Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

Abstract

Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.

Soil fungal community characteristics vary with bamboo varieties and soil compartments

“…Simplicillium and Nectria were the keystone taxa in bulk soil, and Penicillium and Laetisaria in the rhizosphere. Similar findings were reported in previous studies ( Su et al, 2020 ; Liu L. et al, 2021 ; Varsadiya et al, 2021 ; Zheng et al, 2021 ). For instance, Penicillium plays a key role in rhizosphere soil, it can generate products that promote plant health (e.g., soluble phosphorus, iron carriers, plant hormones) and affect plant adaptability through a series of biochemical processes ( Altaf et al, 2018 ; Park et al, 2020 ).…”

“…Bulk soil (B): PE-B, P. edulis; FT-B, P. edulis f. tao kiang; FL-B, P. edulis f. luteosulcata; FP-B, P. edulis f. pachyloen; FG-B, P. edulis f. gracilis. 10.3389/fmicb.2023.1120679 Frontiers in Microbiology frontiersin.org 2020 ;Liu L. et al, 2021;Varsadiya et al, 2021;Zheng et al, 2021). For instance, Penicillium plays a key role in rhizosphere soil, it can generate products that promote plant health (e.g., soluble phosphorus, iron carriers, plant hormones) and affect plant adaptability through a series of biochemical processes (Altaf et al, 2018;Park et al, 2020).…”

From diversity to complexity: Microbial networks in soils

“…Although this concept to interpret nodes with a high connectivity as ‘key taxa’ stems from plant-animal interaction networks, it was later adopted in a large and still growing number of soil ecological studies to identify ‘keystone taxa’ in soil microbial datasets based on co-occurrence networks (e.g. ( Zhou et al, 2011 ; Lu et al, 2013 ; Lupatini et al, 2014 ; Jiang et al, 2016 ; Ling et al, 2016 ; Shi et al, 2016 ; Chen et al, 2018 ; Qi et al, 2019 ; Varsadiya et al, 2021 ; Yuan et al, 2021 )). Other attempts to classify keystone taxa in soil microbial co-occurrence networks select nodes with high degree and high closeness centrality, but low betweenness centrality ( Banerjee et al, 2018 , 2019 ; Lin et al, 2019 ), guided by a theoretical analysis of co-occurrence networks constructed from generalized Lotka-Volterra equations ( Berry and Widder, 2014 ).…”

Fungal plastiphily and its link to generic virulence traits makes environmental microplastics a global health factor

“…6a, Table 1), demonstrating the importance of selective forces in the assembly of mycobiomes and implying the emergence of fundamentally different interaction landscapes on MP. The lower overall size and average path length of the plastisphere network indicates a compact network with 'small world' properties, implying rapid material and information transport among co-occurring species 73,74 , while the higher clustering coefficient suggests a more complex network with stronger interactions than in soil 47,48 . Overall, however, the degree to which these correlations represent real-world organismic interactions remains to be investigated.…”

“…For co-occurrence network construction, the most frequent 10% of OTUs of each MC were chosen. The Spearman correlation matrix was calculated using the psych package 137 in R. To highlight the most important relationships, only strong positive (ρ > 0.6) or strong negative (ρ < −0.6) and highly significant (p < 0.01) correlations were used for network construction 48,74,82 . Network analysis and visualisation was conducted in Gephi 0.9.7 138 .…”