Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient

Abstract

Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.

Reduction of bioavailability and phytotoxicity effect of cadmium in soil by microbial-induced carbonate precipitation using metabolites of ureolytic bacterium Ochrobactrum sp. POC9

“…Most of the so far described MICP applications for heavy metal immobilization in soil utilized culture breeding (bacterial cells suspended in metabolites solution) directly to contaminated soil ( Kumari et al., 2014 ; Liu et al., 2021 ; Qiao et al., 2021 ). In some cases, soil enrichment with the exogenous pool of microbes may have a negative effect on the soil’s autochthonous microbiome condition, by disturbing its natural community structure ( Lourenço et al., 2018 ; Seitz et al., 2022 ). The appropriate microbiome composition is particularly important in the context of the treatment of agricultural soil since microbes directly interact with crop plants and affect their productivity ( Trivedi et al., 2020 ; Glick and Gamalero, 2021 ).…”

Converting Low-Productivity Pasture to Well-Managed Pasture and Silvopastoral System Cause Relevant Changes in Soil Chemical and Microbiological Characteristics

“…Thus, in pastures, soil microbial activity is also influenced by the intensity of grazing [14]. Regarding soil tillage, the proportion of soil microbial biomass tends to increase with less soil disturbance [15], specifically in no-tillage and integrated systems (e.g., integrated crop-livestock (ICL) and silvopastoral systems).…”