Differential Response of Bacterial Microdiversity to Simulated Global Change

Scales, N C; Chase, Alexander B.; Finks, Sarai S.; Malik, Ashish; Weihe, Claudia; Allison, Steven D.; Martiny, Adam C.; Martiny, Jennifer B. H.

doi:10.1128/aem.02429-21

Cited by 13 publications

(12 citation statements)

References 63 publications

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“…Ecotypes will also encompass additional standing genetic variation, or ‘microdiversity’ (Larkin & Martiny, 2017) that can further be grouped into co‐occurring local populations, or what might be considered an evolutionary unit (Arevalo et al, 2019; Chase et al, 2019; Kent et al, 2019). In soils, this microdiversity also responds to environmental changes like drought (Scales et al, 2022). Changes at this level of genetic resolution result in shifts in allele frequencies within populations, a phenomenon that, among larger organisms, would be thought of as an evolutionary process.…”

Section: Evidence For Evolutionary Responses Of Microbiomes To Enviro...mentioning

confidence: 99%

Investigating the eco‐evolutionary response of microbiomes to environmental change

Martiny

Brodie

et al. 2023

Ecology Letters

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Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free‐living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome–functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

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Section: Evidence For Evolutionary Responses Of Microbiomes To Enviro...mentioning

confidence: 99%

Investigating the eco‐evolutionary response of microbiomes to environmental change

Martiny

Brodie

et al. 2023

Ecology Letters

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“…It is possible that our phylogeny could be improved by incorporating accessory genes. However, previous research suggests that the phylogeny produced from an alignment of accessory genes did not substantially differ from a phylogeny constructed with core genes (Batarseh et al, 2022;Scales et al, 2022). It is also possible that our 8 habitat categories (Table 1) may be too broad or too narrow, or perhaps dispersal between sources influences the evolutionary history (Finlay, 2002).…”

Section: Discussionmentioning

confidence: 87%

Variation in Sphingomonas traits across habitats and phylogenetic clades

et al. 2023

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Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.

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“…are nevertheless abundant in soil [ 1 , 2 ], marine sediments [ 3 ] and in the air up to the stratosphere [ 4 ]. Curtobacteria demonstrate enhanced tolerance to drought, salinity, UV irradiation and metal ions, and have been suggested to play an important role in plant adaptation to stress conditions [ 5 , 6 , 7 ]. Being typical inhabitants of the rhizosphere of many plants, Curtobacterium spp.…”

Section: Introductionmentioning

confidence: 99%

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Evseev

Lukianova

Tarakanov

et al. 2023

IJMS

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Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

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Differential Response of Bacterial Microdiversity to Simulated Global Change

Cited by 13 publications

References 63 publications

Investigating the eco‐evolutionary response of microbiomes to environmental change

Investigating the eco‐evolutionary response of microbiomes to environmental change

Variation in Sphingomonas traits across habitats and phylogenetic clades

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

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