Microbe-Microbe Interactions and miscellaneous
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New Phytologist: Small regulatory RNAs and the fine-tuning of plant–bacteria interactions

New Phytologist: Small regulatory RNAs and the fine-tuning of plant–bacteria interactions | Microbe-Microbe Interactions and miscellaneous | Scoop.it

Small regulatory RNAs (sRNAs) play a key role in many physiological and adaptive responses in bacteria. Faced with rapidly changing environments, it is more advantageous for bacteria to use sRNA-mediated responses than regulation by protein transcriptional factors, as sRNAs act at the post-transcriptional level and require less energy and time for their synthesis and turnover. The use of RNA deep sequencing has provided hundreds of sRNA candidates in different bacterial species that interact with plants. Here, we review the most recent results for the involvement of bacterial sRNAs in beneficial as well as deleterious plant–bacteria interactions. We describe the current view for the role of sRNAs, which are suggested to improve competition for both niches and resources in plant-interacting bacteria. These sRNAs also help plant-associated bacteria individually adapt to the rapidly changing conditions to which they are exposed, during different stages of this interaction.


Via Stéphane Hacquard
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Stress as a Normal Cue in the Symbiotic Environment: Trends in Microbiology

Stress as a Normal Cue in the Symbiotic Environment: Trends in Microbiology | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Host tissues may be a source of chemical and/or physical stress. The presence of tissue-associated stress is not dependent on microbes. Microbes that can grow within the constraints of the host tissues may, themselves, produce stress through competitive or antagonistic interactions. Microbial activity in host tissues, or interactions with specific microbial taxa within the community, may induce immune-associated stress.
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Design and synthesis of a minimal bacterial genome

Design and synthesis of a minimal bacterial genome | Microbe-Microbe Interactions and miscellaneous | Scoop.it
A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life. In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function.
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Bacterial Speciation: Genetic Sweeps in Bacterial Species: Current Biology

Bacterial Speciation: Genetic Sweeps in Bacterial Species: Current Biology | Microbe-Microbe Interactions and miscellaneous | Scoop.it
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases | Microbe-Microbe Interactions and miscellaneous | Scoop.it
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
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MetaQUAST: evaluation of metagenome assemblies

MetaQUAST: evaluation of metagenome assemblies | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Summary: During the past years we have witnessed the rapid development of new metagenome assembly methods. While there are many benchmark utilities designed for single-genome assemblies, there is no well-recognised evaluation and comparison tool for metagenomic-specific analogues. In this paper we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (1) unknown species content by detecting and downloading reference sequences, (2) huge diversity by giving comprehensive reports for multiple genomes, (3) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets.
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Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl–coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.
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Frontiers | Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin | Evolutionary and Genomic Microbiology

Frontiers | Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin | Evolutionary and Genomic Microbiology | Microbe-Microbe Interactions and miscellaneous | Scoop.it
The hydrothermal vent system is a typical chemosynthetic ecosystem in which microorganisms play essential roles in the geobiochemical cycling. Although it has been well-recognized that the inorganic sulfur compounds are abundant and actively converted through chemosynthetic pathways, the sulfur budget in a hydrothermal vent is poorly characterized due to the complexity of microbial sulfur cycling resulting from the numerous parties involved in the processes. In this study, we performed an integrated metagenomic and metatranscriptomic analysis on a chimney sample from Guaymas Basin to achieve a comprehensive study of each sulfur metabolic pathway and its hosting microorganisms and constructed the microbial sulfur cycle that occurs in the site. Our results clearly illustrated the stratified sulfur oxidation and sulfate reduction at the chimney wall. Besides, sulfur metabolizing is closely interacting with carbon cycles, especially the hydrocarbon degradation process in Guaymas Basin. This work supports that the internal sulfur cycling is intensive and the net sulfur budget is low in the hydrothermal ecosystem.
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Find it@UT

Find it@UT | Microbe-Microbe Interactions and miscellaneous | Scoop.it

The exchange of chemical compounds is central to the interactions of microalgae with other microorganisms. Although foundational for many food webs, these interactions have been poorly studied compared with higher plant–microbe interactions. Emerging insights have begun to reveal how these interactions and the participating chemical compounds shape microbial communities and broadly impact biogeochemical processes.

Keywordsmicroalgae;symbiosis;syntrophy;secondary metabolism;biogeochemical cycles;chemical ecology
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BMC Biology | Full text | MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes

BMC Biology | Full text | MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Metagenomes provide access to the taxonomic composition and functional capabilities of microbial communities. Although metagenomic analysis methods exist for estimating overall community composition or metabolic potential, identifying specific taxa that encode specific functions or pathways of interest can be more challenging. Here we present MetAnnotate, which addresses the common question: “which organisms perform my function of interest within my metagenome(s) of interest?” MetAnnotate uses profile hidden Markov models to analyze shotgun metagenomes for genes and pathways of interest, classifies retrieved sequences either through a phylogenetic placement or best hit approach, and enables comparison of these profiles between metagenomes.
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The ecology of the microbiome: Networks, competition, and stability

The ecology of the microbiome: Networks, competition, and stability | Microbe-Microbe Interactions and miscellaneous | Scoop.it
The human gut harbors a large and complex community of beneficial microbes that remain stable over long periods. This stability is considered critical for good health but is poorly understood. Here we develop a body of ecological theory to help us understand microbiome stability. Although cooperating networks of microbes can be efficient, we find that they are often unstable. Counterintuitively, this finding indicates that hosts can benefit from microbial competition when this competition dampens cooperative networks and increases stability. More generally, stability is promoted by limiting positive feedbacks and weakening ecological interactions. We have analyzed host mechanisms for maintaining stability—including immune suppression, spatial structuring, and feeding of community members—and support our key predictions with recent data.
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Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle | Microbe-Microbe Interactions and miscellaneous | Scoop.it
A number of organisms synthesize hydrocarbons, but the scale at which this occurs in the environment is unknown. Here, we provide the first global estimates of hydrocarbon production by the two most abundant cyanobacteria on Earth, Prochlorococcus and Synechococcus. We suggest that these organisms represent a significant and widespread source of hydrocarbons to the world’s oceans, which in turn may sustain populations of obligate hydrocarbon-degrading bacteria known to be important in consuming anthropogenic oil spills. Our study demonstrates the role cyanobacteria play in the ocean ‟hydrocarbon cycle” and reveals the massive scale of this process. The widespread distribution of cyanobacteria and hydrocarbon-degrading bacteria in freshwater, marine, and terrestrial environments suggests the hydrocarbon cycle is pervasive in many natural ecosystems.
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The ISME Journal - SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment

The ISME Journal - SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in 13C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments.
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The ISME Journal - Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

The ISME Journal - Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition | Microbe-Microbe Interactions and miscellaneous | Scoop.it
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant–microbe interactions/rhizosphere microbiota/selection.
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Partitioning of Functional and Taxonomic Diversity in Surface-Associated Microbial Communities - Roth-Schulze - 2016 - Environmental Microbiology - Wiley Online Library

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonization by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (>95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. This article is protected by copyright. All rights reserved.
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The ISME Journal - Predicting microbial traits with phylogenies

The ISME Journal - Predicting microbial traits with phylogenies | Microbe-Microbe Interactions and miscellaneous | Scoop.it
phylogenetic trait conservatism is widespread through the tree of life
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Microbial ecology: Linking omics to biogeochemistry

Microbial ecology: Linking omics to biogeochemistry | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Natural volcanic CO2 seeps (mofettes) provided a natural experiment to use omic and biogeochemical approaches to explore how flooding a system with CO2 impacts algal photosynthesis and methanogenesis.
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Networks of energetic and metabolic interactions define dynamics in microbial communities

Networks of energetic and metabolic interactions define dynamics in microbial communities | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Microbial communities are critical to global carbon cycling and particularly important in oxygen-limited environments, such as sediments and parts of the human microbiome. However, the uncultured members of these communities often hinder the study of community composition and interspecies interactions at a deeper level. Here, we integrate metagenomic binning, metatranscriptomic analysis, and metabolic modeling to obtain quantitative information about interspecies interactions between individual species present in methanogenic communities. We found that these communities are defined by not only metabolic interactions but also additional interdependencies, such as amino acid auxotrophies. Strategic usage of antimicrobials by specific community members further reinforces this intricate interspecies network, thereby enforcing strong collaboration among community members.
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The ISME Journal - Bacterial predation in a marine host-associated microbiome

The ISME Journal - Bacterial predation in a marine host-associated microbiome | Microbe-Microbe Interactions and miscellaneous | Scoop.it
In many ecological communities, predation has a key role in regulating community structure or function. Although predation has been extensively explored in animals and microbial eukaryotes, predation by bacteria is less well understood. Here we show that predatory bacteria of the genus Halobacteriovorax are prevalent and active predators on the surface of several genera of reef-building corals. Across a library of 198 16S rRNA samples spanning three coral genera, 79% were positive for carriage of Halobacteriovorax. Cultured Halobacteriovorax from Porites asteroides corals tested positive for predation on the putative coral pathogens Vibrio corallyticus and Vibrio harveyii. Co-occurrence network analysis showed that Halobacteriovorax’s interactions with other bacteria are influenced by temperature and inorganic nutrient concentration, and further suggested that this bacterial predator’s abundance may be driven by prey availability. Thus, animal microbiomes can harbor active bacterial predators, which may regulate microbiome structure and protect the host by consuming potential pathogens.
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Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Oil spills are a significant source of hydrocarbon inputs into the ocean. In response to oil spills, chemical dispersants are applied to the oil-contaminated seawater to disperse surface slicks into smaller droplets that are presumed to be more bioavailable to microorganisms. We provide evidence that chemical dispersants applied to either deep water or surface water from the Gulf of Mexico did not stimulate oil biodegradation. Direct measurement of alkane and aromatic hydrocarbon oxidation rates revealed either suppression or no stimulation of oil biodegradation in the presence of dispersants. However, dispersants affected microbial community composition and enriched bacterial populations with the ability to use dispersant-derived compounds as growth substrates, while oil-alone amendments enriched for natural hydrocarbon degraders.
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A Chemical Perspective on Microalgal–Microbial Interactions

A Chemical Perspective on Microalgal–Microbial Interactions | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Nina Dombrowski's insight:

The exchange of chemical compounds is central to the interactions of microalgae with other microorganisms. Although foundational for many food webs, these interactions have been poorly studied compared with higher plant–microbe interactions. Emerging insights have begun to reveal how these interactions and the participating chemical compounds shape microbial communities and broadly impact biogeochemical processes.

Keywordsmicroalgae;symbiosis;syntrophy;secondary metabolism;biogeochemical cycles;chemical ecology
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BMC Bioinformatics | Full text | Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed. For taxonomic classification of sequence reads, such evaluation should include use of clade exclusion, which better evaluates a method’s accuracy when identical sequences are not present in any reference database, as is common in metagenomic analysis. To date, relatively small evaluations have been performed, with evaluation approaches like clade exclusion limited to assessment of new methods by the authors of the given method. What is needed is a rigorous, independent comparison between multiple major methods, using the same in silico and in vitro test datasets, with and without approaches like clade exclusion, to better characterize accuracy under different conditions.
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Microbiomes in light of traits: A phylogenetic perspective

Microbiomes in light of traits: A phylogenetic perspective | Microbe-Microbe Interactions and miscellaneous | Scoop.it
A focus on the phenotypic characteristics of microorganisms—their traits—offers a path for interpreting the growing amount of microbiome data. We review key aspects of microbial traits, as well as approaches used to assay their phylogenetic distribution. Recent studies reveal that microbial traits are differentially conserved across the tree of life and appear to be conserved in a hierarchical fashion, possibly linked to their biochemical complexity. These results suggest a predictive framework whereby the genetic (or taxonomic) resolution of microbiome variation among samples provides information about the traits under selection. The organizational parallels seen among human and free-living microbiomes seem to support this idea. Developments in this framework may offer predictions not only for how microbial composition responds to changing environmental conditions, but also for how these changes may alter the health or functioning in human, engineered, and environmental systems.
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Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Blooms of phytoplankton can shift the ecosystem state of low-nutrient ocean regions between net heterotrophic and autotrophic conditions, increasing carbon sequestration and driving carbon export to the deep sea. Little is known about the traits that govern the timing and magnitude of these bloom events. We used metatranscriptomics to assess phytoplankton functional group-specific metabolic shifts experimentally during simulated blooms in the North Pacific Subtropical Gyre. The results indicate blooms form when phytoplankton are released from limitation by resources (nutrients, vitamins, and trace metals) and that the mechanistic basis for the success of one functional group over another may be driven by how efficiently the transcriptome is modulated following a nutrient pulse.
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BMC Biology | Full text | Archaeal ancestors of eukaryotes: not so elusive any more

BMC Biology | Full text | Archaeal ancestors of eukaryotes: not so elusive any more | Microbe-Microbe Interactions and miscellaneous | Scoop.it
The origin of eukaryotes is one of the hardest problems in evolutionary biology and sometimes raises the ominous specter of irreducible complexity. Reconstruction of the gene repertoire of the last eukaryotic common ancestor (LECA) has revealed a highly complex organism with a variety of advanced features but no detectable evolutionary intermediates to explain their origin. Recently, however, genome analysis of diverse archaea led to the discovery of apparent ancestral versions of several signature eukaryotic systems, such as the actin cytoskeleton and the ubiquitin network, that are scattered among archaea. These findings inspired the hypothesis that the archaeal ancestor of eukaryotes was an unusually complex form with an elaborate intracellular organization. The latest striking discovery made by deep metagenomic sequencing vindicates this hypothesis by showing that in phylogenetic trees eukaryotes fall within a newly identified archaeal group, the Lokiarchaeota, which combine several eukaryotic signatures previously identified in different archaea. The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis.
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The ISME Journal - Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

The ISME Journal - Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton | Microbe-Microbe Interactions and miscellaneous | Scoop.it
Viral infections dynamically alter the composition and metabolic potential of marine microbial communities and the evolutionary trajectories of host populations with resulting feedback on biogeochemical cycles. It is quite possible that all microbial populations in the ocean are impacted by viral infections. Our knowledge of virus–host relationships, however, has been limited to a minute fraction of cultivated host groups. Here, we utilized single-cell sequencing to obtain genomic blueprints of viruses inside or attached to individual bacterial and archaeal cells captured in their native environment, circumventing the need for host and virus cultivation. A combination of comparative genomics, metagenomic fragment recruitment, sequence anomalies and irregularities in sequence coverage depth and genome recovery were utilized to detect viruses and to decipher modes of virus–host interactions. Members of all three tailed phage families were identified in 20 out of 58 phylogenetically and geographically diverse single amplified genomes (SAGs) of marine bacteria and archaea. At least four phage–host interactions had the characteristics of late lytic infections, all of which were found in metabolically active cells. One virus had genetic potential for lysogeny. Our findings include first known viruses of Thaumarchaeota, Marinimicrobia, Verrucomicrobia and Gammaproteobacteria clusters SAR86 and SAR92. Viruses were also found in SAGs of Alphaproteobacteria and Bacteroidetes. A high fragment recruitment of viral metagenomic reads confirmed that most of the SAG-associated viruses are abundant in the ocean. Our study demonstrates that single-cell genomics, in conjunction with sequence-based computational tools, enable in situ, cultivation-independent insights into host–virus interactions in complex microbial communities.
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