1
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Wang B, Hu K, Li C, Zhang Y, Hu C, Liu Z, Ding J, Chen L, Zhang W, Fang J, Zhang H. Geographic distribution of bacterial communities of inland waters in China. Environ Res 2024; 249:118337. [PMID: 38325783 DOI: 10.1016/j.envres.2024.118337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.
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Affiliation(s)
- Binhao Wang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Kaiming Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chuqiao Li
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yinan Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chao Hu
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhiquan Liu
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Jiafeng Ding
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Wei Zhang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Jing Fang
- Hangzhou Xixi National Wetland Park Ecology & Culture Research Center, Hangzhou, 310030, China; Zhejiang Xixi Wetland Ecosystem National Observation and Research Station, Hangzhou, 310030, China
| | - Hangjun Zhang
- School of Engineering, Hangzhou Normal University, Hangzhou, 310018, China; Hangzhou International Urbanology Research Center and Center for Zhejiang Urban Governance Studies, Hangzhou, 311121, China.
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2
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Macé B, Mouillot D, Dalongeville A, Bruno M, Deter J, Varenne A, Gudefin A, Boissery P, Manel S. The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Mol Ecol 2024:e17373. [PMID: 38703047 DOI: 10.1111/mec.17373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/08/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.
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Affiliation(s)
- Bastien Macé
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | | | - Morgane Bruno
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Andromède Océanologie, Mauguio, France
| | - Alix Varenne
- Université Côte d'Azur, CNRS, ECOSEAS, Nice, France
- Ecocean, Montpellier, France
| | | | - Pierre Boissery
- Agence de l'eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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3
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Logares R. Decoding populations in the ocean microbiome. Microbiome 2024; 12:67. [PMID: 38561814 PMCID: PMC10983722 DOI: 10.1186/s40168-024-01778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.
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Affiliation(s)
- Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, 08003, Spain.
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4
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Wang C, Song Z, Zhang H, Sun Y, Hu X. Deciphering variations in the surficial bacterial compositions and functional profiles in the intersection between North and South Yellow Sea. Mar Environ Res 2024; 195:106355. [PMID: 38244366 DOI: 10.1016/j.marenvres.2024.106355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/22/2024]
Abstract
The coastal ocean systems play paramount role in the nutrient biogeochemistry because of its interconnected environment. To gain a novel insight into coupling relationships between bacterial community, functioning properties and nutrient metabolism, we conducted analysis on the patterns and driving factors of planktonic bacterial functional community across subsurface water of marine ranching near the Yellow Sea in both summer and winter. Illumina HiSeq Sequencing and a corresponding set of biogeochemical data were used to assess distribution patterns of taxa, adaptive mechanism and metabolic function. Results demonstrated that Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota were dominant phyla both in summer and winter. Taxonomic profiles related to nutrient variation were found to be highly correlated with Dissolved Oxygen (DO) and Chlorophyll fluorescence (FLUO), and distinct diversity differences were also found between summer and winter samples. Functional activity in summer associated with the relative abundance of phototrophy and photoautotrophy were the highest in the subsurface water, while in winter the dominant functional properties were mainly include chemoheterotrophy and aerobic_ chemoheterotrophy. A significant difference related to functional activity between summer and winter, mainly representing ligninolysis and iron_respiration. In general, our study provides a framework for understanding the relative importance of environmental factors, temperature variation and nutrient availability in shaping the metabolic processes of aquatic microorganisms, particularly in ocean mariculture systems.
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Affiliation(s)
- Caixia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Yantai Key Laboratory of Pharmacology of Traditional Chinese Medicine in Tumor Metabolism, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, 264003, China
| | - Zenglei Song
- Yantai Vocational College, Yantai, 264003, China
| | - Haikun Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China
| | - Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266237, China.
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5
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Wang J, Zhu YG, Tiedje JM, Ge Y. Global biogeography and ecological implications of cobamide-producing prokaryotes. ISME J 2024; 18:wrae009. [PMID: 38366262 PMCID: PMC10900890 DOI: 10.1093/ismejo/wrae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/01/2024] [Accepted: 01/19/2024] [Indexed: 02/18/2024]
Abstract
Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.
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Affiliation(s)
- Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, United States
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Gralka M. Searching for Principles of Microbial Ecology Across Levels of Biological Organization. Integr Comp Biol 2023; 63:1520-1531. [PMID: 37280177 PMCID: PMC10755194 DOI: 10.1093/icb/icad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/21/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.
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Affiliation(s)
- Matti Gralka
- Systems Biology lab, Amsterdam Institute for Life and Environment (A-LIFE), Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV, The Netherlands
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7
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Campos PM, Lucid MK, Ehlers S, Walke JB. Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs ( Rana luteiventris) in a montane landscape. Curr Res Microb Sci 2023; 6:100213. [PMID: 38187998 PMCID: PMC10770434 DOI: 10.1016/j.crmicr.2023.100213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.
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Affiliation(s)
- Philip M. Campos
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
| | - Michael K. Lucid
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- Selkirk Wildlife Science, LLC, PO Box 733, Sandpoint, ID 83864, USA
| | - Shannon Ehlers
- Idaho Department of Fish and Game, 2885 Kathleen Ave., Coeur d'Alene, ID 83815, USA
- U.S. Fish and Wildlife Service, 287 Westside Rd., Bonners Ferry, ID 83805, USA
| | - Jenifer B. Walke
- Department of Biology, Eastern Washington University, 1175 Washington St., Cheney, WA 99004, USA
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8
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Milke F, Meyerjürgens J, Simon M. Ecological mechanisms and current systems shape the modular structure of the global oceans' prokaryotic seascape. Nat Commun 2023; 14:6141. [PMID: 37783696 PMCID: PMC10545751 DOI: 10.1038/s41467-023-41909-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/24/2023] [Indexed: 10/04/2023] Open
Abstract
Major biogeographic features of the microbial seascape in the oceans have been established and their underlying ecological mechanisms in the (sub)tropical oceans and the Pacific Ocean identified. However, we still lack a unifying understanding of how prokaryotic communities and biogeographic patterns are affected by large-scale current systems in distinct ocean basins and how they are globally shaped in line with ecological mechanisms. Here we show that prokaryotic communities in the epipelagic Pacific and Atlantic Ocean, in the southern Indian Ocean, and the Mediterranean Sea are composed of modules of co-occurring taxa with similar environmental preferences. The relative partitioning of these modules varies along latitudinal and longitudinal gradients and are related to different hydrographic and biotic conditions. Homogeneous selection and dispersal limitation were identified as the major ecological mechanisms shaping these communities and their free-living (FL) and particle-associated (PA) fractions. Large-scale current systems govern the dispersal of prokaryotic modules leading to the highest diversity near subtropical fronts.
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Affiliation(s)
- Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany.
| | - Jens Meyerjürgens
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, D-26129, Oldenburg, Germany.
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9
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Wutkowska M, Vader A, Logares R, Pelletier E, Gabrielsen TM. Linking extreme seasonality and gene expression in Arctic marine protists. Sci Rep 2023; 13:14627. [PMID: 37669980 PMCID: PMC10480425 DOI: 10.1038/s41598-023-41204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023] Open
Abstract
At high latitudes, strong seasonal differences in light availability affect marine organisms and regulate the timing of ecosystem processes. Marine protists are key players in Arctic aquatic ecosystems, yet little is known about their ecological roles over yearly cycles. This is especially true for the dark polar night period, which up until recently was assumed to be devoid of biological activity. A 12 million transcripts catalogue was built from 0.45 to 10 μm protist assemblages sampled over 13 months in a time series station in an Arctic fjord in Svalbard. Community gene expression was correlated with seasonality, with light as the main driving factor. Transcript diversity and evenness were higher during polar night compared to polar day. Light-dependent functions had higher relative expression during polar day, except phototransduction. 64% of the most expressed genes could not be functionally annotated, yet up to 78% were identified in Arctic samples from Tara Oceans, suggesting that Arctic marine assemblages are distinct from those from other oceans. Our study increases understanding of the links between extreme seasonality and biological processes in pico- and nanoplanktonic protists. Our results set the ground for future monitoring studies investigating the seasonal impact of climate change on the communities of microbial eukaryotes in the High Arctic.
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Affiliation(s)
- Magdalena Wutkowska
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway.
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Tove M Gabrielsen
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
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Kim HJ, Kim KE, Kim YJ, Kang H, Shin JW, Kim S, Lee SH, Jung SW, Lee TK. Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding. Int J Mol Sci 2023; 24:13561. [PMID: 37686367 PMCID: PMC10487856 DOI: 10.3390/ijms241713561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.
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Affiliation(s)
- Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hangoo Kang
- Vessel Operation & Observation Team, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea;
| | - Ji Woo Shin
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Soohyun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Sang Heon Lee
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
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11
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Briscoe L, Halperin E, Garud NR. SNV-FEAST: microbial source tracking with single nucleotide variants. Genome Biol 2023; 24:101. [PMID: 37121994 PMCID: PMC10150486 DOI: 10.1186/s13059-023-02927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.
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Affiliation(s)
- Leah Briscoe
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Nandita R Garud
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.
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12
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Power JF, Lowe CL, Carere CR, McDonald IR, Cary SC, Stott MB. Temporal dynamics of geothermal microbial communities in Aotearoa-New Zealand. Front Microbiol 2023; 14:1094311. [PMID: 37020721 PMCID: PMC10068964 DOI: 10.3389/fmicb.2023.1094311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023] Open
Abstract
Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60–70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.
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Affiliation(s)
- Jean F. Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Caitlin L. Lowe
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
| | - Ian R. McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
- S. Craig Cary,
| | - Matthew B. Stott
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- *Correspondence: Matthew B. Stott,
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13
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Doane MP, Ostrowski M, Brown M, Bramucci A, Bodrossy L, van de Kamp J, Bissett A, Steinberg P, Doblin MA, Seymour J. Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions. Environ Microbiol 2023. [PMID: 36700447 DOI: 10.1111/1462-2920.16341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high- and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.
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Affiliation(s)
- Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Martin Ostrowski
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mark Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, New South Wales, Australia
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | | | | | - Peter Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Centre for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
| | - Martina A Doblin
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
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14
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Rogers AD, Appeltans W, Assis J, Ballance LT, Cury P, Duarte C, Favoretto F, Hynes LA, Kumagai JA, Lovelock CE, Miloslavich P, Niamir A, Obura D, O'Leary BC, Ramirez-Llodra E, Reygondeau G, Roberts C, Sadovy Y, Steeds O, Sutton T, Tittensor DP, Velarde E, Woodall L, Aburto-Oropeza O. Discovering marine biodiversity in the 21st century. Adv Mar Biol 2022; 93:23-115. [PMID: 36435592 DOI: 10.1016/bs.amb.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.
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Affiliation(s)
- Alex D Rogers
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom.
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Oostende, Belgium
| | - Jorge Assis
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Lisa T Ballance
- Marine Mammal Institute, Oregon State University, Newport, OR, United States
| | | | - Carlos Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Fabio Favoretto
- Autonomous University of Baja California Sur, La Paz, Baja California Sur, Mexico
| | - Lisa A Hynes
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Joy A Kumagai
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | - Catherine E Lovelock
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Patricia Miloslavich
- Scientific Committee on Oceanic Research (SCOR), College of Earth, Ocean and Environment, University of Delaware, Newark, DE, United States; Departamento de Estudios Ambientales, Universidad Simón Bolívar, Venezuela & Scientific Committee for Oceanic Research (SCOR), Newark, DE, United States
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute, Frankfurt am Main, Germany
| | | | - Bethan C O'Leary
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom; Department of Environment and Geography, University of York, York, United Kingdom
| | - Eva Ramirez-Llodra
- REV Ocean, Lysaker, Norway; Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Gabriel Reygondeau
- Yale Center for Biodiversity Movement and Global Change, Yale University, New Haven, CT, United States; Nippon Foundation-Nereus Program, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Callum Roberts
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Yvonne Sadovy
- School of Biological Sciences, Swire Institute of Marine Science, The University of Hong Kong, Hong Kong
| | - Oliver Steeds
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom
| | - Tracey Sutton
- Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, Dania Beach, FL, United States
| | | | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Veracruz, Mexico
| | - Lucy Woodall
- Nekton Foundation, Begbroke Science Park, Oxford, United Kingdom; Department of Zoology, University of Oxford, Oxford, United Kingdom
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15
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Malard LA, Avila-Jimenez ML, Schmale J, Cuthbertson L, Cockerton L, Pearce DA. Aerobiology over the Southern Ocean - Implications for bacterial colonization of Antarctica. Environ Int 2022; 169:107492. [PMID: 36174481 DOI: 10.1016/j.envint.2022.107492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/27/2022] [Accepted: 08/27/2022] [Indexed: 06/16/2023]
Abstract
Parts of the Antarctic are experiencing dramatic ecosystem change due to rapid and record warming, which may weaken biogeographic boundaries and modify dispersal barriers, increasing the risk of biological invasions. In this study, we collected air samples from 100 locations around the Southern Ocean to analyze bacterial biodiversity in the circumpolar air around the Antarctic continent, as understanding dispersal processes is paramount to assessing the risks of microbiological invasions. We also compared the Southern Ocean air bacterial biodiversity to non-polar ecosystems to identify the potential origin of these Southern Ocean air microorganisms. The bacterial diversity in the air had both local and global origins and presented low richness overall but high heterogeneity, compatible with a scenario whereby samples are composed of a suite of different species in very low relative abundances. Only 4% of Amplicon Sequence Variants (ASVs) were identified in both polar and non-polar air masses, suggesting that the polar air mass over the Southern Ocean can act as a selective dispersal filter. Furthermore, both microbial diversity and community structure both varied significantly with meteorological data, suggesting that regional bacterial biodiversity could be sensitive to changes in weather conditions, potentially altering the existing pattern of microbial deposition in the Antarctic.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | | | - Julia Schmale
- Extreme Environments Research Laboratory, École Polytechnique Fédérale de Lausanne, Sion, Switzerland
| | - Lewis Cuthbertson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom
| | - Luke Cockerton
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom
| | - David A Pearce
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, NEwcastle-upon-Tyne NE1 8ST, United Kingdom; British Antarctic Survey, Natural Environemnt Research Council, High Cross, Madingley Road, Cambridge BCB3 0ET, United Kingdom.
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16
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Castillo DJ, Dithugoe CD, Bezuidt OK, Makhalanyane TP. Microbial ecology of the Southern Ocean. FEMS Microbiol Ecol 2022; 98:6762916. [PMID: 36255374 DOI: 10.1093/femsec/fiac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 09/23/2022] [Accepted: 10/14/2022] [Indexed: 01/21/2023] Open
Abstract
The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.
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Affiliation(s)
- Diego J Castillo
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Choaro D Dithugoe
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Oliver K Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Microbiome Research Group, University of Pretoria, Pretoria 0028, South Africa.,Department of Science and Innovation/South African Research Chair in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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17
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Korlević M, Markovski M, Herndl GJ, Najdek M. Temporal variation in the prokaryotic community of a nearshore marine environment. Sci Rep 2022; 12:16859. [PMID: 36207405 PMCID: PMC9547059 DOI: 10.1038/s41598-022-20954-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Prokaryotic communities inhabiting surface waters of temperate areas exhibit patterns of seasonal succession. Generally, studies describing these temporal changes are not performed in the proximity to the coast. In the present study, temporal variation of these communities was determined in surface waters at two stations located in the close proximity to the eastern shore of the northern Adriatic Sea. Sequencing of the V4 region of the 16S rRNA gene identified the highest community richness in December with distinct shifts in community structure between periods from April to May, June to October, and November to March. Temperature was shown to be the main environmental force explaining community temporal variation. The NS5 marine group, uncultured Cryomorphaceae, SAR86 clade, and Synechococcus were present throughout the year. Members without know relatives within Rhodobacteraceae and the NS4 marine group were more pronounced in the period from April to May, the AEGEAN-169 marine group, SAR11 subclade III, and HIMB11 in the period from June to October, and SAR11 subclade Ia and Archaea in the period from November to March. Litoricola and OM60 (NOR5) clade were characteristic for both the community sampled from April to May and November to March. Taken together, prokaryotic communities inhabiting nearshore surface waters exhibit a general pattern in community structure similar to other surface associated assemblages of temperate areas. However, the identified specific community composition and temporal patterns differ from other coastal areas.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia.
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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18
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Liu J, Qiao Y, Xin Y, Li Y, Zhang XH. 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 DOI: 10.1128/aem.01169-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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19
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Raes EJ, Tolman J, Desai D, Ratten JM, Zorz J, Robicheau BM, Haider D, LaRoche J. Seasonal bacterial niche structures and chemolithoautotrophic ecotypes in a North Atlantic fjord. Sci Rep 2022; 12:15335. [PMID: 36097189 PMCID: PMC9468339 DOI: 10.1038/s41598-022-19165-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022] Open
Abstract
Quantifying the temporal change of bacterial communities is essential to understanding how both natural and anthropogenic pressures impact the functions of coastal marine ecosystems. Here we use weekly microbial DNA sampling across four years to show that bacterial phyla have distinct seasonal niches, with a richness peak in winter (i.e., an inverse relationship with daylength). Our results suggest that seasonal fluctuations, rather than the kinetic energy or resource hypotheses, dominated the pattern of bacterial diversity. These findings supplement those from global analyses which lack temporal replication and present few data from winter months in polar and temperate regions. Centered log-ratio transformed data provided new insights into the seasonal niche partitioning of conditionally rare phyla, such as Modulibacteria, Verrucomicrobiota, Synergistota, Deinococcota, and Fermentibacterota. These patterns could not be identified using the standard practice of ASV generation followed by rarefaction. Our study provides evidence that five globally relevant ecotypes of chemolithoautotrophic bacteria from the SUP05 lineage comprise a significant functional group with varying seasonal dominance patterns in the Bedford Basin.
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Affiliation(s)
- Eric J Raes
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada. .,Flourishing Oceans, Minderoo Foundation, Broadway, WA, 6009, Australia.
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.,Department of Pharmacology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Jackie Zorz
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Brent M Robicheau
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Diana Haider
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.,Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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20
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Xu D, Kong H, Yang EJ, Wang Y, Li X, Sun P, Jiao N, Lee Y, Jung J, Cho KH. Spatial dynamics of active microeukaryotes along a latitudinal gradient: Diversity, assembly process, and co-occurrence relationships. Environ Res 2022; 212:113234. [PMID: 35390306 DOI: 10.1016/j.envres.2022.113234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Recent global warming is profoundly and increasingly influencing the Arctic ecosystem. Understanding how microeukaryote communities respond to changes in the Arctic Ocean is crucial for understanding their roles in the biogeochemical cycles of nutrients and elements. Between July 22 and August 19, 2016, during cruise ARA07, seawater samples were collected along a latitudinal transect extending from the East Sea of Korea to the central Arctic Ocean. Environmental RNA was extracted and the V4 hypervariable regions of the reverse transcribed SSU rRNA were amplified. The sequences generated by high throughput sequencing were clustered into zero-radius OTUs (ZOTUs), and the taxonomic identities of each ZOTU were assigned using SINTAX against the PR2 database. Thus, the diversity, community composition, and co-occurrence networks of size fractionated microeukaryotes were revealed. The present study found: 1) the alpha diversity of pico- and nano-sized microeukaryotes showed a latitudinal diversity gradient; 2) three distinct communities were identified, i.e., the Leg-A, Leg-B surface, and Leg-B subsurface chlorophyll a maximum (SCM) groups; 3) distinct network structure and composition were found in the three groups; and 4) water temperature was identified as the primary factor driving both the alpha and beta diversities of microeukaryotes. This study conducted a comprehensive and systematic survey of active microeukaryotes along a latitudinal gradient, elucidated the diversity, community composition, co-occurrence relationships, and community assembly processes among major microeukaryote assemblages, and will help shed more light on our understanding of the responses of microeukaryote communities to the changing Arctic Ocean.
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Affiliation(s)
- Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
| | - Hejun Kong
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Xinran Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - 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; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
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21
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Wennberg AC, Meland S, Grung M, Lillicrap A. Unravelling reasons for variability in the OECD 306 marine biodegradation test. Chemosphere 2022; 300:134476. [PMID: 35367489 DOI: 10.1016/j.chemosphere.2022.134476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
The recommended test for assessing if a chemical can be biodegraded in the marine environment is performed according to the Organisation for Economic Cooperation and Development Marine biodegradation test guideline (OECD 306). However, this test is known to generate highly variable test results when comparing interlaboratory test results for the same compound. One reason can be the relatively low bacterial content compared to the inoculum used for OECD readily biodegradation tests (OECD 301). Some of the variability in data obtained from OECD 306 tests can also be due to the flexibility on how to store the seawater inoculum before starting a test. Another variable in the seawater inoculum is the source of seawater used by different laboratories, i.e., geographical location and anthropogenic activities at the source. In this study, the effect of aging seawater and the source of seawater (sample time and depth) were investigated to determine differences in the biodegradation of the reference compound aniline. Aging the seawater before starting the test is recommended in OECD 306 to reduce the background levels of organic carbon in the water. However, it also functions to acclimatize the bacterial community from the environmental source temperature to the test temperature (normally 20 °C). Herein, the microbial community was monitored using flowcytometer during the aging process. As expected, the microbial community changed over time. In one experiment, aging significantly improved the biodegradation of aniline, while in two experiments, there was no significant difference in biodegradation. Interestingly however, there was significant variability in the biodegradation of aniline between sampling seasons and depths, even when all experiments were performed in the same lab, by the same operator and seawater obtained from the same source. This highlights the need for a more robust and consistent microbial inoculum source to reduce variability in seawater biodegradation tests.
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Affiliation(s)
| | - Sondre Meland
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway
| | - Merete Grung
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway
| | - Adam Lillicrap
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway
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22
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King NG, Smale DA, Thorpe JM, McKeown NJ, Andrews AJ, Browne R, Malham SK. Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters. Microb Ecol 2022:10.1007/s00248-022-02083-9. [PMID: 35881247 DOI: 10.1007/s00248-022-02083-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK.
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK.
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
| | - Niall J McKeown
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Adam J Andrews
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Ronan Browne
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Shelagh K Malham
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
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23
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Hoarfrost A, Aptekmann A, Farfañuk G, Bromberg Y. Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. Nat Commun 2022; 13:2606. [PMID: 35545619 PMCID: PMC9095714 DOI: 10.1038/s41467-022-30070-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/30/2022] [Indexed: 12/22/2022] Open
Abstract
The majority of microbial genomes have yet to be cultured, and most proteins identified in microbial genomes or environmental sequences cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. Here we present LookingGlass, a deep learning model encoding contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, that distinguishes reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned via transfer learning to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth. Computational methods to analyse microbial systems rely on reference databases which do not capture their full functional diversity. Here the authors develop a deep learning model and apply it using transfer learning, creating biologically useful models for multiple different tasks.
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Affiliation(s)
- A Hoarfrost
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ, 08873, USA. .,NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| | - A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08901, USA
| | - G Farfañuk
- Department of Biological Chemistry, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08901, USA.
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24
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Song W, Liu J, Qin W, Huang J, Yu X, Xu M, Stahl D, Jiao N, Zhou J, Tu Q. Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean. mBio 2022;:e0383221. [PMID: 35285696 DOI: 10.1128/mbio.03832-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.
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25
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Dlugosch L, Poehlein A, Wemheuer B, Pfeiffer B, Badewien TH, Daniel R, Simon M. Significance of gene variants for the functional biogeography of the near-surface Atlantic Ocean microbiome. Nat Commun 2022; 13:456. [PMID: 35075131 PMCID: PMC8786918 DOI: 10.1038/s41467-022-28128-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 01/06/2022] [Indexed: 01/21/2023] Open
Abstract
Microbial communities are major drivers of global elemental cycles in the oceans due to their high abundance and enormous taxonomic and functional diversity. Recent studies assessed microbial taxonomic and functional biogeography in global oceans but microbial functional biogeography remains poorly studied. Here we show that in the near-surface Atlantic and Southern Ocean between 62°S and 47°N microbial communities exhibit distinct taxonomic and functional adaptations to regional environmental conditions. Richness and diversity showed maxima around 40° latitude and intermediate temperatures, especially in functional genes (KEGG-orthologues, KOs) and gene profiles. A cluster analysis yielded three clusters of KOs but five clusters of genes differing in the abundance of genes involved in nutrient and energy acquisition. Gene profiles showed much higher distance-decay rates than KO and taxonomic profiles. Biotic factors were identified as highly influential in explaining the observed patterns in the functional profiles, whereas temperature and biogeographic province mainly explained the observed taxonomic patterns. Our results thus indicate fine-tuned genetic adaptions of microbial communities to regional biotic and environmental conditions in the Atlantic and Southern Ocean. The taxonomic and functional diversity of marine microbial communities are shaped by both environmental and biotic factors. Here, the authors investigate the functional biogeography of epipelagic prokaryotic communities along a 13,000-km transect in the Southern and Atlantic Oceans, showing finely tuned genetic adaptations to regional conditions.
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Affiliation(s)
- Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Birgit Pfeiffer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Thomas H Badewien
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129, Oldenburg, Germany. .,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstr. 231, D-26129, Oldenburg, Germany.
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26
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Aravindraja C, Viszwapriya D, Valliammai A, Pandian SK. Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar. Curr Microbiol 2022; 79:60. [PMID: 34982232 DOI: 10.1007/s00284-021-02692-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 10/01/2021] [Indexed: 11/03/2022]
Abstract
The present study aims to carefully delineate the bacterial community composition in marine sediments from different geographical coastal regions of Palk Bay and Gulf of Mannar that are known for human recreational activities. Bacterial richness in different marine sediments was assessed using 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) which is a widely deployed fingerprinting technique. The DGGE profiles revealed that the bacterial community profiles of sediment from different coastal regions were complex and dynamic. The most dominant phylum present in the marine sediment samples were Proteobacteria followed by Cyanobacteria, Bacteriodetes, Firmicutes, Acidobacteria, and Actinobacteria. Cosmopolitan presence of Thioalkalivibrio sp. was observed in all the marine sediments. Sequencing of the abundant band reveals the presence of Vibrio spp. in all the marine sediments. Comparative illumina data analysis revealed the presence of 51 different Vibrio species in which Vibrio alginolyticus holds the highest abundance (67.2%) followed by V. harveyi (13.5%). This is the one of the very few reports that compared the complex microbial community composition of the marine sediments of different geographical regions of unexplored coastal region. Further in-depth analysis needs to be taken to understand the presence of complex microbial compositions and their functions through high-throughput whole metagenome sequencing and metaproteomic approaches.
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27
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Amaral‐Zettler LA. Latitudinal Diversity Gradients (LDGs) and macroalgal microbiomes: A chimera of biotic and abiotic effects? J Phycol 2021; 57:1679-1680. [PMID: 34875101 PMCID: PMC9300020 DOI: 10.1111/jpy.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Linda A. Amaral‐Zettler
- NIOZ Royal Netherlands Institute for Sea ResearchP.O. Box 59Den Burg1790 ABThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsThe University of AmsterdamAmsterdam1090 GEThe Netherlands
- The Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusetts02543USA
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28
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Erez A, Lopez JG, Meir Y, Wingreen NS. Enzyme regulation and mutation in a model serial-dilution ecosystem. Phys Rev E 2021; 104:044412. [PMID: 34781576 DOI: 10.1103/physreve.104.044412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/20/2021] [Indexed: 11/07/2022]
Abstract
Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in diversity is not a curiosity-microbial diversity has been linked to outcomes of substantial ecological and medical importance. However, the mechanisms underlying microbial diversity are still under debate, as simple mathematical models only permit as many species to coexist as there are resources. A plethora of mechanisms have been proposed to explain the origins of microbial diversity, but many of these analyses omit a key property of real microbial ecosystems: the propensity of the microbes themselves to change their growth properties within and across generations. In order to explore the impact of this key property on microbial diversity, we expand upon a recently developed model of microbial diversity in fluctuating environments. We implement changes in growth strategy in two distinct ways. First, we consider the regulation of a cell's enzyme levels within short, ecological times, and second we consider evolutionary changes driven by mutations across generations. Interestingly, we find that these two types of microbial responses to the environment can have drastically different outcomes. Enzyme regulation may collapse diversity over long enough times while, conversely, strategy-randomizing mutations can produce a "rich-get-poorer" effect that promotes diversity. This paper makes explicit, using a simple serial-dilutions framework, the conflicting ways that microbial adaptation and evolution can affect community diversity.
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Affiliation(s)
- Amir Erez
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.,Racah Institute of Physics, The Hebrew University, Jerusalem 9190401, Israel
| | - Jaime G Lopez
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Yigal Meir
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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29
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Müller O, Seuthe L, Pree B, Bratbak G, Larsen A, Paulsen ML. How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments. Microorganisms 2021; 9:2378. [PMID: 34835503 PMCID: PMC8617753 DOI: 10.3390/microorganisms9112378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022] Open
Abstract
In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton-bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with 'mutualistic phytoplankton'-Gammaproteobacteria interactions dominating in the pre-bloom phase and 'substrate-dependent phytoplankton'-Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics.
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Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (B.P.); (G.B.)
| | - Lena Seuthe
- Department of Arctic and Marine Biology, UiT—The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Bernadette Pree
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (B.P.); (G.B.)
| | - Gunnar Bratbak
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway; (B.P.); (G.B.)
| | - Aud Larsen
- Molecular Ecology Group, NORCE, 5008 Bergen, Norway;
| | - Maria Lund Paulsen
- Arctic Research Center, Department of Ecoscience, Aarhus University, 8600 Silkeborg, Denmark;
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30
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Qin C, Bartelme R, Chung YA, Fairbanks D, Lin Y, Liptzin D, Muscarella C, Naithani K, Peay K, Pellitier P, St. Rose A, Stanish L, Werbin Z, Zhu K. From DNA sequences to microbial ecology: Wrangling NEON soil microbe data with the
neonMicrobe
R package. Ecosphere 2021. [DOI: 10.1002/ecs2.3842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Clara Qin
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
| | - Ryan Bartelme
- BIO5 Institute University of Arizona Tucson Arizona USA
- CyVerse.org Tucson Arizona USA
| | - Y. Anny Chung
- Department of Plant Biology and Department of Plant Pathology University of Georgia Athens Georgia USA
| | - Dawson Fairbanks
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Yang Lin
- Department of Soil and Water Sciences University of Florida Gainesville Florida USA
| | | | - Chance Muscarella
- Department of Environmental Science University of Arizona Tucson Arizona USA
| | - Kusum Naithani
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Kabir Peay
- Department of Biology Stanford University Stanford California USA
| | - Peter Pellitier
- Department of Biology Stanford University Stanford California USA
| | - Ayanna St. Rose
- Department of Biological Sciences University of Arkansas Fayetteville Fayetteville Arkansas USA
| | - Lee Stanish
- Institute of Arctic and Alpine Research University of Colorado Boulder USA
| | - Zoey Werbin
- Department of Biology Boston University Boston Massachusetts USA
| | - Kai Zhu
- Department of Environmental Studies University of California Santa Cruz Santa Cruz California USA
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31
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Muriel-Millán LF, Millán-López S, Pardo-López L. Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics. Appl Microbiol Biotechnol 2021; 105:7171-7185. [PMID: 34515846 DOI: 10.1007/s00253-021-11569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad Universitaria, CDMX, Mexico.
| | - Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
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Yang Y, Wang T, Chen J, Wu L, Wu X, Zhang W, Luo J, Xia J, Meng Z, Liu X. Whole-genome sequencing of brown-marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences. Mol Ecol Resour 2021; 22:711-723. [PMID: 34455708 DOI: 10.1111/1755-0998.13494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/29/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
The brown-marbled grouper (Epinephelus fuscoguttatus) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high-quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among which 23,862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown-marbled grouper and humpback grouper were clustered into one clade that separated approximately 11-23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown-marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown-marbled grouper. A total of 305 expanded gene families were detected in the brown-marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth-related quantitative trait loci was detected in 32,332,447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth-related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Tong Wang
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Jingfang Chen
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Lina Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China
| | - Weiwei Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Key Laboratory of Tropical Biological Resources of Education, Marine Sciences College of Hainan University, Haikou, China
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Life Sciences School, Sun Yat-sen University, Guangzhou, China.,Southern Laboratory of Ocean Science and Engineering, Zhuhai, China
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Wood JL, Neil WC, Wade SA. High Taxonomic Diversity in Ship Bilges Presents Challenges for Monitoring Microbial Corrosion and Opportunity To Utilize Community Functional Profiling. Appl Environ Microbiol 2021; 87:e0089021. [PMID: 34232755 DOI: 10.1128/AEM.00890-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the key areas in which microbially influenced corrosion (MIC) has been found to be a problem is in the bilges of maritime vessels. To establish effective biological monitoring protocols, baseline knowledge of the temporal and spatial biological variation within bilges, as well as the effectiveness of different sampling methodologies, is critical. We used 16S rRNA gene metabarcoding of pelagic and sessile bacterial communities from ship bilges to assess the variation in bilge bacterial communities to determine how the inherent bilge diversity could guide or constrain biological monitoring. Bilge communities exhibited high levels of spatial and temporal variation, with >80% of the community able to be turned over in the space of 3 months, likely due to disturbance events such as cleaning and maintenance. Sessile and pelagic communities within a given bilge were also inherently distinct, with dominant exact sequence variants (ESVs) rarely shared between the two. Taxa containing KEGG orthologies (KOs) associated with dissimilatory sulfate reduction and biofilm production, functions typically associated with MIC, were generally more prevalent in sessile communities. Collectively, our findings indicate that neither bilge water nor an unaffected bilge from within the same vessel would constitute an appropriate reference community for MIC diagnosis. Optimal sampling locations and strategies that could be incorporated into a standardized method for monitoring bilge biology in relation to MIC were identified. Finally, taxonomic and functional comparisons of bilge diversity highlight the potential of functional approaches in future biological monitoring of MIC and MIC mitigation strategies in general. IMPORTANCE Microbially influenced corrosion (MIC) has been estimated to contribute 20 to 50% of the costs associated with corrosion globally. Diagnosis and monitoring of MIC are complex problems requiring knowledge of corrosion rates, corrosion morphology, and the associated microbiology to distinguish MIC from abiotic corrosion processes. Historically, biological monitoring of MIC utilized a priori knowledge to monitor sulfate-reducing bacteria; however, it is becoming widely accepted that a holistic or community-level understanding of corrosion-associated microbiology is needed for MIC diagnosis and monitoring. Before biology associated with MIC attack can be identified, standardized protocols for sampling and monitoring must be developed. The significance of our research is in contributing to the development of robust and repeatable sampling strategies of bilges, which are required for the development of standardized biological monitoring methods for MIC. We achieve this via a biodiversity survey of bilge communities and by comparing taxonomic and functional variation.
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Yan L, Hermans SM, Totsche KU, Lehmann R, Herrmann M, Küsel K. Groundwater bacterial communities evolve over time in response to recharge. Water Res 2021; 201:117290. [PMID: 34130083 DOI: 10.1016/j.watres.2021.117290] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.
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Affiliation(s)
- Lijuan Yan
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Syrie M Hermans
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany
| | - Kai Uwe Totsche
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Germany
| | - Martina Herrmann
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.
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35
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Freedman ZB, McGrew A, Baiser B, Besson M, Gravel D, Poisot T, Record S, Trotta LB, Gotelli NJ. Environment-host-microbial interactions shape the Sarracenia purpurea microbiome at the continental scale. Ecology 2021; 102:e03308. [PMID: 33577089 DOI: 10.1002/ecy.3308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/05/2021] [Accepted: 02/05/2021] [Indexed: 11/10/2022]
Abstract
The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant's cup-shaped leaves fill with rainwater and support a miniature, yet full-fledged, ecosystem with a diverse microbiome that decomposes captured prey and a small network of shredding and filter-feeding aquatic invertebrates that feed on microbes. We characterized pitcher microbiomes of 108 plants sampled at 36 sites from Florida to Quebec. Structural equation models revealed that annual precipitation and temperature, plant size, and midge abundance had direct effects on microbiome taxonomic and phylogenetic diversity. Climate variables also exerted indirect effects through plant size and midge abundance. Further, spatial structure and climate influenced taxonomic composition, but not phylogenetic composition. Our results suggest that direct effects of midge abundance and climate and indirect effects of climate through its effect on plant-associated factors lead to greater richness of microbial phylotypes in warmer, wetter sites.
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Affiliation(s)
- Zachary B Freedman
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Alicia McGrew
- School of Natural Resources and Environment, University of Florida, Gainesville, Florida, 32603, USA.,Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, 32603, USA
| | - Benjamin Baiser
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, 32603, USA
| | - Mathilde Besson
- Département de Sciences Biologiques, Université de Montréal, Montréal, Quebec, H2V 0B3, Canada
| | - Dominique Gravel
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Quebec, J1K 2R1, Canada
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montréal, Quebec, H2V 0B3, Canada
| | - Sydne Record
- Department of Biology, Bryn Mawr College, Bryn Mawr, Pennsylvania, 19010, USA
| | - Lauren B Trotta
- School of Natural Resources and Environment, University of Florida, Gainesville, Florida, 32603, USA
| | - Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, Vermont, 05405, USA
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36
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Gao P, Du G, Zhao D, Wei Q, Zhang X, Qu L, Gong X. Influences of Seasonal Monsoons on the Taxonomic Composition and Diversity of Bacterial Community in the Eastern Tropical Indian Ocean. Front Microbiol 2021; 11:615221. [PMID: 33574800 PMCID: PMC7870504 DOI: 10.3389/fmicb.2020.615221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/22/2020] [Indexed: 01/03/2023] Open
Abstract
The Indian Ocean is characterized by its complex physical systems and strong seasonal monsoons. To better understand effects of seasonal monsoon-driven circulation on the bacterioplanktonic community structure in surface waters and the bacterial distribution response to vertical stratification, patterns of seasonal, and vertical distribution of bacterial communities in the Eastern Tropical Indian Ocean were investigated using 16S rRNA gene profiling. Water samples were collected during the Southwest monsoon (from June to August), the fall inter-monsoon (from October and November) and the Northeast monsoon (from December to January), respectively, onboard during three cruises from July 2016 to January 2018. Surface bacterioplankton communities in these three seasons and in the upper water (3-300 m with six depths) during the Northeast monsoon contained a diverse group of taxa, mainly Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi. Redundancy discriminant analysis (RDA) uncovered that temperature, salinity, and dissolved oxygen (DO) were crucial environmental parameters that affected the structure of bacterial community in overall surface samples. However, significant differences in the composition of the bacterial community are likely due to changes in concentrations of salinity during the fall inter-monsoon, while phosphate for both the Southwest monsoon and the Northeast monsoon. Pearson's analysis revealed that the seasonal variation rather than the vertical variation of environmental factors had a more significant impact on the composition of bacterial community. In addition, a clear seasonal pattern of bacterial co-occurrence showed that inter-taxa associations during the fall inter-monsoon were closer than during the Northeast monsoon and the Southwest monsoon. Overall, our results implied clear differences in the composition of bacterial community, with more pronounced seasonal variation compared to the vertical variation in response to environmental changes.
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Affiliation(s)
- Ping Gao
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China
| | - Guangxun Du
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qinsheng Wei
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xuelei Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Lingyun Qu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), Qingdao, China
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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37
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Hong H, Li J, Wang Q, Lu H, Liu J, Dong YW, Zhang J, Li J, Williams MA, Huang B, Yan C. The legacy of trace metal deposition from historical anthropogenic river management: A regional driver of offshore sedimentary microbial diversity. J Hazard Mater 2020; 400:123164. [PMID: 32563906 DOI: 10.1016/j.jhazmat.2020.123164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/30/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
River management, both modern and historical, have dramatically modified offshore environments. While numerous studies have described the modern impacts, very few have evaluated the legacies remaining from hundreds of years ago. Herein, we show trace metal enrichment in the surface sediment of the abandoned Yellow River Delta, hypothesized to be associated with ancient river management. Essentially, anthropogenic modification caused the river to shift, creating a 12.4×103 km2 area with elevated trace metals; characterized by clear metal deposition gradients. Geographical factors related to the ancient river mouth had the most significant influences on Zn (explained by distance to the river mouth, DTM) and Cd (DTM and sediment salinity), while the sediment absorptive capacity was associated with the reallocation of Cu (clay, silt, and iron), Ni (clay and iron), and Pb (silt and iron). Trace metal legacies showed stronger influences on prokaryotic diversity than on micro-eukaryotic diversity, with the former best described by changes in rare, rather than dominant families and classes, and explainable by an "overlapping micro-niche" model. The ancient river's legacies provide evidence of longer-term human disturbance over hundreds of years; as its impacts on associated benthic microbiomes have led to lessons for modern-day waterway management of benthic ecosystems.
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Affiliation(s)
- Hualong Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061, Virginia, USA.
| | - Junwei Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; Key Laboratory of the Ministry of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Qiang Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Haoliang Lu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Jingchun Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China.
| | - Yun-Wei Dong
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Jie Zhang
- Key Laboratory of Urban Environment Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, Fujian, China.
| | - Jian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| | - Mark A Williams
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061, Virginia, USA.
| | - Bangqin Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Chongling Yan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, Fujian, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
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38
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Wang X, Wang P, Wang C, Chen J, Miao L, Yuan Q, Liu S, Feng T. Do bacterioplankton respond equally to different river regulations? A quantitative study in the single-dammed Yarlung Tsangpo River and the cascade-dammed Lancang River. Environ Res 2020; 191:110194. [PMID: 32919971 DOI: 10.1016/j.envres.2020.110194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/22/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
River damming has raised controversial concerns as it simultaneously contributes to socioeconomic development but may jeopardize aquatic ecology. Since bacterioplankton catalyze vital biogeochemical reactions and play important roles in aquatic ecosystems, more attention has been paid to their responses in dammed rivers. Here, a comparative study was conducted between single-dammed (the Yarlung Tsangpo River) and cascade-dammed (the Lancang River) rivers in Southwest China to investigate whether bacterioplankton respond equally to different river regulations. Our results showed that the decreased bacterioplankton abundance and the increased α-diversity always co-occurred in reservoirs of the Yarlung Tsangpo River and the Lancang River. However, the impact of damming on bacterioplankton abundance and α-diversity were resilient in the Lancang River, which can be attributed to the repeated alterations of environmental heterogeneity in cascade damming reaches. Meanwhile, a generalized additive model (GAM) was applied to identify the important drivers affecting bacterioplankton variation. The abundance was influenced by trophic conditions, such as dissolved silicon, while α-diversity was closely related to the microbial dispersal process, such as elevation and distance-from source. And it is also noted that the bacterioplankton dispersal process was interrupted in cascade damming reaches. In addition, based on their important drivers, variations in abundance and α-diversity were also predicted by GAM. As revealed by the quantitative mutual validation between the two rivers, abundance and α-diversity in the cascade-dammed river can be predicted by their response to single-dammed river, suggesting that the impact of cascade damming on bacterioplankton can be pre-assessed by referring to the single stage damming effect. Therefore, our study provides the first trial of quantitative evidence that bacterioplankton do not respond equally to different river regulations, and the impact of cascade damming on bacterioplankton can be predicted based on single stage damming effect, which can contribute to the protection of aquatic ecology in the cascade hydropower development.
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Affiliation(s)
- Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Lingzhan Miao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Tao Feng
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
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Dini-Andreote F, Kowalchuk GA, Prosser JI, Raaijmakers JM. Towards meaningful scales in ecosystem microbiome research. Environ Microbiol 2020; 23:1-4. [PMID: 33047413 DOI: 10.1111/1462-2920.15276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - George A Kowalchuk
- Ecology & Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
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40
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Ouellet V, St-Hilaire A, Dugdale SJ, Hannah DM, Krause S, Proulx-Ouellet S. River temperature research and practice: Recent challenges and emerging opportunities for managing thermal habitat conditions in stream ecosystems. Sci Total Environ 2020; 736:139679. [PMID: 32474270 DOI: 10.1016/j.scitotenv.2020.139679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
There is growing evidence that river temperatures are increasing under climate change, which is expected to be exacerbated by increased abstractions to satisfy human water demands. Water temperature research has experienced crucial advances, both in terms of developing new monitoring and modelling tools, as well as understanding the mechanisms of temperature feedbacks with biogeochemical and ecological processes. However, water practitioners and regulators are challenged with translating the widespread and complex technological, modelling and conceptual advances made in river temperature research into improvements in management practice. This critical review provides a comprehensive overview of recent advances in the state-of-the-art monitoring and modelling tools available to inform ecological research and practice. In so doing, we identify pressing research gaps and suggest paths forward to address practical research and management challenges. The proposed research directions aim to provide new insights into spatio-temporal stream temperature dynamics and unravel drivers and controls of thermal river regimes, including the impacts of changing temperature on metabolism and aquatic biogeochemistry, as well as aquatic organisms. The findings of this review inform future research into ecosystem resilience in the face of thermal degradation and support the development of new management strategies cutting across spatial and temporal scales.
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Affiliation(s)
- Valerie Ouellet
- University of Birmingham, School of Geography, Earth and Environmental Sciences, Birmingham B15 2TT, UK; Institute for Global Innovation, University of Birmingham, Birmingham B15 2TT, UK.
| | - André St-Hilaire
- INRS Eau Terre Environnement, 490 de la Couronne, Québec, Qc G1K 9A9, Canada; Canadian River Institute, 10 Bailey Drive, P.O. Box 4400, Fredericton, NB E3B 5A3, Canada
| | - Stephen J Dugdale
- University of Nottingham, School of Geography, Nottingham NG7 2RD, UK
| | - David M Hannah
- University of Birmingham, School of Geography, Earth and Environmental Sciences, Birmingham B15 2TT, UK; Institute for Global Innovation, University of Birmingham, Birmingham B15 2TT, UK
| | - Stefan Krause
- University of Birmingham, School of Geography, Earth and Environmental Sciences, Birmingham B15 2TT, UK; Institute for Global Innovation, University of Birmingham, Birmingham B15 2TT, UK
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41
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Erez A, Lopez JG, Weiner BG, Meir Y, Wingreen NS. Nutrient levels and trade-offs control diversity in a serial dilution ecosystem. eLife 2020; 9:e57790. [PMID: 32915132 PMCID: PMC7486120 DOI: 10.7554/elife.57790] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/16/2020] [Indexed: 02/02/2023] Open
Abstract
Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.
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Affiliation(s)
- Amir Erez
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Jaime G Lopez
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
| | | | - Yigal Meir
- Department of Physics, Ben Gurion University of the NegevBeershebaIsrael
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
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42
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Liu Y, Blain S, Crispi O, Rembauville M, Obernosterer I. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environ Microbiol 2020; 22:3968-3984. [PMID: 32755055 DOI: 10.1111/1462-2920.15184] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 11/29/2022]
Abstract
The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high-resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples were collected by a moored remote autonomous sampler over 4 months at 5-11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant amplicon sequence variants, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa. Our study provides the first seasonal picture of microbial community dynamics in the open Southern Ocean and thereby offers biological insights to the cycling of carbon and iron, and to an important puzzling issue that is the modest nitrate decrease associated to iron fertilization.
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Affiliation(s)
- Yan Liu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France.,College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Life Sciences, Ludong University, Yantai, China
| | - Stéphane Blain
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Olivier Crispi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Mathieu Rembauville
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
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43
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Sow SLS, Trull TW, Bodrossy L. Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Front Microbiol 2020; 11:1847. [PMID: 32849444 PMCID: PMC7424020 DOI: 10.3389/fmicb.2020.01847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/15/2020] [Indexed: 01/01/2023] Open
Abstract
The cosmopolitan haptophyte Phaeocystis is recognized as a key contributor to marine biogeochemical cycling and important primary producer within polar marine environments. Yet, little is known about its solitary, non-colonial cell stages or its distribution during the colder, low-productivity seasons. We examined the biogeography of Phaeocystis along a high-resolution (0.5-degree latitudinal interval) transect from the Antarctic ice-edge to the equator of the South Pacific, in the austral autumn-winter. Using high-throughput 18S rRNA gene sequences with single nucleotide variable (zero-radius) operational taxonomic units (zOTUs) allowed us to explore the possibility of strain-level variation. From water samples within the upper water column, we show the presence of an abundant Phaeocystis assemblage that persisted during the colder months, contributing up to 9% of the microbial eukaryote community at high latitudes. The biogeography of Phaeocystis was strongly shaped by oceanographic boundaries, most prominently the polar and subantarctic fronts. Marked changes in dominant Phaeocystis antarctica zOTUs between different frontal zones support the concept that ecotypes may exist within the Phaeocystis assemblage. Our findings also show that the Phaeocystis assemblage did not abide by the classical latitudinal diversity gradient of increasing richness from the poles to the tropics; richness peaked at 30°S and declined to a minimum at 5°S. Another surprise was that P. globosa and P. cordata, previously thought to be restricted to the northern hemisphere, were detected at moderate abundances within the Southern Ocean. Our results emphasize the importance of oceanographic processes in shaping the biogeography of Phaeocystis and highlights the importance of genomics-based exploration of Phaeocystis, which have found the assemblage to be more complex than previously understood. The high winter relative abundance of the Phaeocystis assemblage suggests it could be involved in more complex ecological interactions during the less productive seasons, which should be considered in future studies to better understand the ecological role and strategies of this keystone species.
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Affiliation(s)
- Swan L S Sow
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia.,Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Thomas W Trull
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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44
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Wang X, Liu J, Liang J, Sun H, Zhang XH. Spatiotemporal dynamics of the total and active Vibrio spp. populations throughout the Changjiang estuary in China. Environ Microbiol 2020; 22:4438-4455. [PMID: 33462948 PMCID: PMC7689709 DOI: 10.1111/1462-2920.15152] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/03/2020] [Indexed: 11/27/2022]
Abstract
Vibrio is ubiquitously distributed in marine environments and is the most extensively characterized group within Gammaproteobacteria. Studies have investigated Vibrio spp. worldwide, but mostly focused on pathogenic vibrios and based on cultivation methods. Here, using a combination of molecular and culturing methods, we investigated the dynamics of the total and active Vibrio spp. throughout the Changjiang estuary in China. The total Vibrio abundance was higher in summer (~6.59 × 103 copies ml−1) than in winter (~1.85 × 103 copies ml−1) and increased from freshwater to saltwater (e.g. 8.04 × 101 to 9.39 × 103 copies ml−1 in summer). The ratio of active to total Vibrio (Va/Vt) revealed a high activity of vibrios, with remarkable differences between freshwater and saltwater (p < 0.05). Based on the community compositions of the culturable, total and active Vibrio, Vibrio atlanticus and Vibrio owensii were the dominant and active species in winter and summer, respectively. The distribution of Vibrio was governed by the effects of diverse environmental factors, such as temperature, salinity, pH, dissolved oxygen and SiO32−. Our study clearly demonstrates the spatiotemporal dynamics of total and active Vibrio spp. and lays a foundation for fully understanding the ecological roles of marine Vibrio.
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Affiliation(s)
- Xiaolei Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
| | - Jinchang Liang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Hao Sun
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China
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45
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Sala MM, Ruiz-González C, Borrull E, Azúa I, Baña Z, Ayo B, Álvarez-Salgado XA, Gasol JM, Duarte CM. Prokaryotic Capability to Use Organic Substrates Across the Global Tropical and Subtropical Ocean. Front Microbiol 2020; 11:918. [PMID: 32582044 PMCID: PMC7287293 DOI: 10.3389/fmicb.2020.00918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean.
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Affiliation(s)
- Maria Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Zuriñe Baña
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain.,Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | | | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados-Universitat de les Illes Balears, Consejo Superior de Investigaciones Científicas, Esporles, Spain
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46
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2020; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. Video Abstract
A catalog of 47 million genes was generated from 370 globally distributed metagenomes Meta-omics data integration disentangled the mechanisms of changes in transcript pools Transcript pool changes of metabolic marker genes show distinct mechanistic patterns Community turnover as a response to ocean warming may be strongest in polar regions
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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47
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - 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; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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Ma J, Lu Y, Chen F, Li X, Xiao D, Wang H. Molecular Ecological Network Complexity Drives Stand Resilience of Soil Bacteria to Mining Disturbances among Typical Damaged Ecosystems in China. Microorganisms 2020; 8:E433. [PMID: 32204532 DOI: 10.3390/microorganisms8030433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 12/29/2022] Open
Abstract
Understanding the interactions of soil microbial species and how they responded to disturbances are essential to ecological restoration and resilience in the semihumid and semiarid damaged mining areas. Information on this, however, remains unobvious and deficiently comprehended. In this study, based on the high throughput sequence and molecular ecology network analysis, we have investigated the bacterial distribution in disturbed mining areas across three provinces in China, and constructed molecular ecological networks to reveal the interactions of soil bacterial communities in diverse locations. Bacterial community diversity and composition were classified measurably between semihumid and semiarid damaged mining sites. Additionally, we distinguished key microbial populations across these mining areas, which belonged to Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi. Moreover, the network modules were significantly associated with some environmental factors (e.g., annual average temperature, electrical conductivity value, and available phosphorus value). The study showed that network interactions were completely different across the different mining areas. The keystone species in different mining areas suggested that selected microbial communities, through natural successional processes, were able to resist the corresponding environment. Moreover, the results of trait-based module significances showed that several environmental factors were significantly correlated with some keystone species, such as OTU_8126 (Acidobacteria), OTU_8175 (Burkholderiales), and OTU_129 (Chloroflexi). Our study also implied that the complex network of microbial interaction might drive the stand resilience of soil bacteria in the semihumid and semiarid disturbed mining areas.
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Taylor HB, Kurtz HD. Microbial community structure shows differing levels of temporal stability in intertidal beach sands of the grand strand region of South Carolina. PLoS One 2020; 15:e0229387. [PMID: 32106250 PMCID: PMC7046189 DOI: 10.1371/journal.pone.0229387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Studies of microbial community structure in intertidal and supratidal beach sands along the California and Gulf of Mexico coasts have begun to reveal geographical patterns in microbial diversity through the use of next generation sequencing technology. Only a few studies have targeted communities along the Eastern seaboard, leaving a variety of microbial ecosystems uncharacterized. In this study, we examine the microbial community structure within three South Carolina beaches along the Grand Strand via sequencing of the V4 region of the 16S rRNA gene to discern relationships between diversity and temporal or regional factors. Gammaproteobacteria, Planctomycetes, Acidobacteria, and Actinobacteria dominated the composition of these beaches. Diversity analyses revealed that highly diverse communities were similar in overall composition and diversity but showed different levels of community structure stability over time. The community structure in Pawleys Island sands showed no significant change over time, while Garden City experienced significant shifts between each sampling date. Community structure also differed between beaches and, to a lesser degree, sampling date. These data provide evidence of the high microbial diversity within these beach sands and suggest that even though beaches of the same geographic region can show similarity in composition and diversity at a particular timepoint, the nature of their community structure and underlying diversity may differ comparatively and over time.
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Affiliation(s)
- Harrison B. Taylor
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Harry D. Kurtz
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
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50
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Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE. Iroki: automatic customization and visualization of phylogenetic trees. PeerJ 2020; 8:e8584. [PMID: 32149022 PMCID: PMC7049256 DOI: 10.7717/peerj.8584] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 12/26/2022] Open
Abstract
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
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Affiliation(s)
- Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - Amelia O Harrison
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Sean M McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America
| | - Shawn W Polson
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
| | - K Eric Wommack
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America
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