Adaptation in Natural Microbial Populations

Koskella, Britt; Vos, Michiel

doi:10.1146/annurev-ecolsys-112414-054458

Cited by 53 publications

(56 citation statements)

References 114 publications

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“…If so, we would expect that Methylobacterium from the rice phyllosphere would be similar to other isolates in the local environment. To explore this possibility, we sampled Methylobacterium from various other sources in the Chingarel field in Manipur: (1) the phyllosphere of grasses growing in the same field, (2) the surface of seeds from focal rice landraces, (3) a commercial rice variety cultivated in the same field, and (4) field soil. Based on their taxonomic identity and carbon use profiles (as described above), we removed putative clones (see methods) and obtained 4 distinct isolates from grasses; 5 isolates from seeds of four rice landraces; 4 isolates from the commercial rice variety; and 3 distinct isolates from field soil sampled between rice growing seasons (i.e.…”

Section: Resultsmentioning

confidence: 99%

“…Such spatial structure may reflect neutral or stochastic processes (including dispersal limitation), and/or differential selection imposed by environmental factors (2), including association with eukaryotic hosts. For instance, local adaptation to specific host species or genotypes can drive substantial divergence across bacteria (3), perhaps best exemplified in plant pathogens (4). Association with specific hosts can thus have large impacts on bacterial genomes (5), as well as functional traits such as those reflecting generalist vs. specialist life histories (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…Association with specific hosts can thus have large impacts on bacterial genomes (5), as well as functional traits such as those reflecting generalist vs. specialist life histories (e.g. reviewed in (3,4)). Host association is thus an important context to understand the diversity and distribution of bacteria, because it generates unique selection pressures compared to abiotic environmental factors.…”

Section: Introductionmentioning

confidence: 99%

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Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

Sanjenbam

Buddidathi

Venkatesan

et al. 2019

Preprint

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14The ecology and distribution of many bacteria is strongly associated with specific eukaryotic hosts. 15However, the impact of such host association on bacterial ecology and evolution is not well understood. 16Bacteria from the genus Methylobacterium consume plant-derived methanol, and are some of the most 17 abundant and widespread plant-associated bacteria. In addition, many of these species impact plant 18 fitness. To determine the ecology and distribution of Methylobacterium in nature, we sampled bacteria 19 from 36 distinct rice landraces, traditionally grown in geographically isolated locations in North-East 20(NE) India. These landraces have been selected for diverse phenotypic traits by local communities, and 21we expected that the divergent selection on hosts may have also generated divergence in associated 22Methylobacterium strains. We determined the ability of 91 distinct rice-associated Methylobacterium 23isolates to use a panel of carbon sources, finding substantial variability in carbon use profiles. Consistent 24 with our expectation, across spatial scales this phenotypic variation was largely explained by host 25 landrace identity rather than geographical factors or bacterial taxonomy. However, variation in carbon 26utilisation was not correlated with sugar exudates on leaf surfaces, suggesting that bacterial carbon use 27 profiles do not directly determine bacterial colonization across landraces. Finally, experiments showed 28 that at least some rice landraces gain an early growth advantage from their specific phyllosphere-29colonizing Methylobacterium strains. Together, our results suggest that landrace-specific host-30 microbial relationships may contribute to spatial structure in rice-associated Methylobacterium in a 31 natural ecosystem. In turn, association with specific bacteria may provide new ways to preserve and 32understand diversity in one of the most important food crops of the world . 33 34 35 Keywords 36 Phyllosphere, phenotypic diversity, Methylobacterium, rice landraces, host-microbial association 37 48context to understand the diversity and distribution of bacteria, because it generates unique selection 49pressures compared to abiotic environmental factors. Additionally, strong structure in host populations 50themselves (e.g. due to limited dispersal or local adaptation to environmental conditions) may further 51 enhance population structure in their bacterial associates. 52 53Plant-associated bacteria -especially those occupying aerial niches (the "phyllosphere") -thus 54represent attractive systems to understand the processes and selection pressures that shape natural 55 microbial populations. The phyllosphere is estimated to harbour nearly 10 7 bacterial cells/cm 2 of leaf 56 surface, with both biotic and abiotic factors influencing bacterial communities (reviewed in (6,7). For 57 instance, leaf exudates may include antimicrobials as well as nutrients; and colonization of leaf surfaces 58 exposes bacteria to UV radiation and desiccation. These factors may impose selection...

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

Sanjenbam

Buddidathi

Venkatesan

et al. 2019

Preprint

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“…Fungal microbes are powerful models in genetics and molecular biology and increasingly so in ecological and evolutionary research (Bleuven & Landry, ; Koskella & Vos, ; Landry, Townsend, Hartl, & Cavalieri, ; Marsit et al, ). Among fungi, the genus Saccharomyces , particularly Saccharomyces cerevisiae , is well known for being used as a model system in the laboratory and for being closely associated with other human activities such as beer, wine, and bread making.…”

Section: Introductionmentioning

confidence: 99%

A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology

et al. 2018

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While the use of barcoded collections of laboratory microorganisms and the development of barcode‐based cell tracking are rapidly developing in genetics and genomics research, tools to track natural populations are still lacking. The yeast Saccharomyces paradoxus is an emergent microbial model in ecology and evolution. More than five allopatric and sympatric lineages have been identified and hundreds of strains have been isolated for this species, allowing to assess the impact of natural diversity on complex traits. We constructed a collection of 550 barcoded and traceable strains of S. paradoxus , including all three North American lineages SpB , SpC , and SpC* . These strains are diploid, many have their genome fully sequenced and are barcoded with a unique 20 bp sequence that allows their identification and quantification. This yeast collection is functional for competitive experiments in pools as the barcodes allow to measure each lineage's and individual strains’ fitness in common conditions. We used this tool to demonstrate that in the tested conditions, there are extensive genotype‐by‐environment interactions for fitness among S. paradoxus strains, which reveals complex evolutionary potential in variable environments. This barcoded collection provides a valuable resource for ecological genomics studies that will allow gaining a better understanding of S. paradoxus evolution and fitness‐related traits.

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“…These experiments range from single species grown in flasks (Lenski & Travisano 1994;Levy et al 2015) to more realistic microcosms with manipulated community assemblies (Gomez & Buckling 2011). Yet, whether or not the results of these laboratory studies can be translated into the processes that control natural populations in their ever-changing, complex biotic and abiotic environment is unknown, and some studies suggest they do not (Koskella & Vos 2015).…”

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confidence: 99%

Harnessing the power of digital droplet PCR to conduct real‐world microbial competitions

Murphy

2017

Molecular Ecology Resources

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The budding yeast, Saccharomyces cerevisiae, has a long and storied history as a model organism for genetic, cellular and molecular biological research. More recently, researchers have sought to understand the ecology and evolution of its sister species, Saccharomyces paradoxus, in part to put our vast knowledge of the model yeast into its natural context (Replansky et al. ). However, the research tools have been limited, and most investigations into natural populations have either been descriptions of patterns of biogeography or taken the organism back into the laboratory for mating, growth and competition assays (Kuehne et al. ; Miller & Greig ; Murphy & Zeyl ; Samani et al. ). The link between what occurs out in the real world and what is measured in the laboratory has not yet been made, as so much is still unknown about the natural history of these yeasts. In this issue of Molecular Ecology Resources, Boynton et al. () take a major step towards bridging laboratory studies with field ecological research. By isolating a panel of S. paradoxus strains from a wooded area, culturing them in the laboratory, reintroducing pairs back into their habitat on natural substrate and monitoring the frequency of individual strains using digital droplet PCR, the researchers were able to use the framework of laboratory-based microbial competitions, but conduct them in a natural setting. While there is still more to learn about how to optimize this approach, it represents an exciting step in microbial ecological research and should prove an important tool for other species and numerous ecological questions.

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Adaptation in Natural Microbial Populations

Cited by 53 publications

References 114 publications

Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

Phenotypic diversity of Methylobacterium associated with rice landraces in Northeast India

A collection of barcoded natural isolates of Saccharomyces paradoxus to study microbial evolutionary ecology

Harnessing the power of digital droplet PCR to conduct real‐world microbial competitions

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