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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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Howard-Varona C, Roux S, Bowen BP, Silva LP, Lau R, Schwenck SM, Schwartz S, Woyke T, Northen T, Sullivan MB, Floge SA. Protist impacts on marine cyanovirocell metabolism. ISME COMMUNICATIONS 2022; 2:94. [PMID: 37938263 PMCID: PMC9723779 DOI: 10.1038/s43705-022-00169-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 07/26/2023]
Abstract
The fate of oceanic carbon and nutrients depends on interactions between viruses, prokaryotes, and unicellular eukaryotes (protists) in a highly interconnected planktonic food web. To date, few controlled mechanistic studies of these interactions exist, and where they do, they are largely pairwise, focusing either on viral infection (i.e., virocells) or protist predation. Here we studied population-level responses of Synechococcus cyanobacterial virocells (i.e., cyanovirocells) to the protist Oxyrrhis marina using transcriptomics, endo- and exo-metabolomics, photosynthetic efficiency measurements, and microscopy. Protist presence had no measurable impact on Synechococcus transcripts or endometabolites. The cyanovirocells alone had a smaller intracellular transcriptional and metabolic response than cyanovirocells co-cultured with protists, displaying known patterns of virus-mediated metabolic reprogramming while releasing diverse exometabolites during infection. When protists were added, several exometabolites disappeared, suggesting microbial consumption. In addition, the intracellular cyanovirocell impact was largest, with 4.5- and 10-fold more host transcripts and endometabolites, respectively, responding to protists, especially those involved in resource and energy production. Physiologically, photosynthetic efficiency also increased, and together with the transcriptomics and metabolomics findings suggest that cyanovirocell metabolic demand is highest when protists are present. These data illustrate cyanovirocell responses to protist presence that are not yet considered when linking microbial physiology to global-scale biogeochemical processes.
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Affiliation(s)
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | | | - Leslie P Silva
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Syft Technologies, Ltd, Christchurch, 8024, New Zealand
| | - Rebecca Lau
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cellular and Molecular Medicine and Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Samuel Schwartz
- Department of Biology, Wake Forest University, Winston Salem, NC, USA
| | - Tanja Woyke
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | - Trent Northen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. DOE Joint Genome Institute, Berkeley, CA, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA.
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston Salem, NC, USA.
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Petersen C, Pees B, Martínez Christophersen C, Leippe M. Preconditioning With Natural Microbiota Strain Ochrobactrum vermis MYb71 Influences Caenorhabditis elegans Behavior. Front Cell Infect Microbiol 2021; 11:775634. [PMID: 34976859 PMCID: PMC8718863 DOI: 10.3389/fcimb.2021.775634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
In comparison with the standard monoxenic maintenance in the laboratory, rearing the nematode Caenorhabditis elegans on its natural microbiota improves its fitness and immunity against pathogens. Although C. elegans is known to exhibit choice behavior and pathogen avoidance behavior, little is known about whether C. elegans actively chooses its (beneficial) microbiota and whether the microbiota influences worm behavior. We examined eleven natural C. elegans isolates in a multiple-choice experiment for their choice behavior toward four natural microbiota bacteria and found that microbiota choice varied among C. elegans isolates. The natural C. elegans isolate MY2079 changed its choice behavior toward microbiota isolate Ochrobactrum vermis MYb71 in both multiple-choice and binary-choice experiments, in particular on proliferating bacteria: O. vermis MYb71 was chosen less than other microbiota bacteria or OP50, but only after preconditioning with MYb71. Examining escape behavior and worm fitness on MYb71, we ruled out pathogenicity of MYb71 and consequently learned pathogen avoidance behavior as the main driver of the behavioral change toward MYb71. The change in behavior of C. elegans MY2079 toward microbiota bacterium MYb71 demonstrates how the microbiota influences the worm's choice. These results might give a baseline for future research on host-microbiota interaction in the C. elegans model.
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Affiliation(s)
- Carola Petersen
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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Bock C, Jensen M, Forster D, Marks S, Nuy J, Psenner R, Beisser D, Boenigk J. Factors shaping community patterns of protists and bacteria on a European scale. Environ Microbiol 2020; 22:2243-2260. [PMID: 32202362 DOI: 10.1111/1462-2920.14992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/18/2020] [Indexed: 01/19/2023]
Abstract
Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
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Affiliation(s)
- Christina Bock
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Manfred Jensen
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Str. 14, 67663, Kaiserslautern, Germany
| | - Sabina Marks
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Julia Nuy
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Roland Psenner
- Lake and Glacier Research, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Daniela Beisser
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Jens Boenigk
- Biodiversity, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
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