Revealing regional-scale differences in microbial community structure and metabolic strategies across different land use types and soil types and how these differences relate to soil carbon (C) cycling function is crucial for understanding the mechanisms of soil organic carbon (SOC) sequestration in agroecosystems. However, our understanding of these knowledge still remains unclear. Here, we employed metagenomic methods to explore differences in microbial community structure, functional potential, and ecological strategies in calcareous soil and red soil, as well as the relationships among these factors and SOC stocks. The results showed that the bacterial absolute abundance and diversity were higher and the fungal absolute abundance and diversity were lower in calcareous soil than in red soil. This may be attributed to stochastic processes dominated the assembly of bacterial and fungal communities in calcareous soil and red soil, respectively. This in turn was closely related to soil pH and Ca2 + content. Linear discriminant analysis showed that genes related to microbial growth and reproduction (e.g., amino acid biosynthesis, central carbon metabolism, and membrane transport) were enriched in calcareous soil. While genes related to stress tolerance (e.g., bacterial chemotaxis, DNA damage repair, biofilm formation) were enriched in red soil. The great difference in soil properties between calcareous soil and red soil may be the cause of this result. Compared with red soil, the higher soil pH, SOC, and calcium and magnesium content in calcareous soil increased the bacterial absolute abundance and diversity, thus increasing the SOC sequestration potential of microorganisms, but also increased the decomposition of organic carbon by fungi, thus increasing the SOC loss potential. However, the bacterial absolute abundance and diversity were much higher than that of fungi. Therefore, soil carbon sequestration potential was still greater than its loss potential in karst agroecosystems. Agricultural disturbance intensity may be the main factor affecting these relationships. Overall, these findings advance our understanding of how soil microbial metabolic processes are related to SOC sequestration.

Biological soil crusts (BSCs) play a fundamental role in desert ecosystems by stabilizing soil, cycling nutrients, and retaining moisture. However, the assembly processes governing bacterial communities within BSCs remain largely unknown. This study aimed to reveal the spatiotemporal variations in the bacterial community diversity, co-occurrence patterns, and ecological assembly processes of BSCs and their underlying soils across different desert and seasonal conditions. We systematically analyzed the spatial differences in the bacterial diversity, co-occurrence networks, and community assembly processes of BSCs and their underlying soils using samples collected at various soil depths from different BSC types in different deserts. We discovered that BSC type and soil depth were the primary factors driving bacterial community assembly, while seasonal effects were weaker and more indirect, and mainly regulated community dynamics through changes in resource availability and environmental conditions. The underlying soils of moss- and lichen-BSCs exhibited higher bacterial diversity and richness than those of algae BSCs. In contrast, cyano-BSCs exhibited a lower diversity, but Cyanobacteria demonstrated the highest photosynthetic function. Among the different deserts, the community assembly of samples from the eastern Inner Mongolia deserts was largely influenced by environmental selection, whereas stochastic processes were more prominent in the central and western desert regions. A beta-nearest taxon index (beta NTI) analysis indicated that stochastic processes were dominant in surface BSC samples, while environmental selection played a stronger role in deeper layers. A co-occurrence network analysis revealed that surface BSC samples had a high degree of network connectivity, with those from moss- and lichen-BSCs being particularly high, and they also exhibited high modularity and local clustering that promoted the functional stability of the microbial communities. This study revealed the integrated effects of soil depth, BSC type, desert type, and resource availability on microbial community assembly in desert ecosystems. These findings provide a theoretical basis for the microbial management of BSCs and scientific insights to support restoration strategies in desert ecosystems.

Subsidence from coal mining is a major environmental issue, causing significant damage to soil structure. Soil microorganisms, highly sensitive to environmental changes, adapt accordingly. This study focused on four areas of the Burdai coal mine: a non-subsidence area (CK), half-yearly (HY), 1-year (OY), and 2-year (TY) subsidence areas. Using high-throughput sequencing and molecular ecological network analysis, we examined soil microbial community diversity and structure across these zones, exploring microbial community assembly and functional predictions. Results showed that compared to the control, subsidence areas experienced reduced soil water content, organic matter, available phosphorus, and alkaline nitrogen, with the lowest levels observed at 1 year. These values began to rise after 1 year, suggesting natural recovery after subsidence stabilized. Microbial communities were closely related to soil organic matter, water content, and alkaline nitrogen. At the 1-year mark, soil property changes significantly reduced microbial diversity, which then began to recover after 2 years. The microbial network during 1-year subsidence was simpler, with 102 nodes, 179 edges, and an average degree of 3.51, indicating that early subsidence was unstable, and the microbial community was still adapting. By 1 year, community structure and interactions had begun to stabilize. Stochastic processes played a key role in microbial variability during short-term subsidence.

Snow amounts and duration are susceptible to climate change and may significantly affect plant diversity and biomass in grassland ecosystems. Yet, the combined effects of grassland use (type and intensity) and snow depth on plant diversity and productivity remain poorly understood. We established two complementary field experiments to explore the mechanisms driving the effects of grassland use (type and intensity) and snow manipulation on plant diversity and productivity in the meadow steppe. An experiment on grassland use type and snow manipulation showed that lower snow cover in winter reduced soil moisture in the snowmelt period, significantly increased the abundance of ammonia-oxidizing archaea and ammonia-oxidizing bacteria, and initiated nitrification earlier, resulting in the loss of soil available nitrogen, and then reduced the aboveground biomass of early grasses. An experiment on grassland mowing intensity and snow manipulation showed that moderate mowing intensity can restrain the loss of grass biomass and soil nutrients and maintain grassland sustainability in winters with less snow. Stochasticity has played a more important role in plant community assembly in higher intensity of grassland use. Based on our results, we recommend that optimal defoliation height can restrain the loss of grass biomass and soil nutrients and maintain grassland sustainability in winters with less snow. This study has potential benefits for optimizing sustainable production and maintaining ecosystem function under winter snowfall changes in the future across large regions of arid and semiarid grasslands. (c) 2024 The Society for Range Management. Published by Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Deforestation and slash combustion have substantial adverse impacts on the atmosphere, soil and microbe. Despite this awareness, numerous individuals persist in opting for high-intensity Eucalyptus planting through slash-burning in pursuit of immediate profits while disregarding the environmental significance and destroying the soil. Slash-unburnt agriculture can effectively safeguard the ecological environment, and compared with slash-burning, there remains a limited understanding of its regulatory mechanisms on soil fertility and microbial community. Also, large uncertainty persists regarding the utilization of harvest residues. Thoroughly investigating these questions from various perspectives encompassing physical soil characteristics, nutrient availability, bacterial community structures, and stability is crucial. To explore the ecological advantages of slash-unburnt techniques on microorganisms and their associated ecosystems, we used two slash-unburnt (Unburnt) planting techniques: Spread (naturally and evenly covering the forest floor after logging) and Stack (residues are piled along contour lines) as well as the traditional slash Burnt method (Burnt) in a Eucalyptus plantation. A comparative analysis was conducted between the two methods. We observed that over a span of 4 years, despite the initial lower application of fertilizer in the Unburnt treatments compared with the Burnt treatment during the first 2 years, the Unburnt treatment gradually caught up or even surpassed and attained similar nutrient levels as the Burnt treatment. Alphaproteobacteria was the main phyla that indicated the difference in soil bacterial communities between Burnt and Unburnt treatments. The microbial networks also highlighted the significance of the Unburnt method, as it contributed to the preservation of crucial network nodes and the stability of soil bacterial communities. Therefore, rational utilization of harvest residue may effectively avoid the vast damage caused by slash-burning to Eucalyptus trees and the soil environment but may also increase the potential for restoring soil fertility, improving fertilizer utilization efficiency, and maintaining microbial community stability over time.

Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly. IMPORTANCE Bacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.

Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.

Glaciers, which constitute the world's largest global freshwater reservoir, are also natural microbial repositories. The frequent pandemic in recent years underscored the potential biosafety risks associated with the release of microorganisms from the accelerated melting of glaciers due to global warming. However, the characteristics of pathogenic microorganisms in glaciers are not well understood. The glacier surface is the primary area where glacier melting occurs that is often the main subject of research on the dynamics of pathogenic microbial communities in efforts to assess glacier biosafety risks and devise preventive measures. In this study, high-throughput sequencing and quantitative polymerase chain reaction methods were employed in analyses of the composition and quantities of potential pathogenic bacteria on the surfaces of glaciers in the southeastern Tibetan Plateau. The study identified 441 potential pathogenic species ranging from 215 to 4.39 x 10(11) copies/g, with notable seasonal and environmental variations being found in the composition and quantity of potential pathogens. The highest level of diversity was observed in April and snow, while the highest quantities were observed in October and cryoconite. Host analysis revealed that >70 % of the species were pathogens affecting animals, with the highest proportion of zoonotic pathogens being observed in April. Analysis of aerosols and glacial meltwater dispersion suggested that these microbes originated from West Asia, primarily affecting the central and southern regions of China. Null model analysis indicated that the assembly of potential pathogenic microbial communities on glacier surfaces was largely governed by deterministic processes. In conclusion, potential pathogenic bacteria on glacier surfaces mainly originated from the snow and exhibited significant temporal and spatial variation patterns. These findings can be used to enhance researchers' ability to predict potential biosafety risks associated with pathogenic bacteria in glaciers and to prevent their negative impact on populations and ecological systems.

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

It is generally believed that there is a vegetation succession sequence from alpine marsh meadow to desert in the alpine ecosystem of the Qinghai-Tibet Plateau. However, we still have a limited understanding about distribution patterns and community assemblies of microorganisms' response to such vegetation changes. Hence, across a gradient represented by three types of alpine vegetation from swamp meadow to meadow to steppe, the soil bacterial, fungal and archaeal diversity was evaluated and then associated with their assembly processes, and glacier foreland vegetation was also surveyed as a case out of this gradient. Vegetation biomass was found to decrease significantly along the vegetation gradient. In contrast to irregular shifts in alpha diversity, bacterial and fungal beta diversities that were dominated by species replacement components (71.07-9.08%) significantly increased with the decreasing gradient in vegetation biomass (P < 0.05). These trends of increase were also found in the extent of stochastic bacterial and fungal assembly. Moreover, an increase in microbial beta diversity but a decrease in beta nearest taxon index were observed along with increased discrepancy in vegetation biomass (P < 0.001). Stepwise regression analyses and structural equation models suggested that vegetation biomass was the major variable that was related to microbial distribution and community assembly, and there might be associations between the dominance of species replacements and stochastic assembly. These findings enhanced our recognition of the relationship between vegetation and soil microorganisms and would facilitate the development of vegetation-microbe feedback models in alpine ecosystems.