201
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Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nat Microbiol 2019; 4:1706-1715. [PMID: 31332382 DOI: 10.1038/s41564-019-0507-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/06/2019] [Indexed: 01/29/2023]
Abstract
In the surface ocean, phytoplankton transform inorganic substrates into organic matter that fuels the activity of heterotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon recycling and storage in the ocean. Yet, the diversity of organic molecules and interacting organisms has hindered detection of specific relationships that mediate this large flux of energy and matter. Here, we show that a tightly coupled microbial network based on organic sulfur compounds (sulfonates) exists among key lineages of eukaryotic phytoplankton producers and heterotrophic bacterial consumers in the North Pacific Subtropical Gyre. We find that cultured eukaryotic phytoplankton taxa produce sulfonates, often at millimolar internal concentrations. These same phytoplankton-derived sulfonates support growth requirements of an open-ocean isolate of the SAR11 clade, the most abundant group of marine heterotrophic bacteria. Expression of putative sulfonate biosynthesis genes and sulfonate abundances in natural plankton communities over the diel cycle link sulfonate production to light availability. Contemporaneous expression of sulfonate catabolism genes in heterotrophic bacteria highlights active cycling of sulfonates in situ. Our study provides evidence that sulfonates serve as an ecologically important currency for nutrient and energy exchange between microbial autotrophs and heterotrophs, highlighting the importance of organic sulfur compounds in regulating ecosystem function.
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202
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Lannes R, Olsson-Francis K, Lopez P, Bapteste E. Carbon Fixation by Marine Ultrasmall Prokaryotes. Genome Biol Evol 2019; 11:1166-1177. [PMID: 30903144 PMCID: PMC6475129 DOI: 10.1093/gbe/evz050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin–Benson–Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood–Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle, have been described. Nano-organisms such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described; and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways was quantified and tested for the presence of all key enzymes in nano-organisms from across the World Ocean. The novel marine ultrasmall prokaryotes were demonstrated to collectively harbor the genes required for carbon fixation, in particular the “energetically efficient” dicarboxylate/4-hydroxybutyrate pathway and the 4-hydroxybutyrate pathway. This contrasted with the known carbon metabolic pathways associated with CPR members in aquifers, where they are described as degraders (Castelle CJ, et al. 2015. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 25(6):690–701; Castelle CJ, et al. 2018. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 16(10):629–645; Anantharaman K, et al. 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 7:13219.). Our findings suggest that nano-organisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN superphyla are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nano-organisms by future single cell genomics is anticipated.
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Affiliation(s)
- Romain Lannes
- Sorbonne Université, Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystems, The Open University, Milton Keynes, United Kingdom
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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203
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García-López R, Pérez-Brocal V, Moya A. Beyond cells - The virome in the human holobiont. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:373-396. [PMID: 31528630 PMCID: PMC6717880 DOI: 10.15698/mic2019.09.689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.
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Affiliation(s)
- Rodrigo García-López
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Vicente Pérez-Brocal
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Andrés Moya
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
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204
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Debeljak P, Toulza E, Beier S, Blain S, Obernosterer I. Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environ Microbiol 2019; 21:2360-2374. [PMID: 30958628 PMCID: PMC6618146 DOI: 10.1111/1462-2920.14621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Iron (Fe) is a limiting nutrient in large regions of the ocean, but the strategies of prokaryotes to cope with this micronutrient are poorly known. Using a gene-specific approach from metatranscriptomics data, we investigated seven Fe-related metabolic pathways in microbial communities from high nutrient low chlorophyll and naturally Fe-fertilized waters in the Southern Ocean. We observed major differences in the contribution of prokaryotic groups at different taxonomic levels to transcripts encoding Fe-uptake mechanisms, intracellular Fe storage and replacement and Fe-related pathways in the tricarboxylic acid (TCA) cycle. The composition of the prokaryotic communities contributing to the transcripts of a given Fe-related pathway was overall independent of the in situ Fe supply, indicating that microbial taxa utilize distinct Fe-related metabolic processes. Only a few prokaryotic groups contributed to the transcripts of more than one Fe-uptake mechanism, suggesting limited metabolic versatility. Taxa-specific expression of individual genes varied among prokaryotic groups and was substantially higher for all inspected genes in Fe-limited as compared to naturally fertilized waters, indicating the link between transcriptional state and Fe regime. Different metabolic strategies regarding low Fe concentrations in the Southern Ocean are discussed for two abundant prokaryotic groups, Pelagibacteraceae and Flavobacteriaceae.
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Affiliation(s)
- Pavla Debeljak
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, A‐1090ViennaAustria
| | - Eve Toulza
- Université Perpignan Via DomitiaIHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F‐66860PerpignanFrance
| | - Sara Beier
- Leibniz Institute for Baltic Sea ResearchWarnemündeGermany
| | - Stephane Blain
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
| | - Ingrid Obernosterer
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
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205
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The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea. Sci Rep 2019; 9:9176. [PMID: 31235719 PMCID: PMC6591218 DOI: 10.1038/s41598-019-45512-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/04/2019] [Indexed: 01/05/2023] Open
Abstract
To investigate the interactions between bacterial species in relation to the biotic and abiotic environmental fluctuations, free-living (FL), nanoparticle-associated (NP), and microparticle-associated (MP) bacterial community compositions (BCCs) were analyzed. A total of 267 samples were collected from July to December 2016 in the dynamic and shallow southern coastal water of Korea. The variations in BCC mostly depended on planktonic size fraction. Network analysis revealed water depth-dependent co-occurrence patterns of coastal bacterial communities. Higher interspecies connectivity was observed within FL bacteria than NP/MP bacteria, suggesting that FL bacteria with a streamlined genome may need other bacterial metabolites for survival, while the NP/MP copiotrophs may have the self-supporting capacity to produce the vital nutrients. The analysis of topological roles of individual OTUs in the network revealed that several groups of metabolically versatile bacteria (the marine Roseobacters, Flavobacteriales, Desulfobacterales, and SAR406 clade) acted as module hubs in different water depth. In conclusion, interspecies interactions dominated in FL bacteria, compared to NP and MP bacteria; modular structures of bacterial communities and keystone species strongly depended on the water depth-derived environmental factors. Furthermore, the multifunctional, versatile FL bacteria could play pivotal roles in dynamic shallow coastal ecosystems.
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206
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Becker JW, Hogle SL, Rosendo K, Chisholm SW. Co-culture and biogeography of Prochlorococcus and SAR11. THE ISME JOURNAL 2019; 13:1506-1519. [PMID: 30742057 PMCID: PMC6775983 DOI: 10.1038/s41396-019-0365-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/03/2019] [Accepted: 01/18/2019] [Indexed: 01/07/2023]
Abstract
Prochlorococcus and SAR11 are among the smallest and most abundant organisms on Earth. With a combined global population of about 2.7 × 1028 cells, they numerically dominate bacterioplankton communities in oligotrophic ocean gyres and yet they have never been grown together in vitro. Here we describe co-cultures of Prochlorococcus and SAR11 isolates representing both high- and low-light adapted clades. We examined: (1) the influence of Prochlorococcus on the growth of SAR11 and vice-versa, (2) whether Prochlorococcus can meet specific nutrient requirements of SAR11, and (3) how co-culture dynamics vary when Prochlorococcus is grown with SAR11 compared with sympatric copiotrophic bacteria. SAR11 grew 15-70% faster in co-culture with Prochlorococcus, while the growth of the latter was unaffected. When Prochlorococcus populations entered stationary phase, this commensal relationship rapidly became amensal, as SAR11 abundances decreased dramatically. In parallel experiments with copiotrophic bacteria; however, the heterotrophic partner increased in abundance as Prochlorococcus densities leveled off. The presence of Prochlorococcus was able to meet SAR11's central requirement for organic carbon, but not reduced sulfur. Prochlorococcus strain MIT9313, but not MED4, could meet the unique glycine requirement of SAR11, which could be due to the production and release of glycine betaine by MIT9313, as supported by comparative genomic evidence. Our findings also suggest, but do not confirm, that Prochlorococcus MIT9313 may compete with SAR11 for the uptake of 3-dimethylsulfoniopropionate (DMSP). To give our results an ecological context, we assessed the relative contribution of Prochlorococcus and SAR11 genome equivalents to those of identifiable bacteria and archaea in over 800 marine metagenomes. At many locations, more than half of the identifiable genome equivalents in the euphotic zone belonged to Prochlorococcus and SAR11 - highlighting the biogeochemical potential of these two groups.
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Affiliation(s)
- Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Haverford College, Haverford, PA, USA.
| | - Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kali Rosendo
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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207
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Noell SE, Giovannoni SJ. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ Microbiol 2019; 21:2559-2575. [PMID: 31090982 DOI: 10.1111/1462-2920.14649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 11/29/2022]
Abstract
Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14 C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell-1 h-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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208
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Elemental Composition, Phosphorous Uptake, and Characteristics of Growth of a SAR11 Strain in Batch and Continuous Culture. mSystems 2019; 4:4/4/e00218-18. [PMID: 31117027 PMCID: PMC6589437 DOI: 10.1128/msystems.00218-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While SAR11 bacteria contribute a significant fraction to the total picoplankton biomass in the ocean and likely are major players in organic C and nutrient cycling, the cellular characteristics and metabolic features of most lineages have either only been hypothesized from genomes or otherwise not measured in controlled laboratory experimentation. The dearth of data on even the most basic characteristics for what is arguably the most abundant heterotroph in seawater has limited the specific consideration of SAR11 in ocean ecosystem modeling efforts. In this study, we provide measures of cellular P, N, and C, aerobic respiration, and bacterial production for a SAR11 strain growing in natural seawater medium that can be used to directly relate these features of SAR11 to biogeochemical cycling in the oceans. Through the development of a chemostat system to measure nutrient uptake during steady-state growth, we have also documented inorganic P uptake rates that allude to the importance of organic phosphorous to meet cellular P demands, even in the presence of nonlimiting PO43− concentrations. In this study, a strain of SAR11 subgroup IIIa (termed HIMB114) was grown in seawater-based batch and continuous culture in order to quantify cellular features and metabolism relevant to SAR11 ecology. We report some of the first direct measurements of cellular elemental quotas for nitrogen (N) and phosphorus (P) for SAR11, grown in batch culture: 1.4 ± 0.9 fg N and 0.44 ± 0.01 fg P, respectively, that were consistent with the small size of HIMB114 cells (average volume of 0.09 μm3). However, the mean carbon (C) cellular quota of 50 ± 47 fg C was anomalously high, but variable. The rates of phosphate (PO43−) uptake measured from both batch and continuous cultures were exceptionally slow: in chemostats growing at 0.3 day−1, HIMB114 took up 1.1 ± 0.3 amol P cell−1 day−1, suggesting that <30% of the cellular P requirement of HIMB114 was met by PO43− assimilation. The mean rate of leucine incorporation, a measure of bacterial production, during late-log-phase growth of batch HIMB114 cultures was 0.042 ± 0.02 amol Leu cell−1 h−1. While only weakly correlated with changes in specific growth rates, the onset of stationary phase resulted in decreases in cell-specific leucine incorporation that were proportional to changes in growth rate. The rates of cellular production, respiratory oxygen consumption, and changes in total organic C concentrations constrained cellular growth efficiencies to 13% ± 4%. Hence, despite a small genome and diminutively sized cells, SAR11 strain HIMB114 appears to grow at efficiencies similar to those of naturally occurring bacterioplankton communities. IMPORTANCE While SAR11 bacteria contribute a significant fraction to the total picoplankton biomass in the ocean and likely are major players in organic C and nutrient cycling, the cellular characteristics and metabolic features of most lineages have either only been hypothesized from genomes or otherwise not measured in controlled laboratory experimentation. The dearth of data on even the most basic characteristics for what is arguably the most abundant heterotroph in seawater has limited the specific consideration of SAR11 in ocean ecosystem modeling efforts. In this study, we provide measures of cellular P, N, and C, aerobic respiration, and bacterial production for a SAR11 strain growing in natural seawater medium that can be used to directly relate these features of SAR11 to biogeochemical cycling in the oceans. Through the development of a chemostat system to measure nutrient uptake during steady-state growth, we have also documented inorganic P uptake rates that allude to the importance of organic phosphorous to meet cellular P demands, even in the presence of nonlimiting PO43− concentrations.
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209
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Hurtado-McCormick V, Kahlke T, Petrou K, Jeffries T, Ralph PJ, Seymour JR. Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome. Front Microbiol 2019; 10:1011. [PMID: 31139163 PMCID: PMC6527750 DOI: 10.3389/fmicb.2019.01011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 11/29/2022] Open
Abstract
Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified "core" microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.
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Affiliation(s)
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Thomas Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Robert Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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210
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Abstract
Sometimes, to move ahead, you must take a look at where you have been. Culturing microbes is a foundational underpinning of microbiology. Sometimes, to move ahead, you must take a look at where you have been. Culturing microbes is a foundational underpinning of microbiology. Before genome sequencing, researchers spent countless hours tediously deducing the nutritional requirements of bacterial isolates and tinkering with medium formulations to entice new microbes into culture. This art of cultivation took a back seat to the powerful molecular tools of the last 25 years, and as a result, many researchers have forgotten the utility of having a culture in hand. This perception is changing, as there is clearly a renewed interest in isolating microbes from various environments. Here, I suggest three focus areas to ensure continued growth and success of this “cultural” renaissance, including (i) setting clear cultivation goals, (ii) funding exploratory cultivation, and (iii) culturing and studying unusual organisms. “Unculturable” is a frame of mind, not a state of microbiology; it is time to dust off the bottle of yeast extract.
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211
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Ruiz-González C, Logares R, Sebastián M, Mestre M, Rodríguez-Martínez R, Galí M, Sala MM, Acinas SG, Duarte CM, Gasol JM. Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Mol Ecol 2019; 28:1930-1945. [PMID: 30663830 DOI: 10.1111/mec.15026] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/21/2018] [Accepted: 01/14/2019] [Indexed: 01/21/2023]
Abstract
Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal-like"- abundant and ubiquitous; "logistic"- globally rare, present in few sites; and "bimodal"- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal-like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal-like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.
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Affiliation(s)
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Marta Sebastián
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Mireia Mestre
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Raquel Rodríguez-Martínez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Martí Galí
- Unité Mixte Internationale Takuvik (Université Laval-CNRS) and Québec-Océan, Département de Biologie, Université Laval, Québec City, Québec, Canada.,Barcelona Supercomputing Centre (BSC), Barcelona, Catalonia, Spain
| | | | - Silvia G Acinas
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain.,Centre for Marine Ecosystem Research, Edith Cowan University, Joondalup, Western Australia, Australia
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212
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Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B. Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands. PeerJ 2019; 7:e6800. [PMID: 31086738 PMCID: PMC6487183 DOI: 10.7717/peerj.6800] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/14/2019] [Indexed: 01/18/2023] Open
Abstract
Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.
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Affiliation(s)
- Joanna Warwick-Dugdale
- Plymouth Marine Laboratory, Plymouth, Devon, United Kingdom
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Natalie Solonenko
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Karen Moore
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Lauren Chittick
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Ann C. Gregory
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
| | - Michael J. Allen
- Plymouth Marine Laboratory, Plymouth, Devon, United Kingdom
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH, United States of America
- Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States of America
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
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213
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Teira E, Logares R, Gutiérrez‐Barral A, Ferrera I, Varela MM, Morán XAG, Gasol JM. Impact of grazing, resource availability and light on prokaryotic growth and diversity in the oligotrophic surface global ocean. Environ Microbiol 2019; 21:1482-1496. [DOI: 10.1111/1462-2920.14581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Eva Teira
- Departamento de Ecoloxía e Bioloxía AnimalUniversidade de Vigo Vigo Spain
| | - Ramiro Logares
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
| | | | - Isabel Ferrera
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Instituto Español de OceanografíaCentro Oceanográfico de Málaga Fuengirola Spain
| | - Marta M. Varela
- Instituto Español de OceanografíaCentro Oceanográfico de A Coruña A Coruña Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Josep M. Gasol
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Centre for Marine Ecosystems ResearchEdith Cowan University Joondalup Western Australia Australia
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214
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A Parasitic Arsenic Cycle That Shuttles Energy from Phytoplankton to Heterotrophic Bacterioplankton. mBio 2019; 10:mBio.00246-19. [PMID: 30890605 PMCID: PMC6426599 DOI: 10.1128/mbio.00246-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In many regions of the world oceans, phytoplankton face the problem of discriminating between phosphate, an essential nutrient, and arsenate, a toxic analogue. Many phytoplankton, including the most abundant phytoplankton group known, Prochlorococcus, detoxify arsenate (AsV) by reduction to arsenite (AsIII), followed by methylation and excretion of the methylated arsenic products. We synthesized [14C]dimethyl arsenate (DMA) and used it to show that cultured Pelagibacter strain HTCC7211 (SAR11) cells oxidize the methyl group carbons of DMA, producing 14CO2 and ATP. We measured [14C]DMA oxidation rates in the P-depleted surface waters of the Sargasso Sea, a subtropical ocean gyre. [14C]DMA was oxidized to 14CO2 by Sargasso Sea plankton communities at a rate that would cause turnover of the estimated DMA standing stock every 8.1 days. SAR11 strain HTCC7211, which was isolated from the Sargasso Sea, has a pair of arsenate resistance genes and was resistant to arsenate, showing no growth inhibition at As/P ratios of >65:1. Across the global oceans, there was a strong inverse relationship between the frequency of the arsenate reductase (LMWPc_ArsC) in Pelagibacter genomes and phosphate concentrations. We propose that the demethylation of methylated arsenic compounds by Pelagibacter and possibly other bacterioplankton, coupled with arsenate resistance, results in the transfer of energy from phytoplankton to bacteria. We dub this a parasitic cycle because the release of arsenate by Pelagibacter in principle creates a positive-feedback loop that forces phytoplankton to continually regenerate arsenate detoxification products, producing a flow of energy to P-limited ocean regions.IMPORTANCE In vast, warm regions of the oceans, phytoplankton face the problem of arsenic poisoning. Arsenate is toxic because it is chemically similar to phosphate, a scarce nutrient that phytoplankton cells need for growth. Many phytoplankton, including the commonest phytoplankton type in warm oceans, Prochlorococcus, detoxify arsenate by adding methyl groups. Here we show that the most abundant non-photosynthetic plankton in the oceans, SAR11 bacteria, remove the methyl groups, releasing poisonous forms of arsenic back into the water. We postulate that the methylation and demethylation of arsenic compounds creates a cycle in which the phytoplankton can never get ahead and must continually transfer energy to the SAR11 bacteria. We dub this a parasitic process and suggest that it might help explain why SAR11 bacteria are so successful, surpassing all other plankton in their numbers. Field experiments were done in the Sargasso Sea, a subtropical ocean gyre that is sometimes called an ocean desert because, throughout much of the year, there is not enough phosphorous in the water to support large blooms of phytoplankton. Ocean deserts are expanding as the oceans absorb heat and grow warmer.
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215
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Moelling K, Broecker F. Viruses and Evolution - Viruses First? A Personal Perspective. Front Microbiol 2019; 10:523. [PMID: 30941110 PMCID: PMC6433886 DOI: 10.3389/fmicb.2019.00523] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/28/2019] [Indexed: 01/08/2023] Open
Abstract
The discovery of exoplanets within putative habitable zones revolutionized astrobiology in recent years. It stimulated interest in the question about the origin of life and its evolution. Here, we discuss what the roles of viruses might have been at the beginning of life and during evolution. Viruses are the most abundant biological entities on Earth. They are present everywhere, in our surrounding, the oceans, the soil and in every living being. Retroviruses contributed to about half of our genomic sequences and to the evolution of the mammalian placenta. Contemporary viruses reflect evolution ranging from the RNA world to the DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even in vitro the loss of genes can be recapitulated all the way from coding to non-coding RNA. Furthermore, the giant viruses may indicate that there is no sharp border between living and non-living entities but an evolutionary continuum. Here, it is discussed how viruses can lose and gain genes, and that they are essential drivers of evolution. This discussion may stimulate the thinking about viruses as early possible forms of life. Apart from our view “viruses first”, there are others such as “proteins first” and “metabolism first.”
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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216
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Lee MD, Ahlgren NA, Kling JD, Walworth NG, Rocap G, Saito MA, Hutchins DA, Webb EA. Marine
Synechococcus
isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content. Environ Microbiol 2019; 21:1677-1686. [DOI: 10.1111/1462-2920.14552] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/10/2019] [Accepted: 01/29/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Michael D. Lee
- Department of Biological Sciences University of Southern California Los Angeles CA USA
- Exobiology, Ames Research Center Moffett Field CA USA
| | | | - Joshua D. Kling
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - Nathan G. Walworth
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - Gabrielle Rocap
- School of Oceanography University of Washington Seattle WA USA
| | - Mak A. Saito
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institute Woods Hole MA USA
| | - David A. Hutchins
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - Eric A. Webb
- Department of Biological Sciences University of Southern California Los Angeles CA USA
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217
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Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 2019; 10:1169. [PMID: 30862830 PMCID: PMC6414667 DOI: 10.1038/s41467-019-09106-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production. Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.
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218
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Nowinski B, Motard-Côté J, Landa M, Preston CM, Scholin CA, Birch JM, Kiene RP, Moran MA. Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes. Environ Microbiol 2019; 21:1687-1701. [PMID: 30761723 DOI: 10.1111/1462-2920.14560] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/09/2019] [Indexed: 11/30/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant organic sulfur metabolite produced by many phytoplankton species and degraded by bacteria via two distinct pathways with climate-relevant implications. We assessed the diversity and abundance of bacteria possessing these pathways in the context of phytoplankton community composition over a 3-week time period spanning September-October, 2014 in Monterey Bay, CA. The dmdA gene from the DMSP demethylation pathway dominated the DMSP gene pool and was harboured mostly by members of the alphaproteobacterial SAR11 clade and secondarily by the Roseobacter group, particularly during the second half of the study. Novel members of the DMSP-degrading community emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, including largely uncharacterized gammaproteobacteria and alphaproteobacteria taxa. In the DMSP cleavage pathway, the SAR11 gene dddK was the most abundant early in the study, but was supplanted by dddP over time. SAR11 members, especially those harbouring genes for both DMSP degradation pathways, had a strong positive relationship with the abundance of dinoflagellates, and DMSP-degrading gammaproteobacteria co-occurred with haptophytes. This in situ study of the drivers of DMSP fate in a coastal ecosystem demonstrates for the first time correlations between specific groups of bacterial DMSP degraders and phytoplankton taxa.
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Affiliation(s)
- Brent Nowinski
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Jessie Motard-Côté
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA.,Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA
| | - Marine Landa
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | | | - James M Birch
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, 95039, USA
| | - Ronald P Kiene
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA.,Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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219
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8:e42535. [PMID: 30789345 PMCID: PMC6447387 DOI: 10.7554/elife.42535] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Sebastian Hess
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Institute of ZoologyUniversity of CologneCologneGermany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxCanada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Andrew J Roger
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
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220
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8. [PMID: 30789345 DOI: 10.7554/elife.42535.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Sebastian Hess
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
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221
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Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J. Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean. Front Microbiol 2019; 10:281. [PMID: 30846975 PMCID: PMC6393369 DOI: 10.3389/fmicb.2019.00281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/04/2019] [Indexed: 11/29/2022] Open
Abstract
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.
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Affiliation(s)
- Jackie Zorz
- Department of Biology, Dalhousie University, Halifax, NS, Canada.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Ciara Willis
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - André M Comeau
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Morgan G I Langille
- CGEB-Integrated Microbiome Resource, Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Catherine L Johnson
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - William K W Li
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, NS, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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222
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Fernández-Gómez B, Díez B, Polz MF, Arroyo JI, Alfaro FD, Marchandon G, Sanhueza C, Farías L, Trefault N, Marquet PA, Molina-Montenegro MA, Sylvander P, Snoeijs-Leijonmalm P. Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N. THE ISME JOURNAL 2019; 13:316-333. [PMID: 30228379 PMCID: PMC6331608 DOI: 10.1038/s41396-018-0268-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/11/2018] [Accepted: 07/24/2018] [Indexed: 01/13/2023]
Abstract
Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
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Affiliation(s)
- Beatriz Fernández-Gómez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
- INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile.
- Center for Climate and Resilience Research, Concepción, Chile.
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - José Ignacio Arroyo
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Germán Marchandon
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Cynthia Sanhueza
- Department of Molecular Genetics and Microbiology, Pontifical University Catholic of Chile, Santiago, Chile
| | - Laura Farías
- Center for Climate and Resilience Research, Concepción, Chile
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Pablo A Marquet
- Department of Ecology, Pontifical University Catholic of Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Universidad Católica del Norte, Coquimbo, Chile
| | - Peter Sylvander
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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223
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Liu J, Liu J, Zhang SH, Liang J, Lin H, Song D, Yang GP, Todd JD, Zhang XH. Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea. Front Microbiol 2018; 9:3206. [PMID: 30622530 PMCID: PMC6309047 DOI: 10.3389/fmicb.2018.03206] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 11/18/2022] Open
Abstract
The compatible solute dimethylsulfoniopropionate (DMSP), made by many marine organisms, is one of Earth's most abundant organosulfur molecules. Many marine bacteria import DMSP and can degrade it as a source of carbon and/or sulfur via DMSP cleavage or DMSP demethylation pathways, which can generate the climate active gases dimethyl sulfide (DMS) or methanthiol (MeSH), respectively. Here we used culture-dependent and -independent methods to study bacteria catabolizing DMSP in the East China Sea (ECS). Of bacterial isolates, 42.11% showed DMSP-dependent DMS (Ddd+) activity, and 12.28% produced detectable levels of MeSH. Interestingly, although most Ddd+ isolates were Alphaproteobacteria (mainly Roseobacters), many gram-positive Actinobacteria were also shown to cleave DMSP producing DMS. The mechanism by which these Actinobacteria cleave DMSP is unknown, since no known functional ddd genes have been identified in genome sequences of Ddd+Microbacterium and Agrococcus isolates or in any other sequenced Actinobacteria genomes. Gene probes to the DMSP demethylation gene dmdA and the DMSP lyase gene dddP demonstrated that these DMSP-degrading genes are abundant and widely distributed in ECS seawaters. dmdA was present in relatively high proportions in both surface (19.53% ± 6.70%) and bottom seawater bacteria (16.00% ± 8.73%). In contrast, dddP abundance positively correlated with chlorophyll a, and gradually decreased with the distance from land, which implies that the bacterial DMSP lyase gene dddP might be from bacterial groups that closely associate with phytoplankton. Bacterial community analysis showed positive correlations between Rhodobacteraceae abundance and concentrations of DMS and DMSP, further confirming the link between this abundant bacterial class and the environmental DMSP cycling.
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Affiliation(s)
- Jingli Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Ji Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Sheng-Hui Zhang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Heyu Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Delei Song
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Gui-Peng Yang
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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224
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Zhao Y, Qin F, Zhang R, Giovannoni SJ, Zhang Z, Sun J, Du S, Rensing C. Pelagiphages in thePodoviridaefamily integrate into host genomes. Environ Microbiol 2018; 21:1989-2001. [DOI: 10.1111/1462-2920.14487] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Yanlin Zhao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Fang Qin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental ScienceCollege of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University Xiamen Fujian China
| | | | - Zefeng Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Jing Sun
- Department of MicrobiologyOregon State University Corvallis OR USA
| | - Sen Du
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life SciencesFujian Agriculture and Forestry University Fuzhou Fujian China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and EnvironmentFujian Agriculture and Forestry University Fuzhou Fujian China
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225
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Genome size evolution in the Archaea. Emerg Top Life Sci 2018; 2:595-605. [PMID: 33525826 PMCID: PMC7289037 DOI: 10.1042/etls20180021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/17/2022]
Abstract
What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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226
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Ochsenkühn MA, Schmitt-Kopplin P, Harir M, Amin SA. Coral metabolite gradients affect microbial community structures and act as a disease cue. Commun Biol 2018; 1:184. [PMID: 30417121 PMCID: PMC6218554 DOI: 10.1038/s42003-018-0189-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
Abstract
Corals are threatened worldwide due to prevalence of disease and bleaching. Recent studies suggest the ability of corals to resist disease is dependent on maintaining healthy microbiomes that span coral tissues and surfaces, the holobiont. Although our understanding of the role endosymbiotic microbes play in coral health has advanced, the role surface-associated microbes and their chemical signatures play in coral health is limited. Using minimally invasive water sampling, we show that the corals Acropora and Platygyra harbor unique bacteria and metabolites at their surface, distinctly different from surrounding seawater. The surface metabolites released by the holobiont create concentration gradients at 0–5 cm away from the coral surface. These molecules are identified as chemo-attractants, antibacterials, and infochemicals, suggesting they may structure coral surface-associated microbes. Further, we detect surface-associated metabolites characteristic of healthy or white syndrome disease infected corals, a finding which may aid in describing effects of diseases. Michael Ochsenkühn et al. look at the microbial and metabolic composition of coral surfaces and the surrounding seawater. They find that the metabolites found on the surface of the coral create a concentration gradient that influences the surrounding microbiome.
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Affiliation(s)
- Michael A Ochsenkühn
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Lehrstuhl für Analytische Lebensmittelchemie, Technische Universität München, Alte Akademie 10, 85354, Freising, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Centre Munich, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Shady A Amin
- Biology Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates. .,Chemistry Division, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, 129188, United Arab Emirates.
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227
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Paver SF, Muratore D, Newton RJ, Coleman ML. Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems. mSystems 2018; 3:e00232-18. [PMID: 30443603 PMCID: PMC6234284 DOI: 10.1128/msystems.00232-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.
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Affiliation(s)
- Sara F. Paver
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Daniel Muratore
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA
| | - Maureen L. Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
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228
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Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gómez-Consarnau L. Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ 2018; 6:e5798. [PMID: 30370186 PMCID: PMC6202958 DOI: 10.7717/peerj.5798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
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Affiliation(s)
- Ella T Sieradzki
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Sara Rivero-Calle
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
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229
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Ghuneim LAJ, Jones DL, Golyshin PN, Golyshina OV. Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function. Front Microbiol 2018; 9:1971. [PMID: 30186275 PMCID: PMC6110929 DOI: 10.3389/fmicb.2018.01971] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/06/2018] [Indexed: 11/13/2022] Open
Abstract
Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.
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Affiliation(s)
- Lydia-Ann J. Ghuneim
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - David L. Jones
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, United Kingdom
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, Bangor, United Kingdom
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230
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Zhang C, Dang H, Azam F, Benner R, Legendre L, Passow U, Polimene L, Robinson C, Suttle CA, Jiao N. Evolving paradigms in biological carbon cycling in the ocean. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwy074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO2, CaCO3, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO2. The concepts of the biological carbon pump (BCP) and the microbial loop (ML) shaped our understanding of the marine carbon cycle. The more recent concept of the microbial carbon pump (MCP), which is closely connected to those of the BCP and the ML, explicitly considers the significance of the ocean's RDOC reservoir and provides a mechanistic framework for the exploration of its formation and persistence. Understanding of the MCP has benefited from advanced ‘omics’ and novel research in biological oceanography and microbial biogeochemistry. The need to predict the ocean's response to climate change makes an integrative understanding of the BCP, ML and MCP a high priority. In this review, we summarize and discuss progress since the proposal of the MCP in 2010 and formulate research questions for the future.
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Affiliation(s)
- Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Benner
- Department of Biological Sciences and School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC 29208, USA
| | - Louis Legendre
- Sorbonne Université, Laboratoire d’Océanographie de Villefranche, LOV, 06230 Villefranche-sur-Mer, France
| | - Uta Passow
- Marine Science Institute, University of California Santa Barbara, CA 93106, USA
| | - Luca Polimene
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
| | - Carol Robinson
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Botany, and Microbiology and Immunology, and the Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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231
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Jing X, Gou H, Gong Y, Su X, Xu L, Ji Y, Song Y, Thompson IP, Xu J, Huang WE. Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean. Environ Microbiol 2018; 20:2241-2255. [PMID: 29727057 PMCID: PMC6849569 DOI: 10.1111/1462-2920.14268] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 11/30/2022]
Abstract
It is of great significance to understand CO2 fixation in the oceans. Using single cell Raman spectra (SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here, we show that mini‐metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data. By applying this approach to 13C bicarbonate spiked seawater from euphotic zone of the Yellow Sea of China, the dominant bacteria Synechococcus spp. and Pelagibacter spp. were revealed and both of them contain carotenoid and were able to incorporate 13C into the cells at the same time. Genetic analysis of the reconstructed genomes suggests that both Synechococcus spp. and Pelagibacter spp. contained all genes necessary for carotenoid synthesis, light energy harvesting and CO2 fixation. Interestingly, the reconstructed genome indicates that Pelagibacter spp. harbored intact sets of genes for β‐carotene (precursor of retional), proteorhodopsin synthesis and anaplerotic CO2 fixation. This novel approach shines light on the role of marine ‘microbial dark matter’ in global carbon cycling, by linking yet‐to‐be‐cultured Synechococcus spp. and Pelagibacter spp. to carbon fixation and flow activities in situ.
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Affiliation(s)
- Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Honglei Gou
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaolu Su
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - La Xu
- Disease and Fishery Drugs Research Center, Marine Biology Institute of Shandong Province, Qingdao, Shandong, People's Republic of China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yizhi Song
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
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232
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233
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Coutinho FH, Gregoracci GB, Walter JM, Thompson CC, Thompson FL. Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses. Trends Microbiol 2018; 26:955-965. [PMID: 29937307 DOI: 10.1016/j.tim.2018.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Advances brought about by omics-based approaches have revolutionized our understanding of the diversity and ecological processes involving marine archaea, bacteria, and their viruses. This broad review discusses recent examples of how genomics, metagenomics, and ecogenomics have been applied to reveal the ecology of these biological entities. Three major topics are covered in this revision: (i) the novel roles of microorganisms in ecosystem processes; (ii) virus-host associations; and (iii) ecological associations of microeukaryotes and other microbes. We also briefly comment on the discovery of novel taxa from marine ecosystems; development of a robust taxonomic framework for prokaryotes; breakthroughs on the diversity and ecology of cyanobacteria; and advances on ecological modelling. We conclude by discussing limitations of the field and suggesting directions for future research.
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Affiliation(s)
- Felipe Hernandes Coutinho
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Evolutionary Genomics Group, Departamento de Produccíon Vegetal y Microbiología, Universidad Miguel Hernández (UMH), Alicante, Spain
| | | | - Juline Marta Walter
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Carneiro Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology - CT2, SAGE-COPPE, Federal Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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234
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Gajigan AP, Yñiguez AT, Villanoy CL, San Diego-McGlone ML, Jacinto GS, Conaco C. Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines. PeerJ 2018; 6:e4781. [PMID: 29785352 PMCID: PMC5960264 DOI: 10.7717/peerj.4781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/26/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.
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Affiliation(s)
- Andrian P Gajigan
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines.,Current affiliation: Department of Oceanography, University of Hawaii at Manoa, USA
| | - Aletta T Yñiguez
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Cesar L Villanoy
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | | | - Gil S Jacinto
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
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235
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Pehr K, Love GD, Kuznetsov A, Podkovyrov V, Junium CK, Shumlyanskyy L, Sokur T, Bekker A. Ediacara biota flourished in oligotrophic and bacterially dominated marine environments across Baltica. Nat Commun 2018; 9:1807. [PMID: 29728614 PMCID: PMC5935690 DOI: 10.1038/s41467-018-04195-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 04/13/2018] [Indexed: 11/26/2022] Open
Abstract
Middle-to-late Ediacaran (575–541 Ma) marine sedimentary rocks record the first appearance of macroscopic, multicellular body fossils, yet little is known about the environments and food sources that sustained this enigmatic fauna. Here, we perform a lipid biomarker and stable isotope (δ15Ntotal and δ13CTOC) investigation of exceptionally immature late Ediacaran strata (<560 Ma) from multiple locations across Baltica. Our results show that the biomarker assemblages encompass an exceptionally wide range of hopane/sterane ratios (1.6–119), which is a broad measure of bacterial/eukaryotic source organism inputs. These include some unusually high hopane/sterane ratios (22–119), particularly during the peak in diversity and abundance of the Ediacara biota. A high contribution of bacteria to the overall low productivity may have bolstered a microbial loop, locally sustaining dissolved organic matter as an important organic nutrient. These oligotrophic, shallow-marine conditions extended over hundreds of kilometers across Baltica and persisted for more than 10 million years. The environments and food sources that sustained Ediacara biota 575-541 million years ago remain unclear. Here, the authors perform lipid biomarker and isotopic analyses on biota fossil-containing Ediacaran strata from Baltica and propose the presence of a microbial loop bolstered by bacteria.
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Affiliation(s)
- Kelden Pehr
- Department of Earth Sciences, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Gordon D Love
- Department of Earth Sciences, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| | - Anton Kuznetsov
- Institute of Precambrian Geology and Geochronology, RAS, nab. Makarova 2, St. Petersburg, 199034, Russia
| | - Victor Podkovyrov
- Institute of Precambrian Geology and Geochronology, RAS, nab. Makarova 2, St. Petersburg, 199034, Russia
| | - Christopher K Junium
- Department of Earth Sciences, Syracuse University, 322 Heroy Geology Lab, Syracuse, NY, 13244, USA
| | - Leonid Shumlyanskyy
- M.P. Semenko Institute of Geochemistry, Mineralogy and Ore Formation, National Academy of Sciences of Ukraine, 34 Palladina Av, Kiev, 03142, Ukraine
| | - Tetyana Sokur
- Institute of Geological Sciences, National Academy of Sciences of Ukraine, Olesya Honchara Str., 55-b, Kiev, 01054, Ukraine
| | - Andrey Bekker
- Department of Earth Sciences, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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236
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Carini P, Dupont CL, Santoro AE. Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environ Microbiol 2018; 20:2112-2124. [PMID: 29626379 DOI: 10.1111/1462-2920.14107] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20-like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139-fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea-enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery.
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Affiliation(s)
- Paul Carini
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | | | - Alyson E Santoro
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
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237
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Thiel V, Tank M, Bryant DA. Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:21-49. [PMID: 29505738 DOI: 10.1146/annurev-arplant-042817-040500] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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238
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Mehrshad M, Rodriguez-Valera F, Amoozegar MA, López-García P, Ghai R. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling. THE ISME JOURNAL 2018; 12:655-668. [PMID: 29208946 PMCID: PMC5864207 DOI: 10.1038/s41396-017-0009-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/21/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022]
Abstract
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
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Affiliation(s)
- Maliheh Mehrshad
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | | | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Purificación López-García
- Ecologie, Systématique, Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.
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239
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Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0023-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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240
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The Limnohabitans Genus Harbors Generalistic and Opportunistic Subtypes: Evidence from Spatiotemporal Succession in a Canyon-Shaped Reservoir. Appl Environ Microbiol 2017; 83:AEM.01530-17. [PMID: 28842542 DOI: 10.1128/aem.01530-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/22/2017] [Indexed: 11/20/2022] Open
Abstract
We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.
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241
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Arandia-Gorostidi N, Huete-Stauffer TM, Alonso-Sáez L, G Morán XA. Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom. Environ Microbiol 2017; 19:4493-4505. [PMID: 28836731 DOI: 10.1111/1462-2920.13898] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/27/2022]
Abstract
Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short-term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year-round as analysed by CARD-FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature-sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post-bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy (E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient-sufficient conditions, warming differentially affected distinct bacterioplankton taxa.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain
| | - Tamara Megan Huete-Stauffer
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, Saudi Arabia
| | - Laura Alonso-Sáez
- Plankton Ecology and Pelagic Ecosystem Dynamics Division, Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Marine Research Division, AZTI, Sukarrieta, Bizkaia, Spain
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, Saudi Arabia
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242
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Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 2017; 56:2873-2885. [DOI: 10.1021/acs.biochem.7b00099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas J. Schnicker
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Saumya M. De Silva
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Jonathan D. Todd
- School
of Biological Sciences, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Mishtu Dey
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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243
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Teira E, Hernando-Morales V, Guerrero-Feijóo E, Varela MM. Leucine, starch and bicarbonate utilization by specific bacterial groups in surface shelf waters off Galicia (NW Spain). Environ Microbiol 2017; 19:2379-2390. [PMID: 28370995 DOI: 10.1111/1462-2920.13748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 11/29/2022]
Abstract
The capability of different bacterial populations to degrade abundant polymers, such as algal-derived polysaccharides, or to utilize preferentially polymers over monomers, remains largely unknown. In this study, microautoradiography was combined with fluorescence in situ hybridization (MAR-FISH) to evaluate the ability of Bacteroidetes, SAR11, Roseobacter spp., Gammaproteobacteria and SAR86 cells to use bicarbonate, leucine and starch under natural light conditions at two locations in shelf surface waters off NW Spain. The percentage of cells incorporating bicarbonate was relatively high (mean 32% ± 4%) and was positively correlated with the intensity of solar radiation. The proportion of cells using starch (mean 56% ± 4%) or leucine (mean 47% ± 4%) was significantly higher than that using bicarbonate. On average, SAR11, Roseobacter spp. and Gammaproteobacteria showed a similarly high percentage of cells using leucine (47%-65% of hybridized cells) than using starch (51%-64% of hybridized cells), while Bacteroidetes and SAR86 cells preferentially used starch (53% of hybridized cells) over leucine (34%-40% of hybridized cells). We suggest that the great percentage of bacteria using starch is related to a high ambient availability of polymers associated to algal cell lysis, which, in turn, weakens the short-term coupling between phytoplankton release and bacterial production.
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Affiliation(s)
- E Teira
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - V Hernando-Morales
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - E Guerrero-Feijóo
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
| | - M M Varela
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
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244
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Sun Y, Powell KE, Sung W, Lynch M, Moran MA, Luo H. Spontaneous mutations of a model heterotrophic marine bacterium. ISME JOURNAL 2017; 11:1713-1718. [PMID: 28323279 DOI: 10.1038/ismej.2017.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 11/06/2016] [Accepted: 12/23/2016] [Indexed: 11/09/2022]
Abstract
Heterotrophic marine bacterioplankton populations display substantive genomic diversity that is commonly explained to be the result of selective forces imposed by resource limitation or interactions with phage and predators. Here we use a mutation-accumulation experiment followed by whole-genome sequencing of mutation lines to determine an unbiased rate and molecular spectrum of spontaneous mutations for a model heterotrophic marine bacterium in the globally important Roseobacter clade, Ruegeria pomeroyi DSS-3. We find evidence for mutational bias towards deletions over insertions, and this process alone could account for a sizable portion of genome size diversity among roseobacters and also implies that lateral gene transfer and/or selection must also play a role in maintaining roseobacters with large genome sizes. We also find evidence for a mutational bias in favor of changes from A/T to G/C nucleobases, which explains widespread occurrences of G/C-enriched Roseobacter genomes. Using the calculated mutation rate of 1.39 × 10-10 per base per generation, we implement a 'mutation-rate clock' approach to date the evolution of roseobacters by assuming a constant mutation rate along their evolutionary history. This approach gives an estimated date of Roseobacter genome expansion in good agreement with an earlier fossil-based estimate of ~250 million years ago and is consistent with a hypothesis of a correlated evolutionary history between roseobacters and marine eukaryotic phytoplankton groups.
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Affiliation(s)
- Ying Sun
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kate E Powell
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Way Sung
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences and Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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245
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Enzymology of Microbial Dimethylsulfoniopropionate Catabolism. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:195-222. [DOI: 10.1016/bs.apcsb.2017.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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