Bacterial adaptation is constrained in complex communities

Scheuerl, Thomas; Hopkins, Meirion; Nowell, Reuben W.; Rivett, Damian W.; Barraclough, Timothy G.; Bell, Thomas

doi:10.1038/s41467-020-14570-z

Cited by 128 publications

(120 citation statements)

References 51 publications

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“…Moreover, transcriptome analysis of the endophyte Bacillus mycoides EC18 showed that an upregulation of genes involved in amino acids metabolism, transcriptional regulators, and signal transduction can play an important role in the adaptation of endophytic strains to their ecological niche (Yi et al, 2017). Scheuerl et al (2020) addressed also the question on how the surrounding bacterial community affects evolutionary trajectories of strain adaptation to new niches by studying environmental samples in artificial micro-ecosystems. They found that the diversity of surrounding bacterial communities as well as characteristics of the strain such as genome size are important factors for strain adaptation to new environmental conditions (Scheuerl et al, 2020).…”

Section: Adaptation Of Strains To Environmental Conditionsmentioning

confidence: 99%

“…Scheuerl et al (2020) addressed also the question on how the surrounding bacterial community affects evolutionary trajectories of strain adaptation to new niches by studying environmental samples in artificial micro-ecosystems. They found that the diversity of surrounding bacterial communities as well as characteristics of the strain such as genome size are important factors for strain adaptation to new environmental conditions (Scheuerl et al, 2020). Although this study addressed environmental microorganisms (and not specifically endophytes), this kind of experimental evolutionary approach can help to better understand the required traits for successful penetration and internal plant colonization by endophytes.…”

Section: Adaptation Of Strains To Environmental Conditionsmentioning

confidence: 99%

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The plant endosphere world – bacterial life within plants

Compant

Cambon

Vacher

et al. 2020

Environmental Microbiology

206

104

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The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.

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Section: Adaptation Of Strains To Environmental Conditionsmentioning

confidence: 99%

Section: Adaptation Of Strains To Environmental Conditionsmentioning

confidence: 99%

The plant endosphere world – bacterial life within plants

Compant

Cambon

Vacher

et al. 2020

Environmental Microbiology

206

104

View full text Add to dashboard Cite

show abstract

“…Several studies have focused on genome signatures variations (GC, tetranucleotide signatures, codon usage, purine-pyrimidine ratio) associated with different environments (reviewed in Dutta and Paul (2012) 12 ). Others, have studied bacterial adaptation to shifting environments 13 , or have targeted a specific evolutionary process across several lifestyles (homologous recombination 14 , selection 15 , etc.). Most of these studies, however, considered different species living in different environments, or closely related species with a different lifestyle (i.e.…”

mentioning

confidence: 99%

Evolutionary ecology of natural comammoxNitrospirapopulations

Palomo¹,

Dechesne²,

Cordero

et al. 2020

Preprint

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Microbial life on Earth commonly occurs in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during last decades, but most studies of evolutionary dynamics are based on single species in isolation or experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, favoured by low ammonium concentrations. Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. Nitrospira populations were separated by gene flow boundaries, suggesting natural and cohesive populations. They showed low homologous recombination and strong purifying selection, the latest process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. Additionally, we analysed evolutionary processes in populations from different habitats. Interestingly, our results suggest that in comammox Nitrospira these processes are not an intrinsic feature but greatly vary depending on the habitat they inhabit. Compared to other habitats, groundwater fed sand filters impose strong purifying selection and low recombination. Together, this study improves understanding of interactions and evolution of species in the wild, and sheds light on the environmental dependency of evolutionary processes.

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“…However, it must be re-emphasized that the protective strains studied herein were evolved in the absence of a complex microbial community with the animal host. The community context can alter the evolutionary outcomes of individual microbe species [40,41]. Future research could test whether microbe-mediated protection can be enhanced via evolution in hosts with a resident microbiota.…”

Section: Discussionmentioning

confidence: 99%

Impacts of a novel defensive symbiosis on the nematode host microbiome

Dahan

Preston

Sealey

et al. 2020

Preprint

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Background: Bacteria adapted to live within animals can protect their hosts against harmful infections. Beyond antagonism with pathogens, a ‘defensive’ bacterial symbiont could engage in additional interactions with other colonizing micro-organisms. A single bacterium might thus have cascading ecological impacts on the whole microbiome that are rarely investigated. Here, we assess the role of a defensive symbiont as a driver of host-associated microbiota composition by using a bacterial species ( Enterococcus faecalis ) that was previously experimentally adapted ( Enterococcus faecalis ) to a nematode host model ( Caenorhabditis elegans ). Results: An analysis of 16S rRNA data from C. elegans exposed to E. faecalis and subsequently reared in soil, reveal that symbiont adaptation to host environment or its protective potential had minimal impact on microbiota diversity. Whilst the abundance of Pseudomonas was higher in the microbiota of hosts with protective E.faecalis (and another protective species tested), three other genera – Serratia, Klebsiella and Salinispora – were less abundant in hosts colonized by all E. faecalis strains. In addition, the protective effect of E. faecalis against opportunistic Staphylococcus aureus pathogens was maintained despite multi-species interactions within the microbiota. Conclusions: Our results reveal the degree to which a new, evolving symbiont can colonise and maintain its conferred phenotype (i.e., pathogen-resistance) with minimal disruption to the host microbiota diversity.

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Bacterial adaptation is constrained in complex communities

Cited by 128 publications

References 51 publications

The plant endosphere world – bacterial life within plants

The plant endosphere world – bacterial life within plants

Evolutionary ecology of natural comammoxNitrospirapopulations

Impacts of a novel defensive symbiosis on the nematode host microbiome

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