Ecosystem Microbiome Science

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes

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.IMPORTANCEBacterial 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.

Adaptive shifts in plant traits associated with nitrogen removal driven by phytoremediation strategies in subtropical river restoration

Phytoremediation, which is commonly carried out through hydroponics and substrate-based strategies, is essential for the effectiveness of nature-based engineered solutions aimed at addressing excess nitrogen in aquatic ecosystems. However, the performance and mechanisms of plants involving nitrogen removal between different strategies need to be deeply understood. Here, this study employed in-situ cultivation coupled with static nitrogen tracing experiments to elucidate the influence of both strategies on plant traits associated with nitrogen removal. The results indicated that removal efficiencies in plants with substrate-based strategies for ammonium nitrogen and nitrate nitrogen were 30.51-71.11 % and 16.82-99.95 %, respectively, which were significantly higher than those with hydroponics strategies (25.98-58.18 % and 7.29-79.19 %, respectively). Similarly, the plant nitrogen uptake rates in the substrate-based strategy also generally showed higher levels compared to hydroponics strategies (P < 0.05). Meanwhile, the microorganisms-mediated nitrous oxide emission rates in the substrate-based strategy during summer (unamended: 0.00-0.58 μg/g/d; potential: 3.35-7.65 μg/g/d) were obviously lower than those in the hydroponics strategy (unamended: 2.23-11.70 μg/g/d; potential: 9.72-43.09 μg/g/d) (P < 0.05). Notably, analysis of similarity tests indicated that the influences of strategy on the above parameters generally surpass the effects attributable to interspecies plant differences, particularly during summer (R > 0, P < 0.05). Based on statistical and metagenomic analyses, this study revealed that these differences were driven by the stabilizing influence of substrate-based strategy on plant roots and enhancing synergistic interplay among biochemical factors within plant-root systems. Even so, phytoremediation strategies did not significantly alter the characteristics of plants with regards to their tendency towards ammonium nitrogen uptake (up to 87.68 %) and dissimilatory nitrate reduction to ammonium as primary biological pathway for nitrogen transformation which accounted for 53.66-96.47 % nitrate removal. In summary, this study suggested that the substrate-based strategy should be a more effective strategy for enhancing the nitrogen removal ability of plants in subtropical river restoration practices.

Distribution patterns and functional characteristics of soil bacterial communities in desert ecosystems of northern China

Deserts are extremely arid environments where life is exposed to multiple environmental stresses, including low water availability, high temperatures, intense radiation environments and soil carbon and nitrogen limitation. Microorganisms have enormous potential applications due to their unique physiological adaptation mechanisms, extensive involvement in geochemical cycles and production of new antibiotics, among many other characteristics. With the increasing amount of open data provides unprecedented opportunities to further reveal bacterial biodiversity and its global role in ecosystem function. Through the collection of published high-quality sequencing data supplemented with experimental findings, we investigated the distribution characteristics and functional properties of bacteria in desert ecosystems in northern China. We show that there are significant differences in bacterial diversity among different sandy areas, and that soil properties and climatic factors are the main factors affecting bacterial diversity in desert ecosystems. The mean annual precipitation in growing season, soil organic carbon, total nitrogen and total phosphorus had significant effects on the diversity of desert bacteria and main bacteria. Desert bacteria primarily participate in the macromolecular decomposition, phototrophy, and geochemical cycling of nitrogen. These findings deepen our understanding of the regional-scale soil microbial diversity patterns in Chinese desert ecosystems and broaden our understanding of the ecological functions carried out by bacteria in these environments.

Responses of soil and collembolan (Folsomia candida) gut microbiomes to 6PPD-Q pollution

The potential risk of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) to soil organisms remains poorly understood. Here we showed that 6PPD-Q pollution inhibited the survival of collembolans (Folsomia candida) with the chronic median lethal concentration (LC50) of 16.31 μg kg-1 in a 28-day soil culture. The microbe-microbe interactions between abundant taxa in soil and collembolan gut helped alleviate the negative impact of 6PPD-Q on soil microbial community, while rare taxa contributed to maintaining microbial network complexity and stability under 6PPD-Q stresses. Gammaproteobacteria, Alphaproteobacteria and Actinobacteria in the gut of both adult and juvenile collembolans were identified as potential indicators for 6PPD-Q exposure. Such responses were accompanied by increases in the relative abundances of genes involved in nutrient cycles and their interactions between soil and collembolan gut microbiomes, which enhanced nitrogen and carbon turnover in 6PPD-Q polluted soil, potentially alleviating the stresses caused by 6PPD-Q. Overall, this study sheds new light on the toxicity of 6PPD-Q to soil organisms and links 6PPD-Q stresses to microbial responses and soil functions, thus highlighting the urgency of assessing its potential risk to the terrestrial ecosystem.

Linking biodiversity and ecological function through extensive microeukaryotic movement across different habitats in six urban parks

Highly diverse but divergent microeukaryotes dwell in all types of habitats in urban park ecosystems. Extensive microbial migration occurs between both terrestrial and aquatic habitats. Microbial movement is beneficial to the maintenance of biodiversity and the exchange of functional guilds.