The ecology of heterogeneity: soil bacterial communities and C dynamics

Abstract

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’.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies

“…However, the contribution of endemic links to methanogenesis (36.8%) was far lower than the contribution of common links (53.3%). This result conflicts with the observation that specialists consume resources more rapidly than generalists [64].…”

Continuous Cropping Alters Multiple Biotic and Abiotic Indicators of Soil Health

“…The soil organic matter and C contents are the key drivers and indicators of soil health, as they play a central role in soil fertility, functioning, quality, and sustainability [217][218][219]. There is an emerging consensus that CC with destructive tillage practices may negatively affect soil organic matter in the agricultural soils [207].…”

A critical perspective on interpreting amplicon sequencing data in soil ecological research

“…Several computational tools can correct amplicon datasets for the number of 16S rRNA gene copies based on existing genome information (e.g., PICRUSt2 (Douglas et al, 2020) and CopyRighter (Angly et al, 2014)). However, correcting for 16S rRNA gene copy numbers in sequencing surveys remains challenging, particularly for soil, as the gene copy numbers are only known for a subset of the soil microbes (Louca et al, 2018;Nunan et al, 2020). This challenge becomes even more problematic for marker genes of fungi and other eukaryotes, such as protists, as the copy number here can vary drastically between taxa (Gong et al, 2013;Gong and Marchetti, 2019).…”