Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities

Abstract

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

“…The finding that the cropland-declined microbial cluster drove the degradation of soil ecosystem multifunctionality (Figure b) made sense because the biodiversity of certain microbial clusters, rather than that of the overall microbial communities, were found to significantly correlate with ecosystem multifunctionality. − In the present study, the cropland-declined microbial cluster was positively associated with various ecological processes related with nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles (Figure S11), probably because it contained a variety of taxa capable of improving soil nutrient status (Figures b and S11, and Table S5). Among the prokaryotes within the cropland-declined microbial cluster, the most abundant taxon Rhodoplanes genus was reported to be involved in nitrogen fixation; and Candidatus Solibacter genus was found to participate in the acquisition of carbon, nitrogen, and phosphorus from soils. − We further took Rhizobiales order that the Rhodoplanes genus belonged to as a typical microbial functional population participating in nitrogen fixation and found it indeed significantly and positively ( P = 0.001, R 2 = 0.15) correlated with the normalized abundance of nifH gene (encoding dinitrogenase reductase during nitrogen fixation, Table S2).…”

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

“…This may be because earthworm species distribution is not homogeneous, and therefore may harbor different bacterial communities as well as resistomes at large geographic scale. Moreover, environmental perturbations such as pollution, agricultural practices, and habitat changes can cause significant ecological variations, leading to great fluctuations in microbial diversity and resistome composition at a large scale. , These fluctuations in bacterial communities in the earthworm gut, to which only a part of bacterial species can adapt, may lead to low diversity in both bacteria and resistomes. Furthermore, earthworm gut resistomes displayed random dispersal processes, but these processes were less than soil resistomes.…”