Predictive genomic traits for bacterial growth in culture versus actual growth in soil

Li, Junhui; Mau, Rebecca L.; Dijkstra, Paul; Koch, Benjamin J.; Schwartz, Egbert; Liu, Xiao Jun Allen; Morrissey, Ember M.; Blazewicz, Steven J.; Pett‐Ridge, Jennifer; Stone, Bram WG; Hayer, Michaela; Hungate, Bruce A.

doi:10.1038/s41396-019-0422-z

Cited by 81 publications

(82 citation statements)

References 52 publications

(73 reference statements)

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“…Both maximum growth rate and RRN are expected to be most strongly under selection in lifestyles where resources become episodically available and there is a race to convert them into population. For example, Li et al (2019) showed that RRN was not correlated with growth rates in soil, but became correlated with growth rates following glucose addition.…”

Section: Maximum Growth Ratementioning

confidence: 99%

Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

Westoby

Nielsen

Gillings

et al. 2021

Ecology and Evolution

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Section: Maximum Growth Ratementioning

confidence: 99%

Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

Westoby

Nielsen

Gillings

et al. 2021

Ecology and Evolution

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“…Furthermore, other constraints on growth (lack of resources, external stressors) imposed by the environment may also affect the relationships among traits and the relationship between traits and fitness. It has recently been shown that there is no relationship between the 16S rRNA gene copy number and growth in soil under natural conditions [52]. However, a relationship between growth and the 16S rRNA gene copy number became apparent after the addition of abundant substrate, thus removing the resource constraint.…”

Section: (A) Bacterial Catabolic Breadth Growth Rates and Phylogenymentioning

confidence: 99%

The ecology of heterogeneity: soil bacterial communities and C dynamics

Nunan

Schmidt

Raynaud

2020

Phil. Trans. R. Soc. B

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Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection ( https://metacyc.org/ ). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

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“…imposed by the environment may also affect the relationships among traits and the relationship between traits and fitness. It has recently been shown that there is no relationship between the 16S rRNA gene copy number and growth in soil under natural conditions [52]. However, a relationship between growth and the 16S rRNA gene copy number became apparent after the addition of abundant substrate, thus removing the resource constraint.…”

Section: Bacterial Catabolic Breadth Growth Rates and Phylogenymentioning

confidence: 99%

The ecology of heterogeneity: soil bacterial communities and C dynamics

Raynaud¹,

Schmidt

Nunan³

2021

Preprint

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Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning.Heterogeneity in soils has multiple facets, from the molecular heterogeneity of the diversity of substrate available, the activity heterogeneity due to the activity of microbial species and the spatial heterogeneity of the soil structure and the distribution of organisms.In this contribution we present a simple, spatially explicit model that can be used to understand how the interactions between the heterogeneity of decomposers (in terms of species and spatial distribution) and environmental heterogeneity (in terms of the diversity of substrates and their spatial distribution) affect the bacterial decomposition of organic matter. We found that environmental heterogeneity is a key element in determining the variability of the decomposition process.

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Predictive genomic traits for bacterial growth in culture versus actual growth in soil

Cited by 81 publications

References 52 publications

Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

The ecology of heterogeneity: soil bacterial communities and C dynamics

The ecology of heterogeneity: soil bacterial communities and C dynamics

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