The landscape of microbial phenotypic traits and associated genes

Brbić, Maria; Piškorec, Martija; Vidulin, Vedrana; Kriško, Anita; Šmuc, Tomislav; Supek, Fran

doi:10.1093/nar/gkw964

Cited by 71 publications

(101 citation statements)

References 96 publications

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“…A mapping of EOL‐IDs (according to https://opendata.eol.org/dataset/hierarchy_entries, accessed 04/04/2017) has also been imported, so that full‐text information about taxa is available where EOL offers such (Parr, Wilson, Leary, et al., ). Currently, and as a starting seed, trait data from TraitBank (Parr, Wilson, Schulz, et al., ), EPPO (EPPO, ), the World Crops Database (Bijlmakers, ), the cavity‐nesting bees and wasps database (Budrys, Budriene, & Orlovskyte, , part of the SCALES project (Henle et al., )), IUCN (IUCN, ), and ProTraits (Brbić et al., ) have been imported which is subject to continuous extension. We aim to maintain the high quality of these publicly available traits.…”

Section: Resultsmentioning

confidence: 99%

“…Databases have been developed that provide trait information for eukaryotes and prokaryotes, e.g. LEDA Traitbase (Kleyer et al., ), TRY (Kattge et al., ), and BacDive or ProTraits for microbial traits (Brbić et al., ; Söhngen, Bunk, Podstawka, Gleim, & Overmann, ). On a higher level, TraitBank (Parr, Wilson, Leary, et al., ; Parr, Wilson, Schulz, et al., ) aggregates this information from different sources.…”

Section: Introductionmentioning

confidence: 99%

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Functional exploration of natural networks and ecological communities

Ankenbrand

Hohlfeld

Weber³

et al. 2018

Methods Ecol Evol

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Species composition assessment of ecological communities and networks is an important aspect of biodiversity research. Yet often ecological traits of organisms in a community are more informative than scientific names only. Furthermore, other properties like threat status, invasiveness, or human usage are relevant to many studies, but cannot be evaluated from taxonomy alone. Despite public databases collecting such information, it is still a tedious manual task to enrich community analyses with such, especially for large‐scaled data. Thus we aimed to develop a public and free tool that eases bulk trait mapping of community data in a web browser, implemented with current standard web and database technologies. Here, we present the Fennec (Functional Exploration of Natural Networks and Ecological Communities), a workbench that eases the process of mapping publicly available trait data to the user's communities in an automated process. Usage is either by a local self‐hosted or a public instance ( https://fennec.molecular.eco) covering exemplary traits. Alongside the software, we also provide usage and hosting documentation as well as online tutorials. The Fennec aims to motivate public trait data submission and its reuse in meta‐analyses. Further, it is an open‐source development project with the code freely available to use and open for community contributions ( https://github.com/molbiodiv/fennec).

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Functional exploration of natural networks and ecological communities

Ankenbrand

Hohlfeld

Weber³

et al. 2018

Methods Ecol Evol

View full text Add to dashboard Cite

show abstract

“…Unfortunately, there has been surprisingly little research into the genetic architecture of bacterial traits. Although there is some evidence for the sort of additive gene effects we modeled (Abe & Benedetti, ; Hunter & Keener, ), many traits display more complex interactions (Brbić et al, ). However, we believe our qualitative predictions are likely to hold at the sequence level as well.…”

Section: Discussionmentioning

confidence: 99%

The role of recombination, niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria

Schmutzer

Barraclough

2019

Ecology and Evolution

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Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche‐specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that (a) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect and (b) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche‐specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche‐specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.

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“…36 To repair DSBs, microbes may use one of two pathways: homologous recom-37 bination (HR), or non-homologous end joining (NHEJ) [15]. HR machinery is 38 ubiquitous across microbes [31], although it requires multiple genome copies to 39 function. To-date, much work on GC content has focused on associating rates 40 of HR locally along a genome (inferred using polymorphism data) with local GC 41 content, which would be taken as evidence for the action of BGC [7].…”

Section: Introductionmentioning

confidence: 99%

“…While NHEJ presence is an imperfect indicator of DSB incidence in general, 82 we expect this pathway to be especially common among organisms experiencing 83 many DSBs during periods of slow or no growth [26]. Using a large-scale mi-84 crobial trait database [39] paired with genomes from RefSeq [40], we identified 85 known ecological correlates of NHEJ incidence as well as genomic GC content 86 (some of which were redundant, S1 Fig). A principal component analysis of 87 these traits revealed similar patterns of NHEJ incidence and high genomic GC 88 content in trait-space (Fig 1), consistent with the idea that DNA damage is as-89 sociated with genomic GC content.…”

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confidence: 99%

Potential link between selection for high GC content and repair of double strand breaks in prokaryotic genomes

Weissman

Fagan

Johnson

2019

Preprint

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Genomic GC content varies widely among microbes for reasons unknown. While mutation bias partially explains this variation, prokaryotes near-universally have a higher GC content than predicted solely by this bias. Debate surrounds the relative importance of the remaining explanations of selection versus biased gene conversion favoring GC alleles. Some environments (e.g. soils) are associated with a high genomic GC content of their inhabitants, which implies that either high GC content is a selective adaptation to particular habitats, or that certain habitats favor increased rates of gene conversion. Here, we report a novel association between the presence of the non-homologous end joining DNA doublestrand break repair pathway and GC content; this observation suggests that DNA damage may be a fundamental driver of GC content, leading in part to the many environmental patterns observed to-date. We discuss potential mechanisms accounting for the observed association, and provide preliminary evidence that sites experiencing higher rates of doublestrand breaks are under selection for increased GC content relative to the genomic background.Author Summary The overall nucleotide composition of an organism's genome varies greatly between species. Previous work has identified certain environmental factors (e.g., oxygen availability) associated with the relative number of GC bases as opposed to AT bases in the genomes of species. Many of these environments that are associated with high GC content are also associated with relatively high rates of DNA damage. We show that organisms possessing the non-homologous end-joining DNA repair pathway, which is one mechanism to repair DNA double-strand breaks, have an elevated GC content relative to expectation. We also show that certain sites on the genome that are particularly susceptible to double strand breaks have an elevated GC content. This leads us to suggest that an important underlying driver of variability in nucleotide composition across environments is the rate of DNA damage (specifically doublestrand breaks) to which an organism living in each environment is exposed.

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The landscape of microbial phenotypic traits and associated genes

Cited by 71 publications

References 96 publications

Functional exploration of natural networks and ecological communities

Functional exploration of natural networks and ecological communities

The role of recombination, niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria

Potential link between selection for high GC content and repair of double strand breaks in prokaryotic genomes

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