Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity

Distribution patterns of soil bacteria, fungi, and protists emerge from distinct assembly processes across subcommunities

Environmental change exerts a profound effect on soil microbial domains-including bacteria, fungi, and protists-that each perform vital ecological processes. While these microbial domains are ubiquitous and extremely diverse, little is known about how they respond to environmental changes in urban soil ecosystems and what ecological processes shape them. Here we investigated the community assembly processes governing bacteria, fungi, and protists through the lens of four distinct subcommunities: abundant, conditionally rare, conditionally abundant, and rare taxa. We show that transient taxa, including the conditionally rare and conditionally rare or abundant taxa, were the predominant subcommunities. Deterministic processes (e.g., environmental filtering) had major roles in structuring all subcommunities of fungi, as well as conditionally rare and abundant protists. Stochastic processes had strong effects in structuring all subcommunities of bacteria (except rare taxa) and conditionally rare protists. Overall, our study underscores the importance of complementing the traditional taxonomy of microbial domains with the subcommunity approach when investigating microbial communities in urban soil ecosystems.

Mycorrhizal mediation of soil carbon in permafrost regions depends on soil nutrient stoichiometry and physical protection

Mycorrhizal associations are considered as one of the key drivers for soil carbon (C) accumulation and stability. However, how mycorrhizal associations influence soil organic C (SOC) and its fractions (i.e., particulate organic C [POC] and mineral-associated organic C [MAOC]) remain unclear. In this study, we examined effects of plant mycorrhizal associations with arbuscular mycorrhiza (AM), ectomycorrhiza (ECM), and their mixture (Mixed) on SOC and its fractions as well as soil stoichiometric ratios across 800-km transect in permafrost regions. Our results showed that soil with only ECM-associated trees had significantly higher SOC and POC compared to only AM-associated tree species, while soil in Mixed plots with both AM- and ECM- associated trees tend to be somewhat in the middle. Using structural equation models, we found that mycorrhizal association significantly influenced SOC and its fraction (i.e., POC, MAOC) indirectly through soil stoichiometric ratios (C:N, C:P, and N:P). These results suggest that selecting ECM tree species, characterized by a "slow cycling" nutrient uptake strategy, can effectively enhance accumulation of SOC and its fractions in permafrost forest ecosystems. Our findings provide novel insights for quantitatively assessing the influence of mycorrhiza-associated tree species on the management of soil C pool and biogeochemical cycling.

Chronic exposure to pesticides disrupts the bacterial and fungal co-existence and the cross-kingdom network characteristics of honey bee gut microbiome

Gut microbiome communities have a significant impact on bee health and disease and have been shown to be shaped by a variety of factors, including exposure to pesticides and inhive chemicals. However, it is unknown whether pesticide exposure affects the coexistence and cross-kingdom network parameters of bee gut microbiome communities because microbes may compete in the gut environment under different stressors. Therefore, we conducted additional analysis of the microbiome data from our previous study in which we discovered that exposure to two novel insecticides flupyradifurone (FPF) and sulfoxaflor (Sulf) or/and a fungicide, azoxystrobin (Azoxy) caused dysbiosis of bee gut microbiota that was associated with an increase in the relative abundance of opportunistic pathogens such as Serratia marcescens. We investigated for the first time the potential cross-kingdom fungal-bacterial interactions using co-occurrence pattern correlation and network analysis. We discovered that exposure to FPF or Sulf alone or in combination with Azoxy fungicide influenced the co-existence patterns of fungal and bacterial communities. Significant differences in degree centrality, closeness centrality, and eigenvector centrality distribution indices were also found in single and double-treatment groups compared to controls. The effects of FPF and Sulf alone on cross-kingdom parameters (bacterial to fungal node ratio, degree of centrality, closeness centrality, and eigenvector centrality) were distinct, but this was reversed when they were combined with Azoxy fungicide. The fungal and bacterial hub taxa identified differed, with only a few shared hubs across treatments, suggesting microbial cross-kingdom networks may be disrupted differently under different stressors. Our findings add to our understanding of pesticide effects on the bee gut microbiome and bee health in general, while also emphasizing the importance of cross-kingdom network analysis in future microbiome research.