Niche breadth affects bacterial transcription patterns along a salinity gradient

Rain‐Franco, Angel; Mouquet, Nicolas; Gougat-Barberá, Claire; Bouvier, Thierry; Beier, Sara

doi:10.1111/mec.16316

Cited by 16 publications

(12 citation statements)

References 113 publications

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“…Gene expression variations are key to niche partitioning and ecotype distribution in natural ecosystems [58,59]. It is not yet fully understood whether differences in gene expression could precede genome sequence evolution in response to niche adaptation.…”

Section: Gene Expressionmentioning

confidence: 99%

Respiration-induced biofilm formation as a driver for bacterial niche colonization

Martín‐Rodríguez¹

2023

Trends in Microbiology

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Section: Gene Expressionmentioning

confidence: 99%

Respiration-induced biofilm formation as a driver for bacterial niche colonization

Martín‐Rodríguez¹

2023

Trends in Microbiology

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“…While probabilities do not allow the prediction of a single event, their predictive power increases with the number of considered events. We therefore suggest that resistance or resilience of individual species in a given situation should preferably be evaluated via the regulation of RNA markers in response to a specific environmental change, as detailed in a recent study (Rain-Franco et al, 2021). We however claim that the predictability of functional consequences from genomic traits increases if simultaneously applied for multiple species in a community and genomic traits values are scaled-up to evaluate their distribution at the community level (Box 2).…”

Section: Synthesismentioning

confidence: 99%

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

et al. 2022

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We report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait–trait variations of 11 genomic traits from ~18,000 sequenced genomes. The studied trait–trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an oligotrophic-copiotrophic axis. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from traits associated with resource availability. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. Genome size distributions differ across habitats and our findings therefore point to habitat dependent tradeoffs between resistance and resilience. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.

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“…This classification does not direct mapping onto abundant and rare, as the abundance of generalist or specialist will depend on local environment (McArthur, 2006). The habitat generalists exhibiting broad niche are considered to be less competitive under optimal growth conditions but feature higher resistance against changing conditions, while specialists have narrower range of habitats and specific environment fitness (Rain‐Franco et al ., 2022; Chen et al ., 2021). Compared to generalists, specialists have a faster worldwide decline, promoting the functional homogenization in biodiversity (Clavel et al ., 2011).…”

Section: Introductionmentioning

confidence: 99%

Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes

Liu

et al. 2022

Environmental Microbiology

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Microbial metacommunities normally comprise generalists and specialists. Uncovering the mechanisms underlying the diversity patterns of these two subcommunities is crucial for aquatic biodiversity maintenance. However, little is known about the ecological assembly processes and co-occurrence patterns of the habitat generalists and specialists across large spatial scales in plateau lake sediments, particularly regarding their environmental adaptations. Here, we investigated assembly processes of the habitat generalists and specialists in sediment of Tibetan lakes and their role in the stability of metacommunity cooccurrence network. Our results showed that the habitat generalists exhibited broader environmental thresholds and closer phylogenetic clustering than specialist counterparts. In contrast, the specialists exhibited stronger phylogenetic signals of ecological preferences compared with the habitat generalists. Stochastic processes dominated the habitat generalist (63.2%) and specialist (81.3%) community assembly. Sediment pH was the major factor mediating the balance between stochastic and deterministic processes in the habitat generalists and specialists. In addition, as revealed by network analysis, the habitat specialists played a greater role in maintaining the stability of metacommunity co-occurrence network. The insights gained from this study can be helpful to understand the mechanisms underlying maintenance of sediment microbial diversity in plateau lakes.

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Niche breadth affects bacterial transcription patterns along a salinity gradient

Cited by 16 publications

References 113 publications

Respiration-induced biofilm formation as a driver for bacterial niche colonization

Respiration-induced biofilm formation as a driver for bacterial niche colonization

Trait-trait relationships and tradeoffs vary with genome size in prokaryotes

Distinct strategies of the habitat generalists and specialists in sediment of Tibetan lakes

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