Microbial diversity affects self-organization of the soil–microbe system with consequences for function

Abstract

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits.

Linking microbial community structure to β-glucosidic function in soil aggregates

“…It is suggested that fungi are crucial to the development of soil pore structure and the selforganization of microbial communities in soils (Crawford et al, 2012) and in soil C dynamics (Bailey et al, 2002). However, given our constraints on the DNA yield from the aggregate groups, and the knowledge that fungi are not uniquely associated with the enzyme assayed herein, b-glucosidase, we pyrosequenced only 16S rRNA genes, which does not capture fungal sequences.…”

Understanding mechanisms of soil biota involvement in soil aggregation: A way forward with saprobic fungi?

“…competitors, trophic interactions) and abiotic factors (e.g. soil pH, water content, temperature) in time and space (Naeem and Wright, 2003;Courty et al, 2010;Miller and Fitzsimmons, 2011;Crowther et al, 2012;Crowther and Bradford, 2013). Hence, the expression of fungal traits and their ability to affect soil aggregation has to be evaluated under a variety of conditions, e.g.…”

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes

“…Ecological factors expected to promote diversity [3,4] include spatial structure per se [5] and variable abiotic [4,6,7] and biotic [4,8] environmental features, but the actual contributions of these factors to natural microbial diversity often remain obscure. Among biotic factors, cooperative and competitive social interactions can each affect levels of intra-specific diversity, as can both resource and interference competition [4,7,[9][10][11].…”