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Xie W, Yan Y, Hu J, Dong P, Hou D, Zhang H, Yao Z, Zhu X, Zhang D. Ecological Dynamics and Co-occurrences Among Prokaryotes and Microeukaryotes in a Diatom Bloom Process in Xiangshan Bay, China. MICROBIAL ECOLOGY 2022; 84:746-758. [PMID: 34665286 DOI: 10.1007/s00248-021-01899-1] [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: 08/14/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Diatom blooms can significantly affect the succession of microbial communities, yet little is known about the assembly processes and interactions of microbial communities during autumn bloom events. In this study, we investigated the ecological effects of an autumn diatom bloom on prokaryotic communities (PCCs) and microeukaryotic communities (MECs), focusing on their assembly processes and interactions. The PCCs were largely dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Flavobacteria, while the MECs primarily included Diatomea, Dinoflagellata, and Chlorophyta. The succession of both PCCs and MECs was mainly driven by this diatom bloom and environmental factors, such as nitrate and silicate. Null modeling revealed that homogeneous selection had a more pronounced impact on the structure of PCCs compared with that of MECs. In particular, drift and dispersal limitation cannot be neglected in the assembly processes of MECs. Co-occurrence network analyses showed that Litorimicrobium, Cercozoa, Marine Group I (MGI), Cryptomonadales, Myrionecta, and Micromonas may affect the bloom process. In summary, these results elucidated the complex, robust interactions and obviously distinct assembly mechanisms of PCCs and MECs during a diatom bloom and extend our current comprehension of the ecological mechanisms and microbial interactions involved in an autumn diatom bloom process.
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Affiliation(s)
- Weijuan Xie
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Yi Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Pengsheng Dong
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, 315211, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, 315010, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- School of Marine Sciences, Ningbo University, Ningbo, 315832, China.
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Liu J, Wang X, Liu J, Liu X, Zhang XH, Liu J. Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea. Front Microbiol 2022; 13:1003623. [PMID: 36386657 PMCID: PMC9641972 DOI: 10.3389/fmicb.2022.1003623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2022] [Indexed: 10/10/2023] Open
Abstract
Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.
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Affiliation(s)
- Jinmei Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiao Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoyue Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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Anderson SR, Harvey EL. Estuarine microbial networks and relationships vary between environmentally distinct communities. PeerJ 2022; 10:e14005. [PMID: 36157057 PMCID: PMC9504456 DOI: 10.7717/peerj.14005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/14/2022] [Indexed: 01/19/2023] Open
Abstract
Microbial interactions have profound impacts on biodiversity, biogeochemistry, and ecosystem functioning, and yet, they remain poorly understood in the ocean and with respect to changing environmental conditions. We applied hierarchical clustering of an annual 16S and 18S amplicon dataset in the Skidaway River Estuary, which revealed two similar clusters for prokaryotes (Bacteria and Archaea) and protists: Cluster 1 (March-May and November-February) and Cluster 2 (June-October). We constructed co-occurrence networks from each cluster to explore how microbial networks and relationships vary between environmentally distinct periods in the estuary. Cluster 1 communities were exposed to significantly lower temperature, sunlight, NO3, and SiO4; only NH4 was higher at this time. Several network properties (e.g., edge number, degree, and centrality) were elevated for networks constructed with Cluster 1 vs. 2 samples. There was also evidence that microbial nodes in Cluster 1 were more connected (e.g., higher edge density and lower path length) compared to Cluster 2, though opposite trends were observed when networks considered Prokaryote-Protist edges only. The number of Prokaryote-Prokaryote and Prokaryote-Protist edges increased by >100% in the Cluster 1 network, mainly involving Flavobacteriales, Rhodobacterales, Peridiniales, and Cryptomonadales associated with each other and other microbial groups (e.g., SAR11, Bacillariophyta, and Strombidiida). Several Protist-Protist associations, including Bacillariophyta correlated with Syndiniales (Dino-Groups I and II) and an Unassigned Dinophyceae group, were more prevalent in Cluster 2. Based on the type and sign of associations that increased in Cluster 1, our findings indicate that mutualistic, competitive, or predatory relationships may have been more representative among microbes when conditions were less favorable in the estuary; however, such relationships require further exploration and validation in the field and lab. Coastal networks may also be driven by shifts in the abundance of certain taxonomic or functional groups. Sustained monitoring of microbial communities over environmental gradients, both spatial and temporal, is critical to predict microbial dynamics and biogeochemistry in future marine ecosystems.
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Affiliation(s)
- Sean R. Anderson
- Northern Gulf Institute, Mississippi State University, Mississippi State, MS, United States of America,Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, United States of America
| | - Elizabeth L. Harvey
- Department of Biological Sciences, University of New Hampshire, Durham, NH, United States of America
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Seasonal Succession and Temperature Response Pattern of a Microbial Community in the Yellow Sea Cold Water Mass. Appl Environ Microbiol 2022; 88:e0116922. [PMID: 36000863 PMCID: PMC9469719 DOI: 10.1128/aem.01169-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Explaining the temporal dynamics of marine microorganisms is critical for predicting their changing pattern under environmental disturbances. Although the effect of temperature on microbial seasonality has been widely studied, the phylogenetic structure of the temperature response pattern and the extent to which temperature shift leads to disruptive community changes are still unclear. Here, we explored the microbial seasonal dynamics in the Yellow Sea Cold Water Mass (YSCWM) that occurs in summer and disappears in winter and tested the temperature thresholds and phylogenetic coherence in response to temperature change. The existence of YSCWM generates strong temperature gradients in summer and confers little temperature change during seasonal transition, thus representing a unique intermediate state. The microbial community of YSCWM is more similar to that in the previous YSCWM in winter than that outside YSCWM. Temperature alone explains >50% of the community variation, suggesting that a temperature shift can induce a nearly seasonality-level community variance in summer. Persistence of most previous winter YSCWM inhabitants in YSCWM leads to conservation in predicted functional potentials and cooccurrence patterns, indicating a decisive role of temperature in maintaining functionality. Evaluation of the temperature threshold reveals that a small temperature change can lead to significant community turnover, with most taxa negatively responding to an elevation in temperature. The temperature response pattern is phylogenetically structured, and closely related taxa show an incohesive response. Our study provides novel insights into microbial seasonality and into how marine microorganisms respond to temperature fluctuations. IMPORTANCE Microbial seasonality is driven by a set of covarying factors including temperature. There is still a lack of understanding of the details of the phylogenetic structure and susceptibility of microbial communities in response to temperature variation. Through examination of the microbial community in a seasonally occurring summer cold water mass, which experiences little temperature change during seasonal transition, we show here that the cold water mass leads to nearly seasonality-level variations in community composition and predicted functional profile in summer. Moreover, massive community turnover occurs within a small temperature shift, with most taxa decreasing in abundance in response to increased temperature, and contrasting response patterns are observed between phylogenetically closely related taxa. These results suggest temperature as the fundamental factor over other covarying factors in structuring microbial seasonality, providing important insights into the variation mode of the microbial community under temperature disturbances.
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Abstract
Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.
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The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate. Nat Microbiol 2022; 7:1466-1479. [PMID: 35970961 PMCID: PMC9418006 DOI: 10.1038/s41564-022-01174-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/14/2022] [Indexed: 11/08/2022]
Abstract
Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacterial compounds, yet their native microbiomes remain uncharacterized. Here we report the discovery of a ubiquitous, uncultured bacterial lineage we name Candidatus Comchoanobacterales ord. nov., related to the human pathogen Coxiella and physically associated with the uncultured marine choanoflagellate Bicosta minor. We analyse complete ‘Comchoano’ genomes acquired after sorting single Bicosta cells, finding signatures of obligate host-dependence, including reduction of pathways encoding glycolysis, membrane components, amino acids and B-vitamins. Comchoano encode the necessary apparatus to import energy and other compounds from the host, proteins for host-cell associations and a type IV secretion system closest to Coxiella’s that is expressed in Pacific Ocean metatranscriptomes. Interactions between choanoflagellates and their microbiota could reshape the direction of energy and resource flow attributed to microbial predators, adding complexity and nuance to marine food webs. Choanoflagellates are the closest living unicellular relatives of animals and are important bacterivorous predators in the ocean. Here the authors show that the microbiome of this predator includes an obligate, host resource-dependent bacterial associate.
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Hu R, Liu S, Saleem M, Xiong Z, Zhou Z, Luo Z, Shu L, He Z, Wang C. Environmentally‐induced reconstruction of microbial communities alters particulate carbon flux of deep chlorophyll maxima in the South China sea. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Songfeng Liu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Muhammad Saleem
- Department of Biological Sciences Alabama State University Montgomery AL USA
| | - Zhiyao Xiong
- School of Marine Sciences Sun Yat‐sen University Zhuhai
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat‐sen University Guangzhou China
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Ren Z, Luo W, Zhang C. Rare bacterial biosphere is more environmental controlled and deterministically governed than abundant one in sediment of thermokarst lakes across the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:944646. [PMID: 35958159 PMCID: PMC9358708 DOI: 10.3389/fmicb.2022.944646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Thermokarst lakes are widely distributed in cold regions as a result of ice-rich permafrost thaw. Disentangling the biogeography of abundant and rare microbes is essential to understanding the environmental influences, assembly mechanisms, and responses to climate change of bacterial communities in thermokarst lakes. In light of this, we assessed the abundant and rare bacterial subcommunities in sediments from thermokarst lakes across the Qinghai-Tibet Plateau (QTP). The operational taxonomic unit (OTU) richness was more strongly associated with location and climate factors for abundant subcommunities, while more strongly associated with physicochemical variables for rare subcommunities. The relative abundance of abundant and rare taxa showed opposite patterns with abundant taxa having greater relative abundance at higher latitude and pH, but at lower mean annual precipitation and nutrients. Both the abundant and rare subcommunities had a clear distribution pattern along the gradient of latitude and mean annual precipitation. Abundant subcommunities were dominantly shaped by dispersal limitation processes (80.9%), while rare subcommunities were shaped almost equally by deterministic (47.3%) and stochastic (52.7%) processes. The balance between stochastic and deterministic processes was strongly environmentally adjusted for rare subcommunities, while not associated with environmental changes for abundant subcommunities. The results shed light on biogeography patterns and structuring mechanisms of bacterial communities in thermokarst lakes, improving our ability to predict the influences of future climate change on these lakes.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China
- School of Environment, Beijing Normal University, Beijing, China
- *Correspondence: Ze Ren
| | - Wei Luo
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Wei Luo
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, China
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Zhang H, Yan Y, Lin T, Xie W, Hu J, Hou F, Han Q, Zhu X, Zhang D. Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay. Microbiol Spectr 2022; 10:e0148122. [PMID: 35638815 PMCID: PMC9241920 DOI: 10.1128/spectrum.01481-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/08/2022] [Indexed: 11/24/2022] Open
Abstract
Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.
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Affiliation(s)
- Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Yi Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Tenghui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Weijuan Xie
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Jian Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Fanrong Hou
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Qingxi Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
| | - Xiangyu Zhu
- Environmental Monitoring Center of Ningbo, Ningbo, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Key Laboratory of Applied Marine Biotechnology of Department of Education, Ningbo University, Ningbo, China
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Milke F, Sanchez-Garcia S, Dlugosch L, McNichol J, Fuhrman J, Simon M, Wagner-Döbler I. Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters. Front Microbiol 2022; 13:895875. [PMID: 35836413 PMCID: PMC9273945 DOI: 10.3389/fmicb.2022.895875] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/18/2022] [Indexed: 01/02/2023] Open
Abstract
Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.
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Affiliation(s)
- Felix Milke
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Selene Sanchez-Garcia
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jesse McNichol
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jed Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Meinhard Simon
- Institute for Chmistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Irene Wagner-Döbler
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
- *Correspondence: Irene Wagner-Döbler,
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Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems 2022; 7:e0031622. [PMID: 35730947 PMCID: PMC9426515 DOI: 10.1128/msystems.00316-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
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Yang P, Hao S, Han M, Xu J, Yu S, Chen C, Zhang H, Ning K. Analysis of antibiotic resistance genes reveals their important roles in influencing the community structure of ocean microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153731. [PMID: 35143795 DOI: 10.1016/j.scitotenv.2022.153731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/30/2022] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance gene (ARG) content is a well-established driver of microbial abundance and diversity in an environment. By reanalyzing 132 metagenomic datasets from the Tara Oceans project, we aim to unveil the associations between environmental factors, the ocean microbial community structure and ARG contents. We first investigated the structural patterns of microbial communities including both prokaryotes such as bacteria and eukaryotes such as protists. Additionally, several ARG-dominant horizontal gene transfer events between Protist and Prokaryote have been identified, indicating the potential roles of ARG in shaping the ocean microbial communities. For a deeper insight into the role of ARGs in ocean microbial communities on a global scale, we identified 1926 unique types of ARGs and discovered that the ARGs are more abundant and diverse in the mesopelagic zone than other water layers, potentially caused by limited resources. Finally, we found that ARG-enriched genera were often more abundant compared to their ARG-less neighbors in the same environment (e.g. coastal oceans). A deeper understanding of the ARG-microbiome relationships could help in the conservation of the oceanic ecosystem.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shiguang Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Junjie Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaojun Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Houjin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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63
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Wu B, Wang P, Devlin AT, She Y, Zhao J, Xia Y, Huang Y, Chen L, Zhang H, Nie M, Ding M. Anthropogenic Intensity-Determined Assembly and Network Stability of Bacterioplankton Communities in the Le'an River. Front Microbiol 2022; 13:806036. [PMID: 35602050 PMCID: PMC9114710 DOI: 10.3389/fmicb.2022.806036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/07/2022] [Indexed: 11/26/2022] Open
Abstract
Bacterioplankton are essential components of riverine ecosystems. However, the mechanisms (deterministic or stochastic processes) and co-occurrence networks by which these communities respond to anthropogenic disturbances are not well understood. Here, we integrated niche-neutrality dynamic balancing and co-occurrence network analysis to investigate the dispersal dynamics of bacterioplankton communities along human activity intensity gradients. Results showed that the lower reaches (where intensity of human activity is high) had an increased composition of bacterioplankton communities which induced strong increases in bacterioplankton diversity. Human activity intensity changes influenced bacterioplankton community assembly via regulation of the deterministic-stochastic balance, with deterministic processes more important as human activity increases. Bacterioplankton molecular ecological network stability and robustness were higher on average in the upper reaches (where there is lower intensity of human activity), but a human activity intensity increase of about 10%/10% can reduce co-occurrence network stability of bacterioplankton communities by an average of 0.62%/0.42% in the dry and wet season, respectively. In addition, water chemistry (especially NO3–-N and Cl–) contributed more to explaining community assembly (especially the composition) than geographic distance and land use in the dry season, while the bacterioplankton community (especially the bacterioplankton network) was more influenced by distance (especially the length of rivers and dendritic streams) and land use (especially forest regions) in the wet season. Our research provides a new perspective of community assembly in rivers and important insights into future research on environmental monitoring and classified management of aquatic ecosystems under the influence of human activity.
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Affiliation(s)
- Bobo Wu
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Peng Wang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Adam Thomas Devlin
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China
| | - Yuanyang She
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Jun Zhao
- School of Geography and Ocean Science, Nanjing University, Nanjing, China
| | - Yang Xia
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Yi Huang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Lu Chen
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Hua Zhang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Minghua Nie
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Mingjun Ding
- School of Geography and Environment, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, China
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64
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Maturana-Martínez C, Iriarte JL, Ha SY, Lee B, Ahn IY, Vernet M, Cape M, Fernández C, González HE, Galand PE. Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale. Front Microbiol 2022; 13:862812. [PMID: 35592001 PMCID: PMC9111744 DOI: 10.3389/fmicb.2022.862812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.
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Affiliation(s)
- Claudia Maturana-Martínez
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
| | - José Luis Iriarte
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Sun-Yong Ha
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Boyeon Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - In-Young Ahn
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Maria Vernet
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Mattias Cape
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Camila Fernández
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Humberto E González
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
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65
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Sun P, Wang Y, Huang X, Huang B, Wang L. Water masses and their associated temperature and cross-domain biotic factors co-shape upwelling microbial communities. WATER RESEARCH 2022; 215:118274. [PMID: 35298994 DOI: 10.1016/j.watres.2022.118274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Disentangling the drivers and mechanisms that shape microbial communities in a river-influenced coastal upwelling system requires considering a hydrologic dimension that can drive both deterministic and stochastic community assembly by generating hydrological heterogeneity and dispersal events. Additionally, ubiquitous and complex microbial interactions can play a significant role in community structuring. However, how the hydrology, biotic, and abiotic factors collectively shape microbial distribution in the hydrologically complicated river plume-upwelling coupling system remains unknown. Through underway sampling and daily observations, we employed 16S and 18S ribosomal RNA sequencing to disentangle drivers and mechanisms shaping the protist-bacteria microbiota in a river-influenced coastal upwelling system. Our findings indicate that the composition of microbial communities was water mass specific. Collectively, water mass, local water chemistry (mostly temperature) and biotic interaction (mostly cross-domain biotic interaction) shaped the protistan-bacterial communities. In comparison to protists, bacteria were more influenced by abiotic factors such as temperature than by cross-domain biotic factors, implying a stronger coupling of geochemical cycles. Both deterministic and stochastic processes had an effect on the distribution of microbial communities, but deterministic processes were more important for bacteria and were especially pronounced for upwelling communities. The co-occurrence network revealed strong associations between the protistan assemblages Orchrophyta and Ciliophora and the bacterial assemblages Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which may reflect predation and mutualism interactions. Overall, this study emphasizes the importance of taking water masses, temperature and domains of life into account when seeking to understand the drivers and assemblies of protist-bacteria microbiome dynamics in coastal upwelling systems, which is especially true given the complex and dynamic nature of the coastal ecosystem.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China; Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Xin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen 361102, China
| | - Bangqin Huang
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.
| | - Lei Wang
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
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66
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Krabberød AK, Deutschmann IM, Bjorbækmo MFM, Balagué V, Giner CR, Ferrera I, Garcés E, Massana R, Gasol JM, Logares R. Long-term patterns of an interconnected core marine microbiota. ENVIRONMENTAL MICROBIOME 2022; 17:22. [PMID: 35526063 PMCID: PMC9080219 DOI: 10.1186/s40793-022-00417-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/20/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth's primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. RESULTS Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. CONCLUSIONS We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Marit F M Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Caterina R Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Isabel Ferrera
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Esther Garcés
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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67
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Li Y, Wei J, Yang H, Zhang D, Hu C. Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts. Front Microbiol 2022; 13:848908. [PMID: 35495652 PMCID: PMC9042396 DOI: 10.3389/fmicb.2022.848908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea exhibit strong community heterogeneity with microhabitat gradients and are a non-negligible part of biocrust’s microorganisms. The study on archaeal biogeography in biocrusts could provide new insights for its application in environmental restoration. However, only a few studies on assembly processes and co-occurrence patterns of the archaeal community in patchy biocrusts have been reported, especially considering the number of species pools (SPs). Here, we comprehensively collected biocrusts across 3,500 km of northern China. Different successional biocrusts from various regions contain information of local climate and microenvironments, which can shape multiple unique archaeal SPs. The archaeal community differences in the same successional stage exceeded the variations between successional stages, which was due to the fact that the heterogeneous taxa tended to exchange between unknown patches driven by drift. We also comparatively studied the driving forces of community heterogeneity across three to ten SPs, and assembly and co-occurrence patterns were systematically analyzed. The results revealed that the impact of spatial factors on biogeographic patterns was greater than that of environmental and successional factors and that impact decreased with the number of SPs considered. Meanwhile, community heterogeneity at the phylogenetic facet was more sensitive to these driving factors than the taxonomic facet. Subgroups 1 (SG1) and 2 (SG2) of the archaeal communities in biocrusts were dominated by Nitrososphaeraceae and Haloarchaea, respectively. The former distribution pattern was associated with non-salinity-related variables and primarily assembled by drift, whereas the latter was associated with salinity-related variables and primarily assembled by homogeneous selection. Finally, network analysis indicated that the SG1 network had a higher proportion of competition and key taxa than the SG2 network, but the network of SG2 was more complex. Our study suggested that the development of the archaeal community was not consistent with biocrusts succession. The dominant taxa may determine the patterns of community biogeography, assembly, and co-occurrence.
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Affiliation(s)
- Yuanlong Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyi Wei
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haijian Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Delu Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chunxiang Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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68
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Wang Y, Ren Z, He P, Xu J, Li D, Liu C, Liu B, Wu N. Microeukaryotic Community Shifting Along a Lentic-Lotic Continuum. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.887787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
As an important regulator of ecosystem functions in river systems, microeukaryotes play an important role in energy and material conversion, yet little is known about the shift along a lentic-lotic continuum. In this study, the 18S rRNA genes sequencing was used to identify the microeukaryotic communities at 82 sites along a lentic-lotic continuum with the aim of understanding the impact of upstream inlet river on microeukaryotic communities in Baiyang Lake (BYD) and its downstream. Our results showed that the upstream inlet river affected the diversity and community composition of microeukaryotes in BYD and downstream rivers, and environmental variables greatly affected the composition of microeukaryotic community. The community composition in BYD had lower variabilities. Co-occurrence network analysis revealed that the network was non-random and clearly parsed into three modules, and different modules were relatively more abundant to a particular area. As keystone taxa, some nodes of the upstream microeukaryotic network played an important role in structuring network and maintaining the stability of the ecosystem. In BYD and downstream, the microeukaryotic network was highly fragmented, and the loss of keystone taxa would have an adverse impact on the integrity and function of the microeukaryotic community. Microeukaryotes had strong tendencies to co-occur, which may contribute to the stability and resilience of microeukaryotic communities. Overall, these findings extend the current understanding of the diversity and community composition of microeukaryotic along a lentic-lotic continuum.
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69
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Cruz-Flores R, López-Carvallo JA, Cáceres-Martínez J, Dhar AK. Microbiome analysis from formalin-fixed paraffin-embedded tissues: Current challenges and future perspectives. METHODS IN MICROBIOLOGY 2022; 196:106476. [PMID: 35490989 DOI: 10.1016/j.mimet.2022.106476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in thousands of human and animal pathology laboratories around the globe represent mines of stored genetic information. In recent years, the use of FFPE tissues as a viable source of DNA for diverse genetic studies has attracted attention for interrogating microbiomes from this sample type. These studies have proven that 16S rRNA amplicon sequencing-based microbiome studies are possible from FFPE samples but present some particular challenges. In this review, we summarize all aspects of microbiome studies from FFPE tissues including the challenges associated with working highly degraded DNA, best practices for reducing environmental contamination, and we propose solutions to address these issues. Finally, we discuss how the combination of FFPE microbiome studies and Laser Capture Microdissection and/or Laser Microdissection could enable to determine the spatial heterogeneity underlying complex bacterial communities.
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Affiliation(s)
- Roberto Cruz-Flores
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico.
| | - Jesús Antonio López-Carvallo
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico
| | - Jorge Cáceres-Martínez
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Zona Playitas, 22860 Ensenada, Baja California, Mexico
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, United States of America
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70
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Lv B, Shi J, Li T, Ren L, Tian W, Lu X, Han Y, Cui Y, Jiang T. Deciphering the characterization, ecological function and assembly processes of bacterial communities in ship ballast water and sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:152721. [PMID: 34974026 DOI: 10.1016/j.scitotenv.2021.152721] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Various microorganisms are transported worldwide via the water and sediments inside ship ballast tanks. Nevertheless, the ecological functions and assembly processes of bacterial communities in ballast water and sediments remain poorly understood. Here, we investigated the bacterial composition, community assembly processes, and putative functions through analyses of 70 ballast water and sediment samples obtained from various ships. The results showed that the ballast sediments contained a higher diversity of bacterial communities, whereas the ballast water was characterized by the dominance of Proteobacteria. Both the composition and potential function structures of bacterial communities were clearly different between the ballast water and sediment samples. The ballast water exhibited an abundance of microorganisms that involved in sulfur oxidation, whereas the bacterial species associated with nitrogen metabolism were abundant in the sediments. Co-occurrence network analysis revealed that the communities in ballast sediment samples possessed more complex network structures with higher modularity and positive associations among bacterial populations. Stochastic processes, especially the dispersal limitation process played the most important influence in the assembly of the communities in ballast water. Meanwhile, the bacterial communities in the ballast sediments were primarily governed by the homogeneous selection of determinacy. The results from this study will help us understand the ecological processes related to the bacterial communities in the ballast tanks and provide a foundation for the management of ballast water and sediments.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Jianhong Shi
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Tao Li
- China Waterborne Transport Research Institute, Beijing 100088, China
| | - Lili Ren
- China Waterborne Transport Research Institute, Beijing 100088, China
| | - Wen Tian
- Jiangyin Customs, Jiangyin 214400, China
| | - Xiaolan Lu
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | | | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Ting Jiang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
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71
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Zhao R, Zhao F, Zheng S, Li X, Wang J, Xu K. Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities. Front Microbiol 2022; 13:773487. [PMID: 35464911 PMCID: PMC9024416 DOI: 10.3389/fmicb.2022.773487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022] Open
Abstract
The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.
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Affiliation(s)
- Rongjie Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shan Zheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianing Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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72
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Macroecological distributions of gene variants highlight the functional organization of soil microbial systems. THE ISME JOURNAL 2022; 16:726-737. [PMID: 34580430 PMCID: PMC8857198 DOI: 10.1038/s41396-021-01120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
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Gill JG, Hill-Spanik KM, Whittaker KA, Jones ML, Plante C. Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 2022; 10:e12835. [PMID: 35251777 PMCID: PMC8893026 DOI: 10.7717/peerj.12835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
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Affiliation(s)
- John Geoffrey Gill
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
| | | | - Kerry A. Whittaker
- Sea Education Association, Woods Hole, MA, United States,Maine Maritime Academy, Castine, Maine, United States
| | - Martin L. Jones
- Department of Mathematics, College of Charleston, Charleston, SC, United States
| | - Craig Plante
- Grice Marine Laboratory, College of Charleston, Charleston, SC, United States
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74
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Thomson T, Fusi M, Bennett-Smith MF, Prinz N, Aylagas E, Carvalho S, Lovelock CE, Jones BH, Ellis JI. Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils. Microbiol Spectr 2022; 10:e0090321. [PMID: 34985338 PMCID: PMC8729789 DOI: 10.1128/spectrum.00903-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/11/2021] [Indexed: 12/23/2022] Open
Abstract
Mangrove forests are important biotic sinks of atmospheric CO2 and play an integral role in nutrient-cycling and decontamination of coastal waters, thereby mitigating climatic and anthropogenic stressors. These services are primarily regulated by the activity of the soil microbiome. To understand how environmental changes may affect this vital part of the ecosystem, it is key to understand the patterns that drive microbial community assembly in mangrove forest soils. High-throughput amplicon sequencing (16S rRNA) was applied on samples from arid Avicennia marina forests across different spatial scales from local to regional. Alongside conventional analyses of community ecology, microbial co-occurrence networks were assessed to investigate differences in composition and structure of the bacterial community. The bacterial community composition varied more strongly along an intertidal gradient within each mangrove forest, than between forests in different geographic regions (Australia/Saudi Arabia). In contrast, co-occurrence networks differed primarily between geographic regions, illustrating that the structure of the bacterial community is not necessarily linked to its composition. The local diversity in mangrove forest soils may have important implications for the quantification of biogeochemical processes and is important to consider when planning restoration activities. IMPORTANCE Mangrove ecosystems are increasingly being recognized for their potential to sequester atmospheric carbon, thereby mitigating the effects of anthropogenically driven greenhouse gas emissions. The bacterial community in the soils plays an important role in the breakdown and recycling of carbon and other nutrients. To assess and predict changes in carbon storage, it is important to understand how the bacterial community is shaped by its environment. Here, we compared the bacterial communities of mangrove forests on different spatial scales, from local within-forest to biogeographic comparisons. The bacterial community composition differed more between distinct intertidal zones of the same forest than between forests in distant geographic regions. The calculated network structure of theoretically interacting bacteria, however, differed most between the geographic regions. Our findings highlight the importance of local environmental factors in shaping the microbial soil community in mangroves and highlight a disconnect between community composition and structure in microbial soil assemblages.
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Affiliation(s)
- T. Thomson
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - M. Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - M. F. Bennett-Smith
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - N. Prinz
- University of Waikato, School of Science, Tauranga, New Zealand
| | - E. Aylagas
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - S. Carvalho
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - C. E. Lovelock
- School of Biological Sciences, The University of Queensland, St Lucida, Australia
| | - B. H. Jones
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - J. I. Ellis
- University of Waikato, School of Science, Tauranga, New Zealand
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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75
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Niu L, Xie X, Li Y, Hu Q, Wang C, Zhang W, Zhang H, Wang L. Effects of nitrogen on the longitudinal and vertical patterns of the composition and potential function of bacterial and archaeal communities in the tidal mudflats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151210. [PMID: 34715211 DOI: 10.1016/j.scitotenv.2021.151210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/24/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Increasing attention has been focused on the diminishing health of coastal ecosystems. Understanding the effects of eutrophication on tidal flat ecosystems is beneficial for the restoration and management of coastal ecosystems. However, previous studies did not consider the effects of nitrogen on the structure and function of bacterial and archaeal communities in longitudinal and vertical profiles. Here, the diversity, composition, assembly mechanism, and potential metabolic function of the bacterial and archaeal communities were studied in two longitudinal tidal sections at different eutrophic levels. Nitrogen and salinity were the critical factors that influenced the bacterial and archaeal community composition using canonical correspondence and multivariate regression tree analyses. For the bacterial community, the higher nitrogen loading in tidal mudflats resulted in the convergence of diversity and structure in the longitudinal profile of bacteria, but divergence was detected in the vertical profile. For archaea, the diversity tended to be convergent in longitudinal and vertical profiles in the higher nitrogen area, but the change of structure was similar to that of bacteria. Besides the homogeneous processes influenced by salinity, the assembly process of the bacterial community was mainly influenced by heterogeneous selection (34.8%) and that of archaea by dispersal limitation (19.5%). However, the bacterial and archaeal communities in the higher nitrogen section presented more of an influence of heterogeneous selection (respectively, 39 and 5.6%) than that of the lower nitrogen section (respectively, 10 and 0.2%). Structural equation modeling indicated that nitrogen may have inhibited the effects of the bacterial community on nitrogen turnover in nitrogen-rich anoxic sediment environments, but may have strengthened the effect of the archaeal community on carbon metabolism compared to bacteria. This work deepens our understanding of the responses of bacterial and archaeal community structure and potential function to nitrogen pollution in tidal mudflats.
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Affiliation(s)
- Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Xudong Xie
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Qing Hu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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76
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Gazulla CR, Auladell A, Ruiz-González C, Junger PC, Royo-Llonch M, Duarte CM, Gasol JM, Sánchez O, Ferrera I. Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans. Environ Microbiol 2022; 24:2222-2238. [PMID: 35084095 DOI: 10.1111/1462-2920.15835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/17/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023]
Abstract
The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain.,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Pedro C Junger
- Department of Hydrobiology (DHB), Laboratory of Microbial Processes and Biodiversity (LMPB), Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain.,Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640 Fuengirola, Málaga, Spain
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77
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Quiroga MV, Valverde A, Mataloni G, Casa V, Stegen JC, Cowan D. The ecological assembly of bacterial communities in Antarctic wetlands varies across levels of phylogenetic resolution. Environ Microbiol 2022; 24:3486-3499. [PMID: 35049116 PMCID: PMC9541017 DOI: 10.1111/1462-2920.15912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
As functional traits are conserved at different phylogenetic depths, the ability to detect community assembly processes can be conditional on the phylogenetic resolution; yet most previous work quantifying their influence has focused on a single level of phylogenetic resolution. Here, we have studied the ecological assembly of bacterial communities from an Antarctic wetland complex, applying null models across different levels of phylogenetic resolution (i.e. clustering ASVs into OTUs with decreasing sequence identity thresholds). We found that the relative influence of the community assembly processes varies with phylogenetic resolution. More specifically, selection processes seem to impose stronger influence at finer (100% sequence similarity ASV) than at coarser (99%–97% sequence similarity OTUs) resolution. We identified environmental features related with the ecological processes and propose a conceptual model for the bacterial community assembly in this Antarctic ecosystem. Briefly, eco‐evolutionary processes appear to be leading to different but very closely related ASVs in lotic, lentic and terrestrial environments. In all, this study shows that assessing community assembly processes at different phylogenetic resolutions is key to improve our understanding of microbial ecology. More importantly, a failure to detect selection processes at coarser phylogenetic resolution does not imply the absence of such processes at finer resolutions.
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Affiliation(s)
- María V Quiroga
- Instituto Tecnológico de Chascomús (INTECH, UNSAM - CONICET), Chascomús, Argentina
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | - Gabriela Mataloni
- Instituto de Investigación e Ingeniería Ambiental (IIIA, UNSAM-CONICET), San Martín, Buenos Aires, Argentina
| | - Valeria Casa
- Instituto de Investigación e Ingeniería Ambiental (IIIA, UNSAM-CONICET), San Martín, Buenos Aires, Argentina
| | - James C Stegen
- Pacific Northwest National Laboratory, Ecosystem Science Team, Richland, WA, USA
| | - Don Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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78
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Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean. Microbiol Spectr 2022; 10:e0079821. [PMID: 35019678 PMCID: PMC8754141 DOI: 10.1128/spectrum.00798-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.
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79
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Disentangling the Ecological Processes Shaping the Latitudinal Pattern of Phytoplankton Communities in the Pacific Ocean. mSystems 2022; 7:e0120321. [PMID: 35089068 PMCID: PMC8725599 DOI: 10.1128/msystems.01203-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Phytoplankton diversity and community compositions vary across spaces and are fundamentally affected by several deterministic (e.g., environmental selection) and stochastic (e.g., ecological drift) processes. How this suite of different processes regulates the biogeography of phytoplankton remains to be comprehensively explored. Using high-throughput sequencing data and null model analysis, we revealed the ecological processes shaping the latitudinal community structure of three major phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) across the Pacific Ocean (70°N, 170°W to 35°S, 170°W). At the basin scale, heterogeneous selection (selection under heterogeneous environmental conditions) dominated the assembly processes of all phytoplankton groups; however, its relative importance varied greatly at the climatic zonal scale, explaining the distinct latitudinal α- and β-diversity among phytoplankton groups. Assembly processes in Synechococcus and haptophyte communities were mainly controlled by physical and nutrient factors, respectively. High temperature drove Synechococcus communities to be more deterministic with higher diversity, while haptophyte communities were less environmentally selected at low latitudes due to their wide niche breadth and mixotrophic lifestyle. Diatom communities were overwhelmingly dominated by the selection process but with low correlation of measured environmental factors to their community compositions. This could be attributed to the high growth rate of diatoms, as indicated by their lower site occupation frequency than predicted in the neutral community model. Our study showed that heterogeneous selection is the main force that shaped the biogeography of three key phytoplankton groups in the Pacific Ocean, with a latitudinal variation of relative importance due to the distinct traits among phytoplankton. IMPORTANCE Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored. In this study, we disentangled the ecological processes of three key phytoplankton groups (i.e., diatoms, Synechococcus, and haptophytes) along the same latitudinal gradients in the Pacific Ocean. Heterogeneous selection, by promoting species richness and reducing similarity between communities, was the dominant process shaping the communities of each phytoplankton group at the basin scale. However, its relative importance varied greatly among different phytoplankton groups in different climate zones, explaining the uneven latitudinal α- and β-diversity. We also highlight the importance of identifying key factors mediating the relative importance of assembly processes in phytoplankton communities, which will enhance our understanding of their biogeography in the ocean and future patterns under climate changes.
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80
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Protistan-Bacterial Microbiota Exhibit Stronger Species Sorting and Greater Network Connectivity Offshore than Nearshore across a Coast-to-Basin Continuum. mSystems 2021; 6:e0010021. [PMID: 34636671 PMCID: PMC8510552 DOI: 10.1128/msystems.00100-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Little is known regarding how community assembly and species association vary with habitat and depth. Here, we examined the assembly and association of protistan and bacterial communities across a coast-shelf-slope-basin gradient of the South China Sea using high-throughput sequencing of the V3 and V4 regions of the rRNA gene transcript. Our study revealed that homogenizing dispersal and drift exerted an influence on protistan communities comparable to that on bacterial communities. In contrast, selection and dispersal limitation exerted contrasting effects on the two microbial communities. Community assembly was governed to a greater degree by selection than by dispersal limitation in the bacterial community, and this was much lower in the protistan community. Moreover, this organismal assembly pattern was robust with habitat and depth. However, the relative importance of selection to dispersal limitation varied with habitat and depth in both communities, where horizontally it was higher offshore than nearshore and vertically it was lower in the bottom or deep chlorophyll maximum (DCM) than on the surface. The offshore possessed more microbial network complexity and more associations among microbial taxa than the nearshore, and vertically, the bottom possessed more complexity than the surface and the DCM. Moreover, temperature is strongly associated with the composition and co-occurrence of microbial communities, implying that temperature plays a dominant role in the selection of the protistan-bacterial microbiome across a coast-to-basin continuum. This study contributes to our understanding of the assembly mechanism and species association of protistan-bacterial microbiota across multiple habitats and depths. IMPORTANCE Microbial organisms play a crucial role in global nutrient cycling. Few studies have attempted to simultaneously investigate the community assembly of microeukaryotes and prokaryotes and their association patterns in oceanic waters. This is especially true regarding how they vary with habitats and depths despite the fact that they are essential for developing a more holistic understanding of marine ecosystems. This study revealed the differential actions of selection and dispersal limitation and species association across a coast-to-basin continuum on the marine protistan-bacterial microbiome. Moreover, temperature was identified as a crucial factor driving the structure and co-occurrence of protistan and bacterial communities. The results emphasize that the differences in community assembly and association patterns between nearshore and offshore of the main constituents of the ocean microbiota should be considered to understand their current and future configurations. This is especially crucial in the context of climate change, as the response of ocean microbiota to nearshore and offshore temperature changes remains unknown.
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81
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Liu L, Wang S, Chen J. Transformations from specialists to generalists cause bacterial communities are more stable than micro-eukaryotic communities under anthropogenic activity disturbance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148141. [PMID: 34090161 DOI: 10.1016/j.scitotenv.2021.148141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/07/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Different microbial components have different responses to environmental disturbances. Here, we found that the planktonic bacterial and micro-eukaryotic communities had different responses to anthropogenic activity disturbance in a subtropical river, because they had different survival strategies (generalist and specialist). We used nutrients (nitrogen and phosphorus) as indicators of anthropogenic activities. We found that river stretch 1 showed low nutrient concentrations from October 2018 to September 2019. However, a nutrient disturbance was observed in river stretch 2. The nutrient concentrations increased largely in December and January but recovered to low values in June. Bacterial communities had higher resilience under this disturbance than micro-eukaryotic communities in river stretch 2. The bacterial community composition were quite different between the two river stretches in December and January but were similar in June and July. However, the differences of micro-eukaryotic community composition between the two river stretches were always high during the study period. The bacterial communities in river stretch 2 contained more generalists and nutrient tolerant specialists. The bacterial nutrient tolerant specialists rapidly decreased in the low nutrient months and were replaced by the generalists. Bacteria which were involved in this shifts accounted for 29.3% of the total abundance. However, the micro-eukaryotic communities in river stretch 2 contained more moderate generalists. These moderate generalists were insensitive to the variation of nutrients and only 19.56% of the micro-eukaryotes had significant responses to the disturbance. The survival strategies caused bacterial communities had higher adaptability than eukaryotes to environmental fluctuation.
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Affiliation(s)
- Lemian Liu
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China.
| | - Shanshan Wang
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China
| | - Jianfeng Chen
- Technical Innovation Service Platform for High Value and High Quality Utilization of Marine Organism, Fuzhou University, Fuzhou 350108, China; Fujian Engineering and Technology Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fuzhou 350108, China; Fuzhou Industrial Technology Innovation Center for High Value Utilization of Marine Products, Fuzhou University, Fuzhou 350108, China.
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82
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Chaffron S, Delage E, Budinich M, Vintache D, Henry N, Nef C, Ardyna M, Zayed AA, Junger PC, Galand PE, Lovejoy C, Murray AE, Sarmento H, Acinas SG, Babin M, Iudicone D, Jaillon O, Karsenti E, Wincker P, Karp-Boss L, Sullivan MB, Bowler C, de Vargas C, Eveillard D. Environmental vulnerability of the global ocean epipelagic plankton community interactome. SCIENCE ADVANCES 2021; 7:eabg1921. [PMID: 34452910 PMCID: PMC8397264 DOI: 10.1126/sciadv.abg1921] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/09/2021] [Indexed: 05/05/2023]
Abstract
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
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Affiliation(s)
- Samuel Chaffron
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Erwan Delage
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
| | - Marko Budinich
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Vintache
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Charlotte Nef
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mathieu Ardyna
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Pedro C Junger
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, LECOB, Banyuls-sur-Mer, 66500 Paris, France
| | - Connie Lovejoy
- Département de biologie, Faculté des sciences et Institut de biologie intégrative et des systèmes (IBIS) 1030, ave de la Médecine, Université Laval, Québec, QC, Canada
| | - Alison E Murray
- Division of Earth and Ecosystem Science, Desert Research Institute, Reno, NV 89512, USA
| | - Hugo Sarmento
- Department of Hydrobiology, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, SP, Brazil
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona 08003, Spain
| | - Marcel Babin
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, Paris, France
- Takuvik International Research Laboratory, Université Laval and CNRS, Québec, QC, Canada
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples 80121, Italy
| | - Olivier Jaillon
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Eric Karsenti
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Patrick Wincker
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, 91057 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Damien Eveillard
- Université de Nantes, CNRS UMR 6004, LS2N, F-44000 Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans, Paris, France
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83
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Schwob G, Segovia NI, González-Wevar C, Cabrol L, Orlando J, Poulin E. Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean. Front Microbiol 2021; 12:703792. [PMID: 34335536 PMCID: PMC8317501 DOI: 10.3389/fmicb.2021.703792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.
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Affiliation(s)
- Guillaume Schwob
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Nicolás I. Segovia
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Universidad Católica del Norte, Coquimbo, Chile
| | - Claudio González-Wevar
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Facultad de Ciencias, Centro Fondap IDEAL, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Léa Cabrol
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Julieta Orlando
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
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84
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Latorre F, Deutschmann IM, Labarre A, Obiol A, Krabberød AK, Pelletier E, Sieracki ME, Cruaud C, Jaillon O, Massana R, Logares R. Niche adaptation promoted the evolutionary diversification of tiny ocean predators. Proc Natl Acad Sci U S A 2021; 118:e2020955118. [PMID: 34155140 PMCID: PMC8237690 DOI: 10.1073/pnas.2020955118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Unicellular eukaryotic predators play a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionarily diverse organisms have been combined into a single functional group (heterotrophic flagellates), overlooking their organismal differences. Here, we investigated four evolutionarily related species belonging to one cosmopolitan group of uncultured marine picoeukaryotic predators: marine stramenopiles (MAST)-4 (species A, B, C, and E). Co-occurrence and distribution analyses in the global surface ocean indicated contrasting patterns in MAST-4A and C, suggesting adaptation to different temperatures. We then investigated whether these spatial distribution patterns were mirrored by MAST-4 genomic content using single-cell genomics. Analyses of 69 single cells recovered 66 to 83% of the MAST-4A/B/C/E genomes, which displayed substantial interspecies divergence. MAST-4 genomes were similar in terms of broad gene functional categories, but they differed in enzymes of ecological relevance, such as glycoside hydrolases (GHs), which are part of the food degradation machinery in MAST-4. Interestingly, MAST-4 species featuring a similar GH composition (A and C) coexcluded each other in the surface global ocean, while species with a different set of GHs (B and C) appeared to be able to coexist, suggesting further niche diversification associated with prey digestion. We propose that differential niche adaptation to temperature and prey type has promoted adaptive evolutionary diversification in MAST-4. We show that minute ocean predators from the same phylogenetic group may have different biogeography and genomic content, which needs to be accounted for to better comprehend marine food webs.
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Affiliation(s)
- Francisco Latorre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aurélie Labarre
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Aleix Obiol
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo N-0316, Norway
| | - Eric Pelletier
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Michael E Sieracki
- Ocean Science Division, National Science Foundation, Alexandria, VA 22314
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, 91000 Evry, France
| | - Olivier Jaillon
- Metabolic Genomics, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology & Evolution, FR2022/Tara Oceans Global Ocean System Ecology & Evolution, 75016 Paris, France
| | - Ramon Massana
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona E-08003, Spain;
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85
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Mo Y, Peng F, Gao X, Xiao P, Logares R, Jeppesen E, Ren K, Xue Y, Yang J. Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir. MICROBIOME 2021; 9:128. [PMID: 34082826 PMCID: PMC8176698 DOI: 10.1186/s40168-021-01079-w] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity. RESULTS Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics. CONCLUSIONS Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.
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Affiliation(s)
- Yuanyuan Mo
- 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
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Feng Peng
- 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
| | - Xiaofei Gao
- 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
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xiao
- 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
| | - Ramiro Logares
- Institute of Marine Sciences, CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003 Barcelona, Spain
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, 8600 Silkeborg, Denmark
- Sino-Danish Centre for Education and Research, Beijing, 100049 China
- Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, 06800 Ankara, Turkey
- Institute of Marine Sciences, Middle East Technical University, 33731 Erdemli-Mersin, Turkey
| | - Kexin Ren
- 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
| | - Yuanyuan Xue
- 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
| | - Jun Yang
- 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
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86
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Xiong W, Jousset A, Li R, Delgado-Baquerizo M, Bahram M, Logares R, Wilden B, de Groot GA, Amacker N, Kowalchuk GA, Shen Q, Geisen S. A global overview of the trophic structure within microbiomes across ecosystems. ENVIRONMENT INTERNATIONAL 2021; 151:106438. [PMID: 33621916 DOI: 10.1016/j.envint.2021.106438] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China; Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia, Spain
| | - Benjamin Wilden
- University of Bielefeld, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany
| | - Gerard Arjen de Groot
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA Wageningen, the Netherlands
| | - Nathalie Amacker
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
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87
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Sun P, Zhang S, Wang Y, Huang B. Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea. Microorganisms 2021; 9:1104. [PMID: 34065542 PMCID: PMC8161332 DOI: 10.3390/microorganisms9051104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022] Open
Abstract
Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.
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Affiliation(s)
- Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Silu Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Ying Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
| | - Bangqin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; (S.Z.); (Y.W.); (B.H.)
- Fujian Province Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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88
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Schoenle A, Hohlfeld M, Hermanns K, Mahé F, de Vargas C, Nitsche F, Arndt H. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Commun Biol 2021; 4:501. [PMID: 33893386 PMCID: PMC8065057 DOI: 10.1038/s42003-021-02012-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/08/2021] [Indexed: 02/02/2023] Open
Abstract
Heterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
| | - Manon Hohlfeld
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Karoline Hermanns
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Frédéric Mahé
- CIRAD, UMR BGPI, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Colomban de Vargas
- CNRS, Sorbonne Université, Station Biologique de Roscoff, UMR7144, ECOMAP-Ecology of Marine Plankton, Roscoff, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara GOSEE, Paris, France
| | - Frank Nitsche
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Institute of Zoology, General Ecology, Cologne, Germany.
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89
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Wang J, Wang L, Hu W, Pan Z, Zhang P, Wang C, Wang J, Wu S, Li YZ. Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary. Environ Microbiol 2021; 23:2578-2591. [PMID: 33754415 DOI: 10.1111/1462-2920.15480] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/15/2021] [Accepted: 03/20/2021] [Indexed: 01/04/2023]
Abstract
Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.
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Affiliation(s)
- Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Lidong Wang
- National Nature Reserve Administration of Yellow River Delta, Dongying, 257091, China
| | - Weifeng Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhuo Pan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
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90
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Wan W, Gadd GM, Yang Y, Yuan W, Gu J, Ye L, Liu W. Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:2390-2403. [PMID: 33714213 DOI: 10.1111/mec.15882] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/03/2023]
Abstract
Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, UK.,State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jidong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Environmental Engineering, Guangdong Technion Israel Institute of Technology, Guangdong, China
| | - Luping Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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91
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Vernette C, Henry N, Lecubin J, de Vargas C, Hingamp P, Lescot M. The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms. Mol Ecol Resour 2021; 21:1347-1358. [PMID: 33434383 DOI: 10.1111/1755-0998.13322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 01/04/2023]
Abstract
The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the (i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes; (ii) Tara Oceans 16S/18S rRNA mi Tags; and (iii) 16S-V4 V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode data sets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.
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Affiliation(s)
- Caroline Vernette
- Aix Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nicolas Henry
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, UMR 7144, Roscoff, France
| | | | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, UMR 7144, Roscoff, France
| | - Pascal Hingamp
- Aix Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Magali Lescot
- Aix Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
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92
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Kong J, Liu X, Wang L, Huang H, Ou D, Guo J, Laws EA, Huang B. Patterns of Relative and Quantitative Abundances of Marine Bacteria in Surface Waters of the Subtropical Northwest Pacific Ocean Estimated With High-Throughput Quantification Sequencing. Front Microbiol 2021; 11:599614. [PMID: 33552014 PMCID: PMC7859494 DOI: 10.3389/fmicb.2020.599614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/21/2020] [Indexed: 01/23/2023] Open
Abstract
Bacteria play a pivotal role in shaping ecosystems and contributing to elemental cycling and energy flow in the oceans. However, few studies have focused on bacteria at a trans-basin scale, and studies across the subtropical Northwest Pacific Ocean (NWPO), one of the largest biomes on Earth, have been especially lacking. Although the recently developed high-throughput quantitative sequencing methodology can simultaneously provide information on relative abundance, quantitative abundance, and taxonomic affiliations, it has not been thoroughly evaluated. We collected surface seawater samples for high-throughput, quantitative sequencing of 16S rRNA genes on a transect across the subtropical NWPO to elucidate the distribution of bacterial taxa, patterns of their community structure, and the factors that are potentially important regulators of that structure. We used the quantitative and relative abundances of bacterial taxa to test hypotheses related to their ecology. Total 16S rRNA gene copies ranged from 1.86 × 108 to 1.14 × 109 copies L-1. Bacterial communities were distributed in distinct geographical patterns with spatially adjacent stations clustered together. Spatial considerations may be more important determinants of bacterial community structures than measured environmental variables. The quantitative and relative abundances of bacterial communities exhibited similar distribution patterns and potentially important determinants at the whole-community level, but inner-community connections and correlations with variables differed at subgroup levels. This study advanced understanding of the community structure and distribution patterns of marine bacteria as well as some potentially important determinants thereof in a subtropical oligotrophic ocean system. Results highlighted the importance of considering both the quantitative and relative abundances of members of marine bacterial communities.
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Affiliation(s)
- Jie Kong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xin Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lei Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Hao Huang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Danyun Ou
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jiayu Guo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Edward A Laws
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, United States
| | - Bangqin Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
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93
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Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China. NPJ Biofilms Microbiomes 2021; 7:15. [PMID: 33547284 PMCID: PMC7864921 DOI: 10.1038/s41522-021-00188-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/14/2021] [Indexed: 01/30/2023] Open
Abstract
Biocrusts play critical eco-functions in many drylands, however it is challenging to explore their community assembly, particularly within patched successional types and across climate zones. Here, different successional biocrusts (alga, lichen, and moss-dominated biocrusts) were collected across the northern China, and assembly of biocrust microbial communities was investigated by high-throughput sequencing combined with measurements of soil properties and microclimate environments. Bacterial and eukaryotic communities showed that the maximum and minimum community variation occurred across longitude and latitude, respectively. In the regions where all three stages of biocrusts were involved, the highest community difference existed between successional stages, and decreased with distance. The community assembly was generally driven by dispersal limitation, although neutral processes have controlled the eukaryotic community assembly in hyperarid areas. Along the succession, bacterial community had no obvious patterns, but eukaryotic community showed increasing homogeneity, with increased species sorting and decreased dispersal limitation for community assembly. Compared to early successional biocrusts, there were higher microbial mutual exclusions and more complex networks at later stages, with distinct topological features. Correlation analysis further indicated that the balance between deterministic and stochastic processes might be mediated by aridity, salinity, and total phosphorus, although the mediations were opposite for bacteria and eukaryotes.
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94
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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95
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Comparative genomics reveals new functional insights in uncultured MAST species. ISME JOURNAL 2021; 15:1767-1781. [PMID: 33452482 PMCID: PMC8163842 DOI: 10.1038/s41396-020-00885-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.
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96
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Vendl C, Nelson T, Ferrari B, Thomas T, Rogers T. Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota. BMC Microbiol 2021; 21:20. [PMID: 33421992 PMCID: PMC7796641 DOI: 10.1186/s12866-020-02076-z] [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: 03/09/2020] [Accepted: 12/20/2020] [Indexed: 12/15/2022] Open
Abstract
Background The analysis of blow microbiota has been proposed as a biomarker for respiratory health analysis in cetaceans. Yet, we lack crucial knowledge on the long-term stability of the blow microbiota and its potential changes during disease. Research in humans and mice have provided evidence that respiratory disease is accompanied by a shift in microbial communities of the airways. We investigate here the stability of the community composition of the blow microbiota for 13 captive bottlenose dolphins over eight months including both sick and healthy individuals. We used barcoded tag sequencing of the bacterial 16S rRNA gene. Four of the dolphins experienced distinct medical conditions and received systemic antimicrobial treatment during the study. Results We showed that each dolphin harboured a unique community of zero-radius operational taxonomic units (zOTUs) that was present throughout the entire sampling period (‘intra-core’). Although for most dolphins there was significant variation over time, overall the intra-core accounted for an average of 73% of relative abundance of the blow microbiota. In addition, the dolphins shared between 8 and 66 zOTUs on any of the sampling occasions (‘inter-core’), accounting for a relative abundance between 17 and 41% of any dolphin’s airway microbiota. The majority of the intra-core and all of the inter-core zOTUs in this study are commonly found in captive and free-ranging dolphins and have previously been reported from several different body sites. While we did not find a clear effect of microbial treatment on blow microbiota, age and sex of the dolphins did have such an effect. Conclusions The airways of dolphins were colonized by an individual intra-core ‘signature’ that varied in abundance relative to more temporary bacteria. We speculate that the intra-core bacteria interact with the immune response of the respiratory tract and support its function. This study provides the first evidence of individual-specific airway microbiota in cetaceans that is stable over eight months. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02076-z.
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Affiliation(s)
- Catharina Vendl
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Tiffanie Nelson
- Queensland Facility for Advanced Bioinformatics, Griffith University, Gold Coast, Southport, QLD, 4215, Australia
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Tracey Rogers
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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97
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Lannes R, Cavaud L, Lopez P, Bapteste E. Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur. Genome Biol Evol 2020; 13:6039174. [PMID: 33325996 PMCID: PMC7851587 DOI: 10.1093/gbe/evaa261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
Recently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultrasmall size fractions from marine samples (<0.22 µm) gathered worldwide by the Tara Oceans Expedition. This first finding suggested that prokaryotic nanoorganisms, phylogenetically distantly related to the known CPR and DPANN groups, could collectively impact carbon cycling and carbon fixation across the world's ocean. To extend our mining of the functional and taxonomic microbial dark matter from the ultrasmall size fraction from the Tara Oceans Expedition, we investigated the distribution of 28 metabolic pathways associated with the cycling of carbon, methane, nitrogen, and sulfur. For all of these pathways, we report the existence not only of novel metabolic homologs in the ultrasmall size fraction of the oceanic microbiome, associated with nanoorganisms belonging to the CPR and DPANN lineages, but also of metabolic homologs exclusively found in marine host taxa belonging to other (still unassigned) microbial lineages. Therefore, we conclude that marine nanoorganisms contribute to a greater diversity of key biogeochemical cycles than currently appreciated. In particular, we suggest that oceanic nanoorganisms may be involved in a metabolic loop around Acetyl-CoA, have an underappreciated genetic potential to degrade methane, contribute to sustaining redox-reactions by producing Coenzyme F420, and affect sulfur cycling, notably as they harbor a complete suite of homologs of enzymes of the SOX system.
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Affiliation(s)
- Romain Lannes
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Louise Cavaud
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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98
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Aguirre de Cárcer D. Experimental and computational approaches to unravel microbial community assembly. Comput Struct Biotechnol J 2020; 18:4071-4081. [PMID: 33363703 PMCID: PMC7736701 DOI: 10.1016/j.csbj.2020.11.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Microbial communities have a preponderant role in the life support processes of our common home planet Earth. These extremely diverse communities drive global biogeochemical cycles, and develop intimate relationships with most multicellular organisms, with a significant impact on their fitness. Our understanding of their composition and function has enjoyed a significant thrust during the last decade thanks to the rise of high-throughput sequencing technologies. Intriguingly, the diversity patterns observed in nature point to the possible existence of fundamental community assembly rules. Unfortunately, these rules are still poorly understood, despite the fact that their knowledge could spur a scientific, technological, and economic revolution, impacting, for instance, agricultural, environmental, and health-related practices. In this minireview, I recapitulate the most important wet lab techniques and computational approaches currently employed in the study of microbial community assembly, and briefly discuss various experimental designs. Most of these approaches and considerations are also relevant to the study of microbial microevolution, as it has been shown that it can occur in ecological relevant timescales. Moreover, I provide a succinct review of various recent studies, chosen based on the diversity of ecological concepts addressed, experimental designs, and choice of wet lab and computational techniques. This piece aims to serve as a primer to those new to the field, as well as a source of new ideas to the more experienced researchers.
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99
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Zhang G, Bai J, Tebbe CC, Zhao Q, Jia J, Wang W, Wang X, Yu L. Salinity controls soil microbial community structure and function in coastal estuarine wetlands. Environ Microbiol 2020; 23:1020-1037. [PMID: 33073448 DOI: 10.1111/1462-2920.15281] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig, 38116, Germany
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China.,Ecology Institute of Shandong Academy of Sciences, Jinan, 250103, China
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Walters KE, Martiny JBH. Alpha-, beta-, and gamma-diversity of bacteria varies across habitats. PLoS One 2020; 15:e0233872. [PMID: 32966309 PMCID: PMC7510982 DOI: 10.1371/journal.pone.0233872] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
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Affiliation(s)
- Kendra E. Walters
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
- * E-mail:
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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