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 underlain 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. Previously, 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 the key shifts in microbial inoculant communities altered by soil disturbance using 16S rRNA amplicon sequencing as well as changes in potential functional mechanisms that influence plant growth using long read metagenomics. Across our soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with previous results, the family Acidobacteriaceae, which consists of known plant 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 drives differences in microbial community function. These results indicate that a decrease in plant growth can be linked to changes in the 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.

Current Challenges and Pitfalls in Soil Metagenomics

“…This will allow us to further disentangle soil microbial communities by linking specific microorganisms or functions to precise chemical changes [ 33 ]. Microbial responses are context-dependent; they change with soil disturbance [ 34 ], climate, and nutrient availability [ 26 , 35 ]. Nutrients also determine the abundance of root promoting microorganisms [ 36 ], which can even help explain changes in plant productivity.…”

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes

“…The copyright holder for this this version posted September 22, 2023. ; https://doi.org/10.1101/2023.09.21.558928 doi: bioRxiv preprint research, environmental, and agricultural studies (Michaelsen et al, 2022;Parker et al, 2017;Seitz et al, 2021).…”