Ecological and genomic responses of soil microbiomes to high-severity wildfire: linking community assembly to functional potential

Abstract

Increasing wildfire severity, which is common throughout the western United States, can have deleterious effects on plant regeneration and large impacts on carbon (C) and nitrogen (N) cycling rates. Soil microbes are pivotal in facilitating these elemental cycles, so understanding the impact of increasing fire severity on soil microbial communities is critical. Here, we assess the long-term impact of high-severity fires on the soil microbiome. We find that high-severity wildfires result in a multi-decadal (>25 y) recovery of the soil microbiome mediated by concomitant differences in aboveground vegetation, soil chemistry, and microbial assembly processes. Our results depict a distinct taxonomic and functional successional pattern of increasing selection in post-fire soil microbial communities. Changes in microbiome composition corresponded with changes in microbial functional potential, specifically altered C metabolism and enhanced N cycling potential, which related to rates of potential decomposition and inorganic N availability, respectively. Based on metagenome-assembled genomes, we show that bacterial genomes enriched in our earliest site (4 y since fire) harbor distinct traits such as a robust stress response and a high potential to degrade pyrogenic, polyaromatic C that allow them to thrive in post-fire environments. Taken together, these results provide a biological basis for previously reported process rate measurements and explain the temporal dynamics of post-fire biogeochemistry, which ultimately constrains ecosystem recovery.

Wildfire-dependent changes in soil microbiome diversity and function

“…So far, two studies have applied gene-resolved metagenomic analyses to post-fire soils 23,33 . Genome-resolved metagenomic tools can link potential pyrophilous traits (for example, fast growth rate, heat resistance) to specific organisms that thrive in burned soils and support laboratory observations 34 . Furthermore, this approach enables a broader understanding of microbiome function through identification of co-occurring functional traits, potential interspecies interactions, and viral-host dynamics.…”

Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments

“…To analyze the diversity of different gene categories (e.g., CAZy, nitrogen and sulfur cycling genes), Shannon index was calculated using diversity function in R package of “vegan” ( Oksanen et al, 2020 ). For each sample, the gene counts were normalized to the total number of amino acid coding gene sequences predicted by Prodigal prior to downstream analysis ( McKnight et al, 2019 ; Dove et al, 2022 ).…”

High methane flux in a tropical peatland post-fire is linked to homogenous selection of diverse methanogenic archaea

“…The copyright holder for this preprint this version posted April 10, 2023. ; https://doi.org/10.1101/2023.04. 10.536191 doi: bioRxiv preprint carbon turnover (22,25,26,27), however, this is yet to be established in fire-affected tropical peatlands.…”

“…In addition to effects on microbiome diversity and composition, fires affect the predictability of microbiome compositional shifts by altering the relative balance between deterministic and stochastic assembly processes. A limited number of studies on mineral soil ecosystems have shown that the predictability of microbiome shifts post-fire depends on time since fire (27,28,29). An increase in stochastic processes such as dispersal and ecological drift was observed for a brief period (4-16 weeks) post-fire likely due to limited competition and weak environmental cues (28).…”

“…Phylogenetic-bin based null modelling approaches can provide insights into compositional predictability both at the community and clade levels (32). A recent study showed that individual clades whose members occupy similar ecological niches do indeed respond differently to fires and consequently are shaped by different assembly processes (27). Such approaches thus have the potential to provide an understanding of assembly processes acting on key functional groups such as those that turnover carbon.…”