Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia

Effects of Land Use Type Transformation on the Structure and Diversity of Soil Bacterial Communities

Soil microbiota are significantly influenced by their microenvironments. Therefore, to understand the impacts of various land use patterns on the diversity and composition of soil bacterial communities, this study focused on three typical land use types-NF (natural forest), AF (artificial forests), and FL (farmland)-in the Heilongjiang Central Station Black-billed Capercaillie National Nature Reserve, located in the southwestern part of Heihe City, Heilongjiang Province, China. Using high-throughput sequencing of the 16S rRNA gene, we examined the soil bacterial community structures in these different land use types and explored their correlation with soil environmental factors. The following were our main observations: (1) Significant variations in soil chemical properties among different land use patterns were observed. In artificial forests, total nitrogen (TN), alkali hydrolyzed nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) were higher compared to farmland and significantly higher than those in natural forests. Furthermore, the organic carbon content (SOC) in natural forests was higher than in artificial forests and significantly higher than in farmland. (2) Comparative analysis using the Shannon and Simpson indices revealed that bacterial community diversity was higher in artificial forests than in natural forests, which was significantly higher than in farmland. (3) The effect of different land use types on soil bacterial community structure was not significant. The three land types were dominated by Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria exhibited a higher relative abundance in farmland and artificial forests compared to natural forests, whereas Actinobacteria exhibited the lowest relative abundance in natural forests. (4) Redundancy analysis (RDA) revealed that SOC, TN, AN, and AP were key environmental factors influencing the microbial communities of soil. Collectively, our findings demonstrated that land use practices can significantly alter soil nutrient levels, thereby influencing the structure of bacterial communities.

Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau

The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation

Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.

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

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions of bacteria, archaea, fungi and protists, using a paired sampling of grassland and cropland soils across the agro-pastoral ecotone of northern China. Land-use conversion decreased α diversity of bacteria, fungi and protists, and altered the structures of the entire soil microbial community (archaea, bacteria, fungi and protists). The community assembly of archaea and bacteria was dominated by stochastic processes, and that of protists dominated by deterministic processes in both land-use types. By contrast, the fungal community was governed more strongly by stochastic processes in grassland soil, than by deterministic processes in cropland soil. Our findings support the 'size-plasticity' hypothesis that smaller body-sized microorganisms (archaea and bacteria) are more structured by stochastic processes, and larger one (protist) is more influenced by deterministic processes. Our study demonstrates that distinct ecological processes govern microbial community assembly, and land-use change regulates the balance between determinism and stochasticity.

Soil Microbiomes in Apple Orchards Are Influenced by the Type of Agricultural Management but Never Match the Complexity and Connectivity of a Semi-natural Benchmark

Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.