Linking phylogenetic niche conservatism to soil archaeal biogeography, community assembly and species coexistence

Abstract

Aim A predictive understanding of the mechanisms underlying microbial biogeographical patterns is of great interest, particularly with respect to phylogenetic distributions of their ecological adaptations. Here, we test whether phylogenetic information can predict the biogeographical distributions, community assembly and species co‐occurrence of soil archaea. Location Northern China. Time period July and August 2017. Major taxa studied Archaeal communities. Methods By conducting a large‐scale (transect intervals of 1,257.6 km) study across agricultural field, forest, wetland, grassland and desert biomes, we applied the phylogenetic framework of niche conservatism to investigate archaeal biogeography, community assembly and network topology. We examined the phylogenetic signal based on Blomberg's K to test whether the environmental preference of a given archaeal taxon was related to the phylogeny, corresponding to the degree of phylogenetic conservatism for environmental niches across complex environmental gradients. We evaluated the assembly processes of archaeal communities based on null model and Sloan neutral model analyses. We then explored the major factors that influenced the species coexistence and assembly processes of soil archaeal communities. Results Soil archaeal taxa exhibited strong climate‐related niche conservatism of ecological preferences. Mean annual precipitation (MAP) had the strongest phylogenetic signal, and this mediated both community assembly processes and species coexistence, with stronger deterministic assembly and less species coexistence in environments with lower precipitation. Phylogenetic diversity was closely linked to the balance of community assembly processes; that is, stochastic assembly processes were dominant in low‐diversity communities, whereas variable selection of deterministic processes promoted high phylogenetic diversity. Main conclusions We conclude that strong phylogenetic niche conservatism of soil archaea drives their biogeographical distributions. Our findings represent a considerable advance in linking phylogenetic niche conservatism to soil archaeal biogeography, community assembly and species coexistence, and therefore forecasting soil archaeal evolutionary adaptations in response to ongoing environmental changes.

Aridity Threshold Induces Abrupt Change of Soil Abundant and Rare Bacterial Biogeography in Dryland Ecosystems

“…There is modeling and empirical evidence that multiple ecosystem functional and structural characteristics undergo abrupt discontinuous transitions and follow a series of sequential ecological thresholds in relation to increases in aridity ( 15 , 20 , 38 ). For instance, MAP causes a rapid shift in the diversity and structure of soil microbes, which would trigger changes in microbial interactions and assembly processes ( 39 ). However, few large-scale studies have quantified whether biogeography distribution and ecological assembly of abundant and rare soil bacteria exhibit abrupt changes to increases in aridity in dryland ecosystems.…”

“…Recent studies in a variety of ecosystems (e.g., terrestrial and aquatic) support our findings ( 10 , 49 , 50 ). Those studies have suggested that ecological preferences in evolutionary history determined traits and speciation ( 31 , 39 , 51 ). Evolutionary preferences for salinity ( 52 ), high temperature ( 53 ), and substrate ( 54 ) also supported this insight.…”

“…Chimera detection and removal were accomplished using the USEARCH tool in the UCHIME algorithm ( 73 ). Paired-end sequences that passed quality control were joined, clustered into operational taxonomic units (OTUs) using a 97% identity level cutoff, and assigned to taxonomic groups by SILVA database (release 128) ( 39 ). Counts of individual OTUs were scaled by the total number of reads in each sample to account for sequencing biases using the R package DESeq2 ( 74 ).…”

Biogeographic, Driving Factors, Assembly, and Co-occurrence Patterns of Archaeal Community in Biocrusts

“…Therefore, we assumed that the number of isolated SPs considered could alter biogeographic patterns ( Lennon and Jones, 2011 ; Kramer-Schadt et al, 2013 ). According to our results ( Figure 3 ), successional and spatial factors drove the most apparent biogeographic patterns under the number of three SPs at the taxonomic facet, highlighting the considerable heterogeneity of archaeal assemblage composition suffering from microhabitat changes ( Jiao et al, 2019 , 2021 ). In contrast, at the phylogenetic facet, five SPs were the turning point where the slope of spatial factors began to decrease ( Figure 3 ), and it also indicated the tipping point where the influences of community homogeneity began to emerge, which was mostly contributed by the widely distributed Nitrososphaeraceae ( Figure 4A ).…”

Environmental and Human Microbiome for Health

“…In addition, soil bacterial abundance varies according to carbon input, temperature, soil depth, and hydration status [ 11 ]. The abundance of microorganisms varies depending upon whether they belong to agricultural and forest soil, wetlands, grass, and desert soils [ 12 ]. Apart from that, sewage as an indicator of the human microbiome can be used broadly to obtain an idea of the microbiome of humans residing in a particular area [ 13 , 14 , 15 ].…”