivity related to nutrients carried by the Changjiang River and physical mixing in the Changjiang River plume and inner/middle shelves of the ECS, whereas temperature was the dominant factor determining pCO2 distributions in the ECS outer shelf waters influenced by the Kuroshio Current. Overall, the entire study area shifted from a CO2 sink (-4.18 ± 5.60 mmol m-2 d-1) to a weak source (1.02 ± 4.87 mmol m-2 d-1) from spring to summer. Specifically, the SYS and ECS offshore waters changed from CO2 sinks in spring to sources in summer, while the Changjiang River plume was always a CO2 sink.
Collapse
Affiliation(s)
- Xue Deng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States
| | - Gui-Ling Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| | - Ming Xin
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Key Laboratory for Marine Bioactive Substances and Modern Analytical Technology, the First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, PR China
| | - Chun-Ying Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, PR China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China.
| | - Wei-Jun Cai
- School of Marine Science and Policy, University of Delaware, Newark, DE 19716, United States
| |
Collapse
|
14
|
Vaulot D, Geisen S, Mahé F, Bass D. pr2-primers: An 18S rRNA primer database for protists. Mol Ecol Resour 2021; 22:168-179. [PMID: 34251760 DOI: 10.1111/1755-0998.13465] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023]
Abstract
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R-based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set (https://app.pr2-primers.org). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.
Collapse
Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France.,Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.,Nanjing Agricultural University, Nanjing, China
| | - Frédéric Mahé
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.,Department of Life Sciences, The Natural History Museum, London, UK
| |
Collapse
|
15
|
The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean. BIOLOGY 2021; 10:biology10030248. [PMID: 33810062 PMCID: PMC8005183 DOI: 10.3390/biology10030248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 11/29/2022]
Abstract
Simple Summary Marine microbes are regarded as the most diverse organisms in the biosphere and drive biogeochemical cycles through their metabolism. It is essential to understand the structure and metabolic function of microbial communities. The Indian Ocean is the third largest ocean in the world, and it possesses unique hydrographical properties. So far, assessments of microbial diversity and metabolism need to be improved in the Indian Ocean. Therefore, we carried out a series of investigations in the equatorial eastern Indian Ocean in order to clarify the local microbial communities and detect the genetic potential for microbial functions. The obtained results suggested Cyanobacteria was the dominant microbial group, and predicted the Calvin cycle and the assimilatory nitrate and nitrite reduction played important role in the pathway of carbon fixation and nitrogen metabolism respectively. This study provides insights into microbial community structures as well as the metabolic potential that may be active in the local environment, and lays the groundwork for understanding the roles of microbes in energy and resource cycling in this habitat. Abstract Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.
Collapse
|
16
|
Pujari L, Narale D, Kan J, Wu C, Zhang G, Ding C, Li L, Sun J. Distribution of Chromophytic Phytoplankton in the Eddy-Induced Upwelling Region of the West Pacific Ocean Revealed Using rbcL Genes. Front Microbiol 2021; 12:596015. [PMID: 33737916 PMCID: PMC7960667 DOI: 10.3389/fmicb.2021.596015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Marine chromophytic phytoplankton are a diverse group of algae and contribute significantly to the total oceanic primary production. However, the spatial distribution of chromophytic phytoplankton is understudied in the West Pacific Ocean (WPO). In this study, we have investigated the community structure and spatial distribution of chromophytic phytoplankton using RuBisCO genes (Form ID rbcL). Our results showed that Haptophyceae, Pelagophyceae, Cyanophyceae, Xanthophyceae, and Bacillariophyceae were the dominant groups. Further, chromophytic phytoplankton can be distinguished between upwelling and non-upwelling zones of the WPO. Surface and 75 m depths of a non-upwelling area were dominated by Prochlorococcus strains, whereas chromophytic phytoplankton were homogenously distributed at the surface layer in the upwelling zone. Meanwhile, Pelagomonas-like sequences were dominant at DCM (75 m) and 150 m depths of the upwelling zone. Non-metric multidimensional scaling (NMDS) analysis did not differentiate between chromophytic phytoplankton in the upwelling and non-upwelling areas, however, it showed clear trends of them at different depths. Further, redundancy analysis (RDA) showed the influence of physicochemical parameters on the distribution of chromophytic phytoplankton. Along with phosphate (p < 0.01), temperature and other dissolved nutrients were important in driving community structure. The upwelling zone was impacted by a decrease in temperature, salinity, and re-supplement of nutrients, where Pelagomonas-like sequences outnumbered other chromophytic groups presented.
Collapse
Affiliation(s)
- Laxman Pujari
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Dhiraj Narale
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, United States
| | - Chao Wu
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Changling Ding
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Liuyang Li
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
| |
Collapse
|
17
|
Wang Y, Hu X, Sun Y, Wang C. Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143496. [PMID: 33248757 DOI: 10.1016/j.scitotenv.2020.143496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
The formation and presence of the cold bottom water (Yellow Sea Cold Water Mass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on the marine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deep water communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic α-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic α-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment.
Collapse
Affiliation(s)
- Yibo Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|