Abstract: Background: The rRNA operon (rrn) copy number is associated with protein synthesis and reproduction, reflecting microbial r- and K-life strategies and influencing soil ecosystem function. Although the positive relationship between microbial community-level rrn copy numbers and nutrient availability has been reported, the association between rrn copy number and soil stoichiometry or environmental stress remains largely unknown, particularly in the context of long-term nutrient inputs. Results: Using long-term (> 30 years) field experiments across three agro-ecosystems, we consistently found that N fertilization increased the microbial community-level rrn copy number. This increase was equivalently explained by soil CN stoichiometry (22%) and soil acidification (21%). Balanced soil CN stoichiometry favored the growth of N-dependent copiotrophs such as Bacilliand Flavobacteriia containing high rrn copy numbers (an average of 2.5), and enhanced their nutrient competition ability. Moreover, N fertilization-induced soil acidification, as an environmental stressor, increased the abundance of pH-negative responders such as Clostridia and Ktedonobacteria which also contained high rrn copy numbers (2.8), and threatened rare taxa with low rrn copy numbers. Conclusions: Consequently, our finding challenges the concept of microbial life-strategy regulation solely by nutrient availability, highlighting the novelty of significant contributions of soil stoichiometric balance and environmental stress to microbial strategies in agro-ecosystems under long-term nutrient inputs.

Soil ecological functions are largely determined by the activities of soil microorganisms, which, in turn, are regulated by relevant interactions between genes and their corresponding pathways. Therefore, the genetic network can theoretically elucidate the functional organization that supports complex microbial community functions, although this has not been previously attempted. We generated a genetic correlation network based on 5421 genes derived from metagenomes of forest soils, identifying 7191 positive and 123 negative correlation relationships. This network consisted of 27 clusters enriched with sets of genes within specific functions, represented with corresponding cluster hubs. The clusters revealed a hierarchical architecture, reflecting the functional organization in the soil metagenomes. Positive correlations mapped functional associations, whereas negative correlations often mapped regulatory processes. The potential functions of uncharacterized genes were predicted based on the functions of located clusters. The global genetic correlation network highlights the functional organization in soil metagenomes and provides a resource for predicting gene functions. We anticipate that the genetic correlation network may be exploited to comprehensively decipher soil microbial community functions.

Biochar greatly influences the soil bacterial community and nutrient transformations, while our knowledge of the responses of fungal lifestyles to biochar is still in its infancy. Here, we used experimental pre-treatments (acetone extraction) of nutrient-rich biochars to identify which major biochar properties influence fungi the most: the easily mineralizable C, fused aromatic backbone, or the inorganic nutrients of biochars. Our objective was to investigate how different biochar fractions (easily mineralizable C, fused aromatic C, nutrients) structure the fungal taxonomic and functional communities. The easily mineralizable C of biochars induced greater short-term changes in fungal community composition compared to the fused aromatic C. The easily mineralizable C significantly decreased the relative abundance of Basidiomycota by avg. 10.6%, while it had no effects on Ascomycota and Zygomycota. Co-occurrence network indicated that saprophytic fungi were self-assembled in the easily mineralizable C-sufficient environment, whereas they were the connectors to interact with other groups when lower amounts of energy in form of mineralizable C were present. Thus, the easily mineralizable C in biochar as a microbial C source probably promoted saprotroph growth, caused them to self-assemble and to enhance their competitive capacity, leading to overall diversity decrease and relative decline of fungal pathogens. The inorganic nutrients had no effects on fungal diversity and saprotroph abundance, while they decreased the relative abundance of Zygomycota. Our study highlighted the important roles of both mineralizable C and inorganic nutrients in modification of the fungal community, and demonstrated that biochar probably favors the growth of saprotrophs over soil-borne fungal pathogens.

Soil microbiota play a critical role in soil biogeochemical processes and have a profound effect on soil functions. Recent studies have revealed microbial co-occurrence patterns in soil microbial communities, yet the geographic pattern of topological features in soil microbial co-occurrence networks at the continental scale are largely unknown. Here, we investigated the shifts of topological features in co-occurrence networks inferred from soil microbiota along a continental scale in eastern China. Integrating archaeal, bacterial and fungal community datasets, we inferred a meta-community co-occurrence network and analyzed node-level and network-level topological shifts associated with five climatic regions. Both node-level and network-level topological features revealed geographic patterns wherein microorganisms in the northern regions had closer relationships but had a lower interaction influence than those in the southern regions. We further identified topological differences associated with taxonomic groups and demonstrated that co-occurrence patterns were random for archaea and non-random for bacteria and fungi. Given that microbial interactions may contribute to soil functions more than species diversity, this geographic shift of topological features provides new insight into studying microbial biogeographic patterns, their organization and impacts on soil-associated function.

There is growing global interest in the bioremediation of cadmium (Cd) using combinations of biochar and microorganisms. However, the interactions among biochar, introduced and indigenous microorganisms remain unclear. Accordingly, a 90 day microcosm experiment was conducted to investigate this by adding Bacillus sp. K1 strain inoculated rice straw biochar (SBB) and magnetic straw biochar (MBB) into a Cd contaminated paddy soil from Hunan, China. All treatments were incubated aerobically (60% water holding capacity) or anaerobically for 90 d. During both soil incubations, Bacillus sp. K1 successfully colonized in soil with composites applications. Soil pH was significantly increased from acid to neutral, and available Cd decreased with the addition of both composites. The better remediation efficiency of MBB than SBB under anerobic conditions was attributed to the transformation of acetic acid-extractable Cd into the residual fraction, caused by Cd²⁺ bonding with crystal Fe₃O₄. The application of the two kinds of composites caused similar changes to both microbial communities. There was a slight decrease in indigenous microbial alpha diversity with the MBB aerobic application, while the total population number of bacteria was increased by 700%. Both the redundancy analysis and Mantel analyses indicated that pH and microbial biomass C contributed to the colonization of Bacillus sp. K1 with SBB under aerobic conditions, and with MBB under anerobic conditions, respectively. The research provides a new insight into interactive effects and investigates immobilization mechanisms involved of bacterial/biochar composites in anaerobic and aerobic soils.

The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem's decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change.

Systematic studies on the genesis, properties, and distribution of natural nanoparticles (NNPs) in soil remain scarce. This study examined a soil chronosequence of continuous paddy field land use for periods ranging from 0 to 1 000 years to determine how NNPs in soil changed at the early stages of soil genesis in eastern China. Soil samples were collected from coastal reclaimed paddy fields that were cultivated for 0, 50, 100, 300, 700, and 1 000 years. Natural nanoparticles were isolated and characterized along with bulk soil samples (< 2-mm fraction) for selected physical and chemical properties. The NNP content increased with increasing soil cultivation age at 60 g m−2 year−1, which was related to decreasing soil electrical conductivity (172–1 297 µS cm−1) and NNP zeta potentials (from –22 to –36 mV) with increasing soil cultivation age. Changes in several NNP properties, such as pedogenic iron oxide and total organic carbon contents, were consistent with those of the bulk soils across the soil chronosequence. Notably, changes in NNP iron oxide content were obvious and illustrated active chemical weathering, pedogenesis, and potential impacts on the microbial community. Redundancy analysis demonstrated that the soil cultivation age was the most important factor affecting NNP properties, contributing 60.7% of the total variation. Cluster and principal component analysis (PCA) revealed splitting of NNP samples into age groups of 50–300 and 700–1 000 years, indicating rapid evolution of NNP properties, after an initial period of desalinization (approximately 50 years). Overall, this study provides new insights into NNP evolution in soil during pedogenesis and predicting their influences on agriculture and ecological risks over millennial-scale rice cultivation.

We assessed the response of soil microbial nitrogen (N) cycling and associated functional genes to elevated temperature at the global scale. A meta-analysis of 1,270 observations from 134 publications indicated that elevated temperature decreased soil microbial biomass N and increased N mineralization rates, both in the presence and absence of plants. These findings infer that elevated temperature drives microbially mediated N cycling processes from dominance by anabolic to catabolic reaction processes. Elevated temperature increased soil nitrification and denitrification rates, leading to an increase in N₂ O emissions of up to 227%, whether plants were present or not. Rates of N mineralization, denitrification and N₂ O emission demonstrated significant positive relationships with rates of CO₂ emissions under elevated temperatures, suggesting that microbial N cycling processes were associated with enhanced microbial carbon (C) metabolism due to soil warming. The response in the abundance of relevant genes to elevated temperature was not always consistent with changes in N cycling processes. While elevated temperature increased the abundances of the nirS gene with plants and nosZ genes without plants, there was no effect on the abundances of the ammonia-oxidizing archaea amoA gene, ammonia-oxidizing bacteria amoA and nirK genes. This study provides the first global-scale assessment demonstrating that elevated temperature shifts N cycling from microbial immobilization to enhanced mineralization, nitrification and denitrification in terrestrial ecosystems. These findings infer that elevated temperatures have a profound impact on global N cycling processes with implications of a positive feedback to global climate and emphasize the close linkage between soil microbial C and N cycling.