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Chang T, Gavelis GS, Brown JM, Stepanauskas R. Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton. MICROBIOME 2024; 12:126. [PMID: 39010229 PMCID: PMC11247762 DOI: 10.1186/s40168-024-01848-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/28/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment. RESULTS We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages. CONCLUSIONS Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.
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Affiliation(s)
- Tianyi Chang
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Gregory S Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
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Henson MW, Thrash JC. Microbial ecology of northern Gulf of Mexico estuarine waters. mSystems 2024:e0131823. [PMID: 38980056 DOI: 10.1128/msystems.01318-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/19/2024] [Indexed: 07/10/2024] Open
Abstract
Estuarine and coastal ecosystems are of high economic and ecological importance, owing to their diverse communities and the disproportionate role they play in carbon cycling, particularly in carbon sequestration. Organisms inhabiting these environments must overcome strong natural fluctuations in salinity, nutrients, and turbidity, as well as numerous climate change-induced disturbances such as land loss, sea level rise, and, in some locations, increasingly severe tropical cyclones that threaten to disrupt future ecosystem health. The northern Gulf of Mexico (nGoM) along the Louisiana coast contains dozens of estuaries, including the Mississippi-Atchafalaya River outflow, which dramatically influence the region due to their vast upstream watershed. Nevertheless, the microbiology of these estuaries and surrounding coastal environments has received little attention. To improve our understanding of microbial ecology in the understudied coastal nGoM, we conducted a 16S rRNA gene amplicon survey at eight sites and multiple time points along the Louisiana coast and one inland swamp spanning freshwater to high brackish salinities, totaling 47 duplicated Sterivex (0.2-2.7 µm) and prefilter (>2.7 µm) samples. We cataloged over 13,000 Amplicon Sequence ariants (ASVs) from common freshwater and marine clades such as SAR11 (Alphaproteobacteria), Synechococcus (Cyanobacteria), and acI and Candidatus Actinomarina (Actinobacteria). We observed correlations with freshwater or marine habitats in many organisms and characterized a group of taxa with specialized distributions across brackish water sites, supporting the hypothesis of an endogenous brackish-water community. Additionally, we observed brackish-water associations for several aquatic clades typically considered marine or freshwater taxa, such as SAR11 subclade II, SAR324, and the acI Actinobacteria. The data presented here expand the geographic coverage of microbial ecology in estuarine communities, help delineate the native and transitory members of these environments, and provide critical aquatic microbiological baseline data for coastal and estuarine sites in the nGoM.IMPORTANCEEstuarine and coastal waters are diverse ecosystems influenced by tidal fluxes, interconnected wetlands, and river outflows, which are of high economic and ecological importance. Microorganisms play a pivotal role in estuaries as "first responders" and ecosystem architects, yet despite their ecological importance, they remain underrepresented in microbial studies compared to open ocean environments. This leads to substantial knowledge gaps that are important for understanding global biogeochemical cycling and making decisions about conservation and management strategies in these environments. Our study makes key contributions to the microbial ecology of estuarine and coastal habitats in the northern Gulf of Mexico. Our microbial community data support the concept of a globally distributed, core brackish microbiome and emphasize previously underrecognized brackish-water taxa. Given the projected worsening of land loss, oil spills, and natural disasters in this region, our results will serve as important baseline data for researchers investigating the microbial communities found across estuaries.
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Affiliation(s)
- Michael W Henson
- Department of Biological Sciences, Northern University, DeKalb, Illinois, USA
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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3
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Bandekar M, More KD, Seleyi SC, Ramaiah N, Kekäläinen J, Akkanen J. Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106615. [PMID: 38941665 DOI: 10.1016/j.marenvres.2024.106615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/04/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024]
Abstract
We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.
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Affiliation(s)
- Mandar Bandekar
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland; Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India.
| | - Kuldeep D More
- Business Development Group, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Seyieleno C Seleyi
- Marine Biotechnology Division, National Institute of Ocean Technology, Ministry of Earth Sciences, Chennai, India
| | - Nagappa Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403004, India
| | - Jukka Kekäläinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland
| | - Jarkko Akkanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Kuopio, Finland
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4
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Ma JG, Wang XB, Hou FJ. A general pattern of plant traits and their relationships with environmental factors and microbial life-history strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172670. [PMID: 38679109 DOI: 10.1016/j.scitotenv.2024.172670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/31/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
The trait-based unidimensional plant economics spectrum provides a valuable framework for understanding plant adaptation strategies to the environment. However, it is still uncertain whether there is a general multidimensionality of how variation of both leaf and fine root traits are influenced by environmental factors, and how these relate to microbial resource strategies. Here, we examined the coordination patterns of four pairs of similar leaf and fine root traits of herbaceous plants in an alpine meadow at the community-level, and their environmental driving patterns. We then assessed their correlation with microbial life-history strategies, as these exhibit analogous resource strategies with plants in terms of growth and resource utilization efficiency. Results exhibited an analogous multidimensionality of the economics spectrum for leaf and fine root traits: the first dimension, collaboration gradient, primarily represented a tradeoff between lifespan and resource foraging efficiency; the second dimension, conservation gradient, primarily represented a tradeoff between conservation and acquisition in resource uptake. Climate variables had a stronger impact on both dimensions for leaf and fine root traits than soil variables did; whereas, the primary drivers were more complex for fine root traits than for leaf traits. The collaboration gradient of leaf and fine root traits exhibited consistent relationships with soil microbial life-history strategies, both showed negative and positive correlation with bacterial and fungal strategies, respectively. Our findings suggest that both leaves and fine roots have general multidimensional strategies for adapting to new environments and provide a solid basis for further understanding the relationships between the adaptive strategies of plants and microbes.
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Affiliation(s)
- Jian-Guo Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Xiao-Bo Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Fu-Jiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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5
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Romera‐Castillo C, Birnstiel S, Sebastián M. Diversity of marine bacteria growing on leachates from virgin and weathered plastic: Insights into potential degraders. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13305. [PMID: 38923399 PMCID: PMC11194452 DOI: 10.1111/1758-2229.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Plastic debris in the ocean releases chemical compounds that can be toxic to marine fauna. It was recently found that some marine bacteria can degrade such leachates, but information on the diversity of these bacteria is mostly lacking. In this study, we analysed the bacterial diversity growing on leachates from new low-density polyethylene (LDPE) and a mix of naturally weathered plastic, collected from beach sand. We used a combination of Catalysed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH), BioOrthogonal Non-Canonical Amino acid Tagging (BONCAT), and 16S rRNA gene amplicon sequencing to analyse bacterioplankton-groups specific activity responses and the identity of the responsive taxa to plastic leachates produced under irradiated and non-irradiated conditions. We found that some generalist taxa responded to all leachates, most of them belonging to the Alteromonadales, Oceanospirillales, Nitrosococcales, Rhodobacterales, and Sphingomonadales orders. However, there were also non-generalist taxa responding to specific irradiated and non-irradiated leachates. Our results provide information about bacterial taxa that could be potentially used to degrade the chemicals released during plastic degradation into seawater contributing to its bioremediation.
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Zhu M, Dai X. Shaping of microbial phenotypes by trade-offs. Nat Commun 2024; 15:4238. [PMID: 38762599 PMCID: PMC11102524 DOI: 10.1038/s41467-024-48591-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Growth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticide, School of Life Sciences, Central China Normal University, Wuhan, PR China.
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7
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Blais MA, Vincent WF, Vigneron A, Labarre A, Matveev A, Coelho LF, Lovejoy C. Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum. Microbiol Spectr 2024; 12:e0416023. [PMID: 38511950 PMCID: PMC11210273 DOI: 10.1128/spectrum.04160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season. IMPORTANCE Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Warwick F. Vincent
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Aurélie Labarre
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
| | - Alex Matveev
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Lígia Fonseca Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
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Brüwer JD, Sidhu C, Zhao Y, Eich A, Rößler L, Orellana LH, Fuchs BM. Globally occurring pelagiphage infections create ribosome-deprived cells. Nat Commun 2024; 15:3715. [PMID: 38698041 PMCID: PMC11066056 DOI: 10.1038/s41467-024-48172-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Phages play an essential role in controlling bacterial populations. Those infecting Pelagibacterales (SAR11), the dominant bacteria in surface oceans, have been studied in silico and by cultivation attempts. However, little is known about the quantity of phage-infected cells in the environment. Using fluorescence in situ hybridization techniques, we here show pelagiphage-infected SAR11 cells across multiple global ecosystems and present evidence for tight community control of pelagiphages on the SAR11 hosts in a case study. Up to 19% of SAR11 cells were phage-infected during a phytoplankton bloom, coinciding with a ~90% reduction in SAR11 cell abundance within 5 days. Frequently, a fraction of the infected SAR11 cells were devoid of detectable ribosomes, which appear to be a yet undescribed possible stage during pelagiphage infection. We dubbed such cells zombies and propose, among other possible explanations, a mechanism in which ribosomal RNA is used as a resource for the synthesis of new phage genomes. On a global scale, we detected phage-infected SAR11 and zombie cells in the Atlantic, Pacific, and Southern Oceans. Our findings illuminate the important impact of pelagiphages on SAR11 populations and unveil the presence of ribosome-deprived zombie cells as part of the infection cycle.
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Affiliation(s)
- Jan D Brüwer
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Yanlin Zhao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Andreas Eich
- PSL Research University: EPHE-UPVD-CNRS,UAR 3278 CRIOBE, Moorea, French Polynesia
| | - Leonard Rößler
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Luis H Orellana
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
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9
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He C, Li G, Zou S, Zheng P, Song Q, Li G, Yu Q, Yu Y, Zhang Q, Zhang X, Shen Z, Gong J. Spatial and diel variations of bacterioplankton and pico-nanoeukaryote communities and potential biotic interactions during macroalgal blooms. MARINE POLLUTION BULLETIN 2024; 202:116409. [PMID: 38663343 DOI: 10.1016/j.marpolbul.2024.116409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024]
Abstract
We investigated spatial heterogeneity and diel variations in bacterioplankton and pico-nanoeukaryote communities, and potential biotic interactions at the extinction stage of the Ulva prolifera bloom in the Jiaozhou Bay, Yellow Sea. It was found that the presence of Ulva canopies significantly promoted the cell abundance of heterotrophic bacteria, raised evenness, and altered the community structure of bacterioplankton. A diel pattern was solely significant for pico-nanoeukaryote community structure. >50 % of variation in the heterotrophic bacterial abundance was accounted for by the ratio of Bacteroidota to Firmicutes, and dissolved organic nitrogen effectively explained the variations in cell abundances of phytoplankton populations. The factors representing biotic interactions frequently contributed substantially more than environmental factors in explaining the variations in diversity and community structure of both bacterioplankton and pico-nanoeukaryotes. There were higher proportions of eukaryotic pathogens compared to other marine systems, suggesting a higher ecological risk associated with the Ulva blooms.
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Affiliation(s)
- Cui He
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
| | - Guihao Li
- Zhuhai Doumen Agricultural Technology Extension, Zhuhai, Guangdong, China
| | - Songbao Zou
- Zhejiang Institute of Freshwater Fisheries, Huzhou, Zhejiang, China
| | - Pengfei Zheng
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536007, China
| | - Qinqin Song
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536007, China
| | - Guanzhe Li
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
| | - Qin Yu
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Yunjun Yu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510535, China
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Xiaoli Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Zhuo Shen
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Jun Gong
- School of Marine Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China.
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10
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Serra Moncadas L, Hofer C, Bulzu PA, Pernthaler J, Andrei AS. Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis. Nat Commun 2024; 15:3421. [PMID: 38653968 PMCID: PMC11039613 DOI: 10.1038/s41467-024-47767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.
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Affiliation(s)
- Lucas Serra Moncadas
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Cyrill Hofer
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.
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11
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Harbeitner RC, Wittmers F, Yung CCM, Eckmann CA, Hehenberger E, Blum M, Needham DM, Worden AZ. Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions. PLoS One 2024; 19:e0298139. [PMID: 38564528 PMCID: PMC10986988 DOI: 10.1371/journal.pone.0298139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024] Open
Abstract
Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.
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Affiliation(s)
- Rachel C. Harbeitner
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Fabian Wittmers
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
- Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Charmaine C. M. Yung
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Charlotte A. Eckmann
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Marguerite Blum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
| | - David M. Needham
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
| | - Alexandra Z. Worden
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, United States of America
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, DE, Germany
- Marine Biological Laboratory, Woods Hole, MA, United States of America
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12
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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] [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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13
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024:S0966-842X(24)00057-X. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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14
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Dragone NB, Hoffert M, Strickland MS, Fierer N. Taxonomic and genomic attributes of oligotrophic soil bacteria. ISME COMMUNICATIONS 2024; 4:ycae081. [PMID: 38988701 PMCID: PMC11234899 DOI: 10.1093/ismeco/ycae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
Not all bacteria are fast growers. In soil as in other environments, bacteria exist along a continuum-from copiotrophs that can grow rapidly under resource-rich conditions to oligotrophs that are adapted to life in the "slow lane." However, the field of microbiology is built almost exclusively on the study of copiotrophs due, in part, to the ease of studying them in vitro. To begin understanding the attributes of soil oligotrophs, we analyzed three independent datasets that represent contrasts in organic carbon availability. These datasets included 185 samples collected from soil profiles across the USA, 950 paired bulk soil and rhizosphere samples collected across Europe, and soils from a microcosm experiment where carbon availability was manipulated directly. Using a combination of marker gene sequencing and targeted genomic analyses, we identified specific oligotrophic taxa that were consistently more abundant in carbon-limited environments (subsurface, bulk, unamended soils) compared to the corresponding carbon-rich environment (surface, rhizosphere, glucose-amended soils), including members of the Dormibacterota and Chloroflexi phyla. In general, putative soil oligotrophs had smaller genomes, slower maximum potential growth rates, and were under-represented in culture collections. The genomes of oligotrophs were more likely to be enriched in pathways that allow oligotrophs to metabolize a range of energy sources and store carbon, while genes associated with energy-intensive functions like chemotaxis and motility were under-represented. However, few genomic attributes were shared, highlighting that oligotrophs likely use a range of different metabolic strategies and regulatory pathways to thrive in resource-limited soils.
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Affiliation(s)
- Nicholas B Dragone
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Michael Hoffert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, United States
| | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, United States
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, United States
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15
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Tamayo-Leiva J, Alcorta J, Sepúlveda F, Fuentes-Alburquenque S, Arroyo JI, González-Pastor JE, Díez B. Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton. ISME COMMUNICATIONS 2024; 4:ycae059. [PMID: 38770060 PMCID: PMC11104534 DOI: 10.1093/ismeco/ycae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question. The aim of this study was to characterize the structure of the conjugative mobilome in the ocean surface bacterioplankton by searching the publicly available marine metagenomes from the TARA Oceans survey, together with molecular markers, such as relaxases and type IV coupling proteins of the type IV secretion system (T4SS). The T4SS machinery was retrieved in more abundance than relaxases in the surface marine bacterioplankton. Moreover, among the identified MGEs, mobilizable elements were the most abundant, outnumbering self-conjugative sequences. Detection of a high number of incomplete T4SSs provides insight into possible strategies related to trans-acting activity between MGEs, and accessory functions of the T4SS (e.g. protein secretion), allowing the host to maintain a lower metabolic burden in the highly dynamic marine system. Additionally, the results demonstrate a wide geographical dispersion of MGEs throughout oceanic regions, while the Southern Ocean appears segregated from other regions. The marine mobilome also showed a high similarity of functions present in known plasmid databases. Moreover, cargo genes were mostly related to DNA processing, but scarcely associated with antibiotic resistance. Finally, within the MGEs, integrative and conjugative elements showed wider marine geographic dispersion than plasmids.
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Affiliation(s)
- Javier Tamayo-Leiva
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
| | - Jaime Alcorta
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Felipe Sepúlveda
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
| | - Sebastián Fuentes-Alburquenque
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O’Higgins, Santiago, Chile
- Departamento de Matemáticas y Ciencias de la Ingeniería, Facultad de Ingeniería, Ciencia y Tecnología, Universidad Bernardo O’Higgins, Santiago, Chile
| | - José Ignacio Arroyo
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- The Santa Fe Institute, Santa Fe, NM 87131, United States
- Centro de Modelamiento Matemático, Universidad de Chile, IRL 2807 CNRS Beauchef 851, Santiago, Chile
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA. Carretera de Ajalvir km 4, Torrejón de Ardoz 28850 Madrid, Spain
| | - Beatriz Díez
- Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG) , Santiago, Chile
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16
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Sebastián M, Giner CR, Balagué V, Gómez-Letona M, Massana R, Logares R, Duarte CM, Gasol JM. The active free-living bathypelagic microbiome is largely dominated by rare surface taxa. ISME COMMUNICATIONS 2024; 4:ycae015. [PMID: 38456147 PMCID: PMC10919342 DOI: 10.1093/ismeco/ycae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 03/09/2024]
Abstract
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.
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Affiliation(s)
- Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Caterina R Giner
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Vanessa Balagué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Markel Gómez-Letona
- Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Parque Científico Tecnológico Marino de Taliarte, s/n, Telde, Las Palmas 35214, Spain
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
| | - Carlos M Duarte
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Pg Marítim de la Barceloneta 37-49, Barcelona, Catalunya E08003, Spain
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17
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Liu L, Zhong KX, Chen Q, Wang Y, Zhang T, Jiao N, Zheng Q. Selective cell lysis pressure on rare and abundant prokaryotic taxa across a shelf-to-slope continuum in the Northern South China Sea. Appl Environ Microbiol 2023; 89:e0139323. [PMID: 38014961 PMCID: PMC10734510 DOI: 10.1128/aem.01393-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Virus-induced host lysis contributes up to 40% of total prokaryotic mortality and plays crucial roles in shaping microbial composition and diversity in the ocean. Nonetheless, what taxon-specific cell lysis is caused by viruses remains to be studied. The present study, therefore, examined the taxon-specific cell lysis and estimated its contribution to the variations in the rare and abundant microbial taxa. The results demonstrate that taxon-specific mortality differed in surface and bottom of the coastal environment. In addition, active rare taxa are more susceptible to heightened lytic pressure and suggested the importance of viral lysis in regulating the microbial community composition. These results improve our understanding of bottom-up (abiotic environmental variables) and top-down (viral lysis) controls contributing to microbial community assembly in the ocean.
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Affiliation(s)
- Lu Liu
- State Key Laboratory for 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
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Qi Chen
- State Key Laboratory for 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
| | - Yu Wang
- State Key Laboratory for 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
| | - Ting Zhang
- State Key Laboratory for 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
| | - Nianzhi Jiao
- State Key Laboratory for 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
| | - Qiang Zheng
- State Key Laboratory for 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
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18
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Marín-Vindas C, Sebastián M, Ruiz-González C, Balagué V, Vega-Corrales L, Gasol JM. Shifts in bacterioplankton community structure between dry and wet seasons in a tropical estuary strongly affected by riverine discharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166104. [PMID: 37558065 DOI: 10.1016/j.scitotenv.2023.166104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Estuaries are among the most productive ecosystems in the world and are highly dynamic due to the interaction of freshwater and seawater, which results in strong spatial gradients in physico-chemical conditions. Bacterioplankton play a central role in these systems, driving the fluxes of carbon and energy, and being central for contaminant removal in human-impacted areas. Most studies on bacterioplankton dynamics have been carried out in temperate estuaries, and they show that salinity is a major factor driving bacterioplankton distribution. Tropical estuaries, although largely understudied, experience drastic variations in river discharge between the dry and the rainy seasons, influencing the spatial distribution of the salinity gradient and thus likely impacting bacterioplankton communities. Using Illumina sequencing of the 16S rRNA gene, here we studied bacterial communities from the Nicoya's Gulf (Costa Rica), a large tropical estuary characterized by high riverine discharge during the rainy season, to explore seasonal changes in the spatial distribution and connectivity of these communities along the Gulf. Our results show pronounced differences in bacterial diversity and community structure between seasons and zones within the estuary (the shallow upper Gulf, the middle zone and the lower zone, located in the marine end of the estuary). Bacterial communities from the different regions were more similar during the rainy season, suggesting a larger degree of microbial connectivity likely driven by the fast water circulation fueled by the riverine discharge. In the dry season, Enterobacteriales and Cyanobacteria dominated bacterial communities, whereas in the rainy season Alphaproteobacteria was the dominant group. These contrasting seasonal trends were consistent with the seasonal variations observed in bacterial assemblages during a year at a single station in the upper region of the Gulf. We conclude that the Gulf is highly dynamic in both the spatial and temporal scale and that bacterioplankton communities are strongly influenced by the riverine and tidal inputs during both seasons. This study sheds light on the sources of variability in the structure of bacterial communities in tropical estuarine systems, an understudied type of aquatic ecosystem, and sets the basis to design further comprehensive studies on their microbial diversity.
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Affiliation(s)
- Carolina Marín-Vindas
- Universidad Nacional, Escuela de Ciencias Biológicas, Heredia, Costa Rica; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain.
| | - Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Vanessa Balagué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Luis Vega-Corrales
- Universidad Nacional, Escuela de Ciencias Biológicas, Heredia, Costa Rica
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
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19
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Carrión O, Li CY, Peng M, Wang J, Pohnert G, Azizah M, Zhu XY, Curson ARJ, Wang Q, Walsham KS, Zhang XH, Monaco S, Harvey JM, Chen XL, Gao C, Wang N, Wang XJ, Wang P, Giovanonni SJ, Lee CP, Suffridge CP, Zhang Y, Luo Z, Wang D, Todd JD, Zhang YZ. DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms. Nat Microbiol 2023; 8:2326-2337. [PMID: 38030907 PMCID: PMC10686828 DOI: 10.1038/s41564-023-01526-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.
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Affiliation(s)
- Ornella Carrión
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
| | - Ming Peng
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jinyan Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Muhaiminatul Azizah
- Institute of Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Jena, Germany
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Qing Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Keanu S Walsham
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - James M Harvey
- Department of Chemistry, King's College London, London, UK
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Juan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | | | - Chih-Ping Lee
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | | | - Yu Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ziqi Luo
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jonathan D Todd
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Qingdao, China.
- Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao, China.
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20
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Zheng N, Hu W, Zhou X, Liu Y, Bartlam M, Wang Y. Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival. ENVIRONMENTAL RESEARCH 2023; 237:117060. [PMID: 37659640 DOI: 10.1016/j.envres.2023.117060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/01/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.
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Affiliation(s)
- Ningning Zheng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Xinzhu Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yu Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), College of Life Sciences, Nankai University, Tianjin, 300350, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Nankai International Advanced Research Institute (Shenzhen Futian), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300350, China.
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21
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Gronniger JL, Gray PC, Niebergall AK, Johnson ZI, Hunt DE. A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters. PLoS One 2023; 18:e0293334. [PMID: 37943816 PMCID: PMC10635494 DOI: 10.1371/journal.pone.0293334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 phylotypes) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception. Additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.
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Affiliation(s)
| | - Patrick C. Gray
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
| | | | - Zackary I. Johnson
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
| | - Dana E. Hunt
- Marine Laboratory, Duke University, Beaufort, NC, United States of America
- Biology and Civil & Environmental Engineering, Duke University, Durham, NC, United States of America
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22
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Dželalija M, Kvesić-Ivanković M, Jozić S, Ordulj M, Kalinić H, Pavlinović A, Šamanić I, Maravić A. Marine resistome of a temperate zone: Distribution, diversity, and driving factors across the trophic gradient. WATER RESEARCH 2023; 246:120688. [PMID: 37806125 DOI: 10.1016/j.watres.2023.120688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
Marine and ocean environments are the most widespread habitats in the world but are still the least studied from the aspect of antibiotic resistance. The indigenous and tetracycline (TET)- and sulfamethoxazole (SXT)-resistant planktonic bacterial communities were simultaneously investigated for the first time along a trophic gradient of a temperate zone, regarding their taxonomic and functional structures as well as biotic and abiotic factors affecting their dynamics as vehicles of antibiotic resistance genes (ARGs), thus impacting the ARGs distribution at seasonal and spatial scales. A total of 80 microbiomes, recovered seasonally from bottom layer and surface waters along a 68-km transect from wastewater-impacted estuary to coastal and pristine open sea in the central Adriatic (Mediterranean Sea), were analysed using 16S rRNA amplicon sequencing, PICRUSt2 bioinformatics and extensive biostatistics. Eighty-one bacterial phyla were identified, with majority (n = 49) in summer when communities were found to be more species enriched across the gradient. Microbial diversity was more site-specific and pronounced in surface microbiomes in winter. Nevertheless, both richness and community diversity decreased with distance from the coast. Although the microbiomes from human-influenced sites significantly differed from those in oligotrophic offshore area, Proteobacteria were still the most abundant phylum during both seasons at the surface and seabed along the gradient, and the major contributors to the marine resistome regarding native and TET- and SXT-resistant microbial communities. Resistome structure was more diverse in winter, whereas peptide, vancomycin and multidrug resistance modules predominated regardless of season, trophic status, or antibiotic. However, multidrug, beta-lactam resistance modules as well as macrolide, phenicol, aminoglycoside, and particularly imipenem resistance genes were much more frequent in winter, suggesting that the diversity of indigenous resistomes is highly dependent on seasonal variations of the water column, driven by thermohaline stratification and nutrients. Moreover, several pathogenic genera stood out as important carriers of multiple resistance traits in TET- and SXT-related resistomes in both seasons, particularly Acinetobacter, Vibrio, Bacillus and Pseudomonas, beside which Proteus, Serratia and Bacteroides prevailed in native resistomes. This study evidenced seasonal and spatial variations of the marine microbiome and resistome and their driving forces along the trophic gradient, providing a comprehensive insight into the diversity and distribution of antibiotic resistance in the marine ecosystem of a temperate zone.
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Affiliation(s)
- Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Marija Kvesić-Ivanković
- Center of Excellence for Science and Technology-Integration of Mediterranean Region, University of Split, Ruđera Boškovića 31, 21000 Split, Croatia; Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Slaven Jozić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - Marin Ordulj
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, 21000 Split, Croatia
| | - Hrvoje Kalinić
- Department of Informatics, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Antonio Pavlinović
- Faculty of Electrical Engineering, Mechanical Engineering and Naval Architecture, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia.
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23
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Grabowska-Grucza K, Kiersztyn B. Relationships between Legionella and Aeromonas spp. and associated lake bacterial communities across seasonal changes in an anthropogenic eutrophication gradient. Sci Rep 2023; 13:17076. [PMID: 37816753 PMCID: PMC10564844 DOI: 10.1038/s41598-023-43234-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
Anthropogenic eutrophication of lakes threatens their homeostasis and carries an increased risk of development of potentially pathogenic microorganisms. In this paper we show how eutrophication affects seasonal changes in the taxonomic structure of bacterioplankton and whether these changes are associated with the relative abundance of pathogenic bacteria of the genera Legionella and Aeromonas. The subject of the study was a unique system of interconnected lakes in northern Poland (Great Masurian Lakes system), characterized by the presence of eutrophic gradient. We found that the taxonomic structure of the bacterial community in eutrophic lakes was significantly season dependent. No such significant seasonal changes were observed in meso-eutrophic lakes. We found that there is a specific taxonomic composition of bacteria associated with the occurrence of Legionella spp. The highest positive significant correlations were found for families Pirellulaceae, Mycobacteriaceae and Gemmataceae. The highest negative correlations were found for the families Sporichthyaceae, Flavobacteriaceae, the uncultured families of class Verrucomicrobia and Chitinophagaceae. We used also an Automatic Neural Network model to estimate the relative abundance of Legionella spp. based on the relative abundance of dominant bacterial families. In the case of Aeromonas spp. we did not find a clear relationship with bacterial communities inhabiting lakes of different trophic state. Our research has shown that anthropogenic eutrophication causes significant changes in the taxonomic composition of lake bacteria and contributes to an increase in the proportion of potentially pathogenic Legionella spp.
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Affiliation(s)
- Karolina Grabowska-Grucza
- Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
| | - Bartosz Kiersztyn
- Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland
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24
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Mendoza-Cano F, Encinas-García T, Muhlia-Almazán A, Porchas-Cornejo M, de la Re-Vega E, Sánchez-Paz A. Development and validation of a real-time PCR assay protocol for the specific detection and quantification of pelagiphages in seawater samples. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106168. [PMID: 37708616 DOI: 10.1016/j.marenvres.2023.106168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/16/2023]
Abstract
Earth is inhabited by numerous adaptations of cellular forms shaped by the persistent scrutiny of natural selection. Thus, as natural selection has fixed beneficial adaptations of functional traits, cellular life has conquered almost all environmental niches on our planet. However, cellular life succumbs in number and genetic diversity to viruses. Among all viruses, phages are highly prevalent in diverse environments, and due to their vast genetic diversity and abundance, their relevant role as significant players in several ecological processes is now fully recognized. Pelagiphages, bacteriophages infecting bacteria of the SAR11 clade, are the most abundant viruses in the oceans. However, the ecological contribution of pelagiphages on populations of Pelagibacterales remains largely underestimated. An essential aspect of estimating the impact of bacteriophages is their absolute and precise quantification, which provides relevant information about the host-virus interactions and the structure of viral assemblages. Consequently, due to its abundance and claimed influence in the biogeochemical cycling of elements, the accurate quantification of pelagiphages results in an essential task. This study describes the development and validation of a sensitive, specific, accurate and reproducible qPCR platform targeting pelagiphages. Moreover, this method allowed the detection and quantification of pelagiphages in the Gulf of California for the first time.
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Affiliation(s)
- F Mendoza-Cano
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México
| | - T Encinas-García
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México; Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Muhlia-Almazán
- Bioenergetics and Molecular Genetics Lab, Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C. Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo, Sonora, 83304, México
| | - M Porchas-Cornejo
- Centro de Investigaciones Biológicas del Noroeste, S.C. Km 2.35 Carretera a Las Tinajas, S/N Colonia Tinajas, Guaymas, Sonora, C.P. 85460, México
| | - E de la Re-Vega
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Hermosillo, Sonora, 83000, México
| | - A Sánchez-Paz
- Laboratorio de Virología, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C. (Campus Hermosillo), Calle Hermosa 101, Fraccionamiento Los Ángeles, Hermosillo, Sonora, C.P. 83206, México.
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25
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Zhang R, Debeljak P, Blain S, Obernosterer I. Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling. Environ Microbiol 2023; 25:1816-1829. [PMID: 37157891 DOI: 10.1111/1462-2920.16397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Iron (Fe) governs the cycling of organic carbon in large parts of the Southern Ocean. The strategies of diverse microbes to acquire the different chemical forms of Fe under seasonally changing organic carbon regimes remain, however, poorly understood. Here, we report high-resolution seasonal metagenomic observations from the region off Kerguelen Island (Indian Sector of the Southern Ocean) where natural Fe-fertilization induces consecutive spring and summer phytoplankton blooms. Our data illustrate pronounced, but distinct seasonal patterns in the abundance of genes implicated in the transport of different forms of Fe and organic substrates, of siderophore biosynthesis and carbohydrate-active enzymes. The seasonal dynamics suggest a temporal decoupling in the prokaryotic requirements of Fe and organic carbon during the spring phytoplankton bloom and a concerted access to these resources after the summer bloom. Taxonomic assignments revealed differences in the prokaryotic groups harbouring genes of a given Fe-related category and pronounced seasonal successions were observed. Using MAGs we could decipher the respective Fe- and organic substrate-related genes of individual taxa assigned to abundant groups. The ecological strategies related to Fe-acquisition provide insights on how this element could shape microbial community composition with potential implications on organic matter transformations in the Southern Ocean.
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Affiliation(s)
- Rui Zhang
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
| | - Pavla Debeljak
- Sorbonne Université, Muséum National d'Histoire, Naturelle, CNRS, EPHE, Université des Antilles, Institut de Systématique, Evolution, Biodiversité (ISYEB), Paris, France
- SupBiotech, Villejuif, France
| | - Stephane Blain
- 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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26
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes. THE ISME JOURNAL 2023; 17:1660-1670. [PMID: 37452097 PMCID: PMC10504331 DOI: 10.1038/s41396-023-01466-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.
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Affiliation(s)
| | | | - Ashley G Bell
- School of Biosciences, University of Exeter, Exeter, UK
| | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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27
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Arcadi E, Buschi E, Rastelli E, Tangherlini M, De Luca P, Esposito V, Calogero R, Andaloro F, Romeo T, Danovaro R. Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field. Microorganisms 2023; 11:2464. [PMID: 37894122 PMCID: PMC10608945 DOI: 10.3390/microorganisms11102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.
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Affiliation(s)
- Erika Arcadi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Valentina Esposito
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale—OGS Borgo Grotta Gigante 42/C, 34010 Sgonico, Italy;
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Via dei Mille 46, 98057 Milazzo, Italy
- National Institute for Environmental Protection and Research, Via dei Mille 46, 98057 Milazzo, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
- National Biodiversity Future Centre (NBFC), 90133 Palermo, Italy
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28
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Chen X, Hu C, Wei W, Yang Y, Weinbauer MG, Li H, Ren S, Ma R, Huang Y, Luo T, Jiao N, Zhang R. Virus-Host Interactions Drive Contrasting Bacterial Diel Dynamics in the Ocean. RESEARCH (WASHINGTON, D.C.) 2023; 6:0213. [PMID: 37614364 PMCID: PMC10443526 DOI: 10.34133/research.0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
Marine organisms perform a sea of diel rhythmicity. Planktonic diel dynamics have been shown to be driven by light, energy resources, circadian rhythms, and the coordinated coupling of photoautotrophs and heterotrophic bacterioplankton. Here, we explore the diel fluctuation of viral production and decay and their impact on the total and active bacterial community in the coastal and open seawaters of the South China Sea. The results showed that the night-production diel pattern of lytic viral production was concurrent with the lower viral decay at night, contributing to the accumulation of the viral population size during the night for surface waters. The diel variations in bacterial activity, community composition, and diversity were found highly affected by viral dynamics. This was revealed by the finding that bacterial community diversity was positively correlated to lytic viral production in the euphotic zone of the open ocean but was negatively related to lysogenic viral production in the coastal ocean. Such distinct but contrasting correlations suggest that viral life strategies can not only contribute to diversifying bacterial community but also potentially piggyback their host to dominate bacterial community, suggesting the tightly synchronized depth-dependent and habitat-specific diel patterns of virus-host interactions. It further implies that viruses serve as an ecologically important driver of bacterial diel dynamics across the ocean, highlighting the viral roles in bacterial ecological and biogeochemical processes in the ocean.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wei Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, PR China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, PR China
| | - Markus G Weinbauer
- Sorbonne Universités, UPMC, Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV), Villefranche-sur-Mer 06230, France
| | - Hongbo Li
- National Marine Environmental Monitoring Center, Ministry of Ecological Environment, Dalian 116023, PR China
| | - Shiying Ren
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Yibin Huang
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
- NOAA/OAR Pacific Marine Environmental Laboratory, Seattle, WA, USA
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, PR China
- Institute for Advanced Study, Shenzhen University, Shenzhen 518055, PR China
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29
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Doane MP, Reed MB, McKerral J, Farias Oliveira Lima L, Morris M, Goodman AZ, Johri S, Papudeshi B, Dillon T, Turnlund AC, Peterson M, Mora M, de la Parra Venegas R, Pillans R, Rohner CA, Pierce SJ, Legaspi CG, Araujo G, Ramirez-Macias D, Edwards RA, Dinsdale EA. Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome. Sci Rep 2023; 13:12747. [PMID: 37550406 PMCID: PMC10406844 DOI: 10.1038/s41598-023-39184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/20/2023] [Indexed: 08/09/2023] Open
Abstract
Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.
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Affiliation(s)
| | - Michael B Reed
- North Carolina Agricultural and Technical State University, Greensboro, NC, USA
| | | | | | - Megan Morris
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Shaili Johri
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | | | | | - Abigail C Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD, Australia
| | | | - Maria Mora
- San Diego State University, San Diego, CA, USA
| | | | | | | | | | | | - Gonzalo Araujo
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
- Marine Research and Conservation Foundation, Lydeard St Lawrence, Somerset, UK
| | - Deni Ramirez-Macias
- Tiburon Ballena Mexico de Conciencia Mexico, La Paz, Baja California Sur, Mexico
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30
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Brüwer JD, Orellana LH, Sidhu C, Klip HCL, Meunier CL, Boersma M, Wiltshire KH, Amann R, Fuchs BM. In situ cell division and mortality rates of SAR11, SAR86, Bacteroidetes, and Aurantivirga during phytoplankton blooms reveal differences in population controls. mSystems 2023; 8:e0128722. [PMID: 37195198 PMCID: PMC10308942 DOI: 10.1128/msystems.01287-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023] Open
Abstract
Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence in situ hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum Bacteroidetes, and its genus Aurantivirga. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and Aurantivirga of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (-0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom-up and top-down controls. IMPORTANCE The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom-up and top-down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates in situ. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (Bacteroidetes and Aurantivirga) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top-down control. Microscopy remains the method of choice to understand ecological processes like top-down and bottom-up control on a cellular level.
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Affiliation(s)
- Jan D. Brüwer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helena C. L. Klip
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Cédric L. Meunier
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- University of Bremen, Bremen, Germany
| | - Karen H. Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wattenmeerstation, List auf Sylt, Bremerhaven, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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31
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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Mohapatra M, Manu S, Kim JY, Rastogi G. Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163109. [PMID: 36996988 DOI: 10.1016/j.scitotenv.2023.163109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2-97.8 %) was greater than nestedness (2.2-27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500048, India
| | - Ji Yoon Kim
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
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33
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Sun CC, Zhao WJ, Yue WZ, Cheng H, Sun FL, Wang YT, Wu ML, Engel A, Wang YS. Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China. Front Microbiol 2023; 14:1180321. [PMID: 37425997 PMCID: PMC10322874 DOI: 10.3389/fmicb.2023.1180321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.
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Affiliation(s)
- Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Jie Zhao
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhong Yue
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Yu-Tu Wang
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
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34
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Abreu CI, Dal Bello M, Bunse C, Pinhassi J, Gore J. Warmer temperatures favor slower-growing bacteria in natural marine communities. SCIENCE ADVANCES 2023; 9:eade8352. [PMID: 37163596 PMCID: PMC10171810 DOI: 10.1126/sciadv.ade8352] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.
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Affiliation(s)
- Clare I Abreu
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Martina Dal Bello
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carina Bunse
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution of Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
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35
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Mitra A, Flynn KJ. Low rates of bacterivory enhances phototrophy and competitive advantage for mixoplankton growing in oligotrophic waters. Sci Rep 2023; 13:6900. [PMID: 37106077 PMCID: PMC10140275 DOI: 10.1038/s41598-023-33962-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/21/2023] [Indexed: 04/29/2023] Open
Abstract
With climate change, oceans are becoming increasingly nutrient limited, favouring growth of prokaryotic picoplankton at the expense of the larger protist plankton whose growth support higher trophic levels. Constitutive mixoplankton (CM), microalgal plankton with innate phototrophic capability coupled with phagotrophy, graze on these picoplankton, indirectly exploiting the excellent resource acquisition abilities of the prokaryotes. However, feeding rates can be very low (e.g., a few bacteria d-1). For the first time, the significance of such low consumption rates has been quantified. We find that while prokaryote-carbon (C) supply to CM grown at non-limiting light was so low that it may appear insignificant (< 10%), contributions of nitrogen (N) and phosphorus (P) from ingestions of 1-12 prokaryotes d-1 were significant. Under limiting light, contributions of ingested C increased, also raising the contributions of N and P. The order of nutritional importance for CM growth from predation was P > N > C. Further, provision of N through internal recycling of ingested prey-N stimulates C-fixation through photosynthesis. Importantly, coupled photo-phago-mixoplanktonic activity improved CM resource affinities for both inorganic and prey-bound nutrients, enhancing the nutritional status and competitiveness of mixoplankton. With warming oceans, with increased prokaryote abundance, we expect CM to exhibit more phagotrophy.
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Affiliation(s)
- Aditee Mitra
- School of Earth and Environmental Sciences, Cardiff University, Park Place, Cardiff, CF10 3AT, Wales, UK.
| | - Kevin J Flynn
- Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth, PL1 3DH, UK
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36
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Lanclos VC, Rasmussen AN, Kojima CY, Cheng C, Henson MW, Faircloth BC, Francis CA, Thrash JC. Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. THE ISME JOURNAL 2023; 17:620-629. [PMID: 36739346 PMCID: PMC10030771 DOI: 10.1038/s41396-023-01376-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
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Affiliation(s)
- V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Conner Y Kojima
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chuankai Cheng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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37
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME COMMUNICATIONS 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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38
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Cai L, Xu B, Li H, Xu Y, Wei W, Zhang R. Spatiotemporal Shift of T4-Like Phage Community Structure in the Three Largest Estuaries of China. Microbiol Spectr 2023; 11:e0520322. [PMID: 36877016 PMCID: PMC10101079 DOI: 10.1128/spectrum.05203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
Estuaries are one of the most highly productive and economically important ecosystems at the continent-ocean interface. Estuary productivity is largely determined by the microbial community structure and activity. Viruses are major agents of microbial mortality and are key drivers of global geochemical cycles. However, the taxonomic diversity of viral communities and their spatial-temporal distribution in estuarine ecosystems have been poorly studied. In this study, we investigated the T4-like viral community composition at three major Chinese estuaries in winter and in summer. Diverse T4-like viruses, which were divided into three main clusters (Clusters I to III), were revealed. The Marine Group of Cluster III, with seven identified subgroups, was the most dominant (averaging 76.5% of the total sequences) in the Chinese estuarine ecosystems. Significant variations of T4-like viral community composition were observed among estuaries and seasons, with higher diversity occurring in winter. Among various environmental variables, temperature was a main driver of the viral communities. This study demonstrates viral assemblage diversification and seasonality in Chinese estuarine ecosystems. IMPORTANCE Viruses are ubiquitous but largely uncharacterized members of aquatic environments that cause significant mortality in microbial communities. Recent large-scale oceanic projects have greatly advanced our understanding of viral ecology in marine environments, but those studies mostly focused on oceanic regions. There have yet to be spatiotemporal studies of viral communities in estuarine ecosystems, which are unique habitats that play a significant role in global ecology and biogeochemistry. This work is the first comprehensive study that provides a detailed picture of the spatial and seasonal variation of viral communities (specifically, T4-like viral communities) in three major estuarine ecosystems in China. These findings provide much-needed knowledge regarding estuarine viral ecosystems, which currently lags in oceanic ecosystem research.
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Affiliation(s)
- Lanlan Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Bu Xu
- School of Environment, Harbin Institute of Technology, Harbin, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Key Laboratory of Coastal Salt Marsh Ecosystems and Resources, Ministry of Natural Resources, Jiangsu Ocean University, Lianyungang, China
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Shandong, China
| | - Wei Wei
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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39
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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40
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Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
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41
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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42
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Kiefl E, Esen OC, Miller SE, Kroll KL, Willis AD, Rappé MS, Pan T, Eren AM. Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. SCIENCE ADVANCES 2023; 9:eabq4632. [PMID: 36812328 DOI: 10.1126/sciadv.abq4632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
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Affiliation(s)
- Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ozcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Samuel E Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Kourtney L Kroll
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96822, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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43
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Roda-Garcia JJ, Haro-Moreno JM, Rodriguez-Valera F, Almagro-Moreno S, López-Pérez M. Single-amplified genomes reveal most streamlined free-living marine bacteria. Environ Microbiol 2023. [PMID: 36755376 DOI: 10.1111/1462-2920.16348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.
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Affiliation(s)
- Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.,National Center for Integrated Coastal Research, University of Central Florida, Orlando, Florida, USA
| | - Mario López-Pérez
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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44
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Iriarte J, Dachs J, Casas G, Martínez-Varela A, Berrojalbiz N, Vila-Costa M. Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1625-1636. [PMID: 36655903 PMCID: PMC9893724 DOI: 10.1021/acs.est.2c05583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 05/28/2023]
Abstract
The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.
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45
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Vincent F, Gralka M, Schleyer G, Schatz D, Cabrera-Brufau M, Kuhlisch C, Sichert A, Vidal-Melgosa S, Mayers K, Barak-Gavish N, Flores JM, Masdeu-Navarro M, Egge JK, Larsen A, Hehemann JH, Marrasé C, Simó R, Cordero OX, Vardi A. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun 2023; 14:510. [PMID: 36720878 PMCID: PMC9889395 DOI: 10.1038/s41467-023-36049-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
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Affiliation(s)
- Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Systems Biology Lab, Amsterdam Institute for Life and Environment (A-Life)/Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Sichert
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Kyle Mayers
- NORCE Norwegian Research Centre, 5008, Bergen, Norway
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - J Michel Flores
- Department of Earth and Planetary Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Jorun Karin Egge
- Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008, Bergen, Norway.,Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Celia Marrasé
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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46
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Herndl GJ, Bayer B, Baltar F, Reinthaler T. Prokaryotic Life in the Deep Ocean's Water Column. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:461-483. [PMID: 35834811 DOI: 10.1146/annurev-marine-032122-115655] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The oceanic waters below a depth of 200 m represent, in terms of volume, the largest habitat of the biosphere, harboring approximately 70% of the prokaryotic biomass in the oceanic water column. These waters are characterized by low temperature, increasing hydrostatic pressure, and decreasing organic matter supply with depth. Recent methodological advances in microbial oceanography have refined our view of the ecology of prokaryotes in the dark ocean. Here, we review the ecology of prokaryotes of the dark ocean, present data on the biomass distribution and heterotrophic and chemolithoautotrophic prokaryotic production in the major oceanic basins, and highlight the phylogenetic and functional diversity of this part of the ocean. We describe the connectivity of surface and deep-water prokaryotes and the molecular adaptations of piezophilic prokaryotes to high hydrostatic pressure. We also highlight knowledge gaps in the ecology of the dark ocean's prokaryotes and their role in the biogeochemical cycles in the largest habitat of the biosphere.
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Affiliation(s)
- 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
| | - Barbara Bayer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria;
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47
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Dunn AK. Alternative oxidase in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148929. [PMID: 36265564 DOI: 10.1016/j.bbabio.2022.148929] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
While alternative oxidase (AOX) was discovered in bacteria in 2003, the expression, function, and evolutionary history of this protein in these important organisms is largely unexplored. To date, expression and functional analysis is limited to studies in the Proteobacteria Novosphingobium aromaticivorans and Vibrio fischeri, where AOX likely plays roles in maintenance of cellular energy homeostasis and supporting responses to cellular stress. This review describes the history of the study of AOX in bacteria, details current knowledge of the predicted biochemical and structural characteristics, distribution, and function of bacterial AOX, and highlights interesting areas for the future study of AOX in bacteria.
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Affiliation(s)
- Anne K Dunn
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA.
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48
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Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. MICROBIOME 2022; 10:212. [PMID: 36464731 PMCID: PMC9721005 DOI: 10.1186/s40168-022-01410-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes. RESULTS We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies. CONCLUSIONS We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.
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Affiliation(s)
- Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Quentin Clayssen
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marisa Isabell Keller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel R. Mende
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
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49
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Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D'Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764-770. [PMID: 36477536 PMCID: PMC9771814 DOI: 10.1038/s41586-022-05505-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
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Affiliation(s)
| | | | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma, Spain
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Joe Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - 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
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Dinasquet J, Landa M, Obernosterer I. SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:907-916. [PMID: 36028477 DOI: 10.1111/1758-2229.13117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
The ecology of the SAR11 clade, the most abundant bacterial group in the ocean, has been intensively studied in temperate and tropical regions, but its distribution remains largely unexplored in the Southern Ocean. Through amplicon sequencing of the 16S rRNA gene, we assessed the contribution of the SAR11 clade to bacterial community composition in the naturally iron fertilized region off Kerguelen Island. We investigated the upper 300 m at seven sites located in early spring phytoplankton blooms and at one high-nutrient low-chlorophyll site. Despite pronounced vertical patterns of the bacterioplankton assemblages, the SAR11 clade had high relative abundances at all depths and sites, averaging 40% (±15%) of the total community relative abundance. Micro-autoradiography combined with CARD-FISH further revealed that the clade had an overall stable contribution (45%-60% in surface waters) to bacterial biomass production (determined by 3 H-leucine incorporation) during different early bloom stages. The spatio-temporal partitioning of some of the SAR11 subclades suggests a niche specificity and periodic selection of different subclades in response to the fluctuating extreme conditions of the Southern Ocean. These observations improve our understanding of the ecology of the SAR11 clade and its implications in biogeochemical cycles in the rapidly changing Southern Ocean.
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Affiliation(s)
- Julie Dinasquet
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Marine Biology Research Division and Climate, Atmospheric Science & Physical Oceanography Department, Scripps Institution of Oceanography, San Diego, California, USA
| | - Marine Landa
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
- Sorbonne Université/Centre National de la Recherche Scientifique, UMR7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, Banyuls-sur-Mer, France
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