Conversion of natural grassland to cropland alters microbial community assembly across northern China

Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability

Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.

Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally

Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.

Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale

Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes

The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.

Carbon Amendments Shape the Bacterial Community Structure in Salinized Farmland Soil

Practical, effective, and economically feasible salt reclamation and amelioration methods are in great demand in arid and semiarid areas. Energy amendments may be more appropriate than alternatives for improving salinized farmland soil because of their effects on soil microbes. We investigated the effects of biochar (Carbon) addition and desulfurization (noncarbon) on the soil bacterial community associated with Zea mays seedlings. Proteobacteria, Firmicutes, and Actinobacteriota were the dominant soil bacterial phyla. Biochar significantly increased soil bacterial biodiversity but desulfurization did not. The application of both amendments stimulated a soil bacterial community shift, and biochar amendments relieved selection pressure and increased the stochasticity of community assembly of bacterial communities. We concluded that biochar amendment can improve plant salt resistance by increasing the abundance of bacteria associated with photosynthetic processes and alter bacterial species involved in carbon cycle functions to reduce the toxicity of soil salinity to plants. IMPORTANCE Farmland application of soil amendments is a usual method to mitigate soil salinization. Most studies have concluded that soil properties can be improved by soil amendment, which indirectly affects the soil microbial community structures. In this study, we applied carbon and noncarbon soil amendments and analyzed the differences between them on the soil microbial community. We found that carbon soil amendment distinctly altered the soil microbial community. This finding provides key theoretical and technical support for using soil amendments in the future.