Soil disturbance affects plant growth via soil microbial community shifts

Abstract

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant growth by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant growth was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased growth compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost have differences in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant growth can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant growth in Boreal forests and more broadly, ecosystem health.

Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska

“…The link between host phylogeny and ARG abundance demonstrates how a loss of Firmicutes and enrichment of Proteobacteria as a result of community shifts could increase the abundance of ARGs within a community. Although we cannot say from this specific dataset of cultured isolates which taxa are enriched across FPES sites, previous analyses conducted on uncultured metagenomic data from across 48 FPES cores in Seitz et al, 2020 identified over-representation of the phylum Proteobacteria in the disturbed cores and of the order Bacillales in undisturbed cores [ 24 ]. This enrichment in the metagenomic data parallels the enrichment of these taxa in this cultured subset of the community.…”

“…This gene encodes fosfomycin thiol transferase that confers resistance to an antibiotic derived from secondary metabolites produced by soil-dwelling bacteria including Streptomyces and pseudomonads [ 42 ]. Both Streptomyces and pseudomonads have been found to be abundant in FPES metagenomic datasets [ 24 ] highlighting the taxonomic potential for the production of fosfomycin at this locale. This potential along with the high abundance of fosB found in this study is suggestive of the selective advantage encoding antibiotic inactivating enzymes may have in competing against antibiotic producing bacterial taxa in the soil community.…”

“…This shift in both biotic and abiotic factors has the potential to enrich ARGs by selecting for their host taxa. For example, the phylum Proteobacteria is significantly enriched with plasmid-borne resistance determinants compared to other bacterial phyla [ 23 ] and over-represented in terms of abundance in active layer soils associated with disturbance-induced thaw [ 24 ]. This connection between ARGs, phylogeny, and community shifts observed in disturbed soils of Alaska makes it imperative to assess how thaw will affect bacteria from active layer soils as a reservoir of resistance.…”

“…The location’s distinctive gradient of disturbance-induced thaw makes it fitting for research on the effect of disturbance on permafrost, vegetation, soils, and microbial communities. Previous culture-independent metagenomic analyses conducted at this site found distinct shifts in microbial community composition, such as an enrichment of Proteobacteria in the disturbed soils [ 24 ], necessitating more research into how this site has affected antibiotic resistance.…”

Soil Disturbance Affects Plant Productivity via Soil Microbial Community Shifts

“…This research was supported by the Alaska BLaST program, the Institute of Arctic Biology, and Alaska INBRE. The content of this manuscript has previously appeared as a preprint in bioRxiv ( Seitz et al, 2020 ).…”