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PubMed2025

Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.

Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.

Wetlands↗
PubMed2025

Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.

The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ13C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.

Soil Pollutants↗
PubMed2026

Electron shuttles facilitate methane-dependent arsenate reduction in paddy soils.

Methane-dependent arsenate reduction (M-AsR) occurs widely in paddy soils and can substantially enhance arsenic mobilization, posing potential ecological risks. However, the role of electron shuttles in this process remains poorly understood. In this study, we investigated the influence of anthraquinone-2,6-disulfonate (AQDS) on M-AsR in paddy soils. Fourteen-day incubation showed that 1 mmol/L AQDS facilitated 50.88 % of arsenate reduction and 31.31 % of methane oxidation. Quantitative polymerase chain reaction analysis revealed that AQDS significantly increased the abundance of functional genes associated with arsenate reduction (arrA, arsC) and anaerobic methane oxidation (mcrA) (P < 0.05). Microbial community analysis revealed that AQDS addition enriched Cloacibacterium, Sphingorhabdus, and Methylocystis, while decreasing the relative abundance of Methylobacter and Methylomonas. These findings indicate that electron shuttles facilitate M-AsR by modulating functional microbial populations, providing valuable insights into arsenic biogeochemistry and the coupled cycling of methane and arsenic in paddy soils.

Methane↗
PubMed2026

Description of two nitrogen-fixing bacteria, Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov., isolated from paddy soils.

Two novel aerobic, rod-shaped, motile bacterial strains, designated as sgz302134T and sgz301742T, were isolated from paddy soil in Fujian Province. Strains sgz302134T and sgz301742T shared the highest 16S rRNA gene sequence similarities with the type strains Azospirillum isscasi C340-1T (98.2%) and Azospirillum thiophilum DSM 21654T (97.4%), respectively. The phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Azospirillum. Growth of strains sgz302134T and sgz301742T was observed at 10-45 &#xb0;C, pH 5.0-9.5 and 0-0.5% (w/v) NaCl and 15-37 &#xb0;C, pH 6.0-9.0 and 0-1.0% (w/v) NaCl, respectively. Strains sgz302134T and sgz301742T contained Q-10 as the main quinone. The main fatty acids (>10%) of both strains were summed feature 2 (C12 : 0 aldehyde), summed feature 3 (C16 : 1 &#x3c9;7c and/or C16 : 1 &#x3c9;6c), summed feature 8 (C18 : 1 &#x3c9;7c and/or C18 : 1 &#x3c9;6c) and C16 : 0. The genomic DNA G+C content of strains sgz302134T and sgz301742T was 68.4 and 68.3%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between the two strains and their related reference strains were 27.8 and 87.4% and 22.0 and 84.3%, respectively. Both strains possessed nif genes nifBDEHKN. Based on the above results, these two strains represent two novel species of the genus Azospirillum, for which the names Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov. are proposed. The type strains are sgz302134T (=MCCC 1K09520T=KCTC 8840T) and sgz301742T (=MCCC 1K09804T=KCTC 18149T), respectively.

Soil Microbiology↗
PubMed2026

Isolation and characterization of two novel species Neorhizobium fuzhouense sp. nov. and Neotabrizicola paludis sp. nov.

Two novel aerobic bacterial strains, designated SGZ-38T and sgz301269T, were isolated from the root of Pennisetum sp. and paddy soil, respectively. Strain SGZ-38T grew at 10-40&#xa0;&#x2103; (optimum 30&#xa0;&#xb0;C) and pH 5.0-12.0 (optimum 6.5) and tolerated up to 1.0% NaCl (w/v), whereas strain sgz301269T grew at 15-37&#xa0;&#xb0;C (optimum 30&#xa0;&#xb0;C), pH 5.0-9.5 (optimum 7.0) and 0-2% NaCl (optimum 0%). Phylogenetic trees based on the 16S rRNA gene and genomes placed both strains into distinct lineages, forming separated clades from their closest relatives. Strain SGZ-381T exhibited the highest 16S rRNA gene similarities to "Neorhizobium deserti" ACCC 61627T (97.4%), and strain sgz301269T had the highest 16S rRNA gene sequence similarity to Neotabrizicola shimadae N10T (97.6%). The respiratory quinone in both strains was ubiquinone-10. The main fatty acids of SGZ-381T were Summed feature 8, Summed feature 2 and C16:0, whereas strain sgz301269T included C10:0 3OH, C18:0 3OH and Summed feature 8. The DNA G+C content of SGZ-381T and sgz301269T was 62.1% and 65.5%, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between each strain and their respective closest species were 74.6% and 20.1%, 75.3% and 17.4% respectively, below the thresholds for species delineation. Based on the comprehensive chemotaxonomic, phylogenetic, and phenotypic evidence, proposed names of the novel strains are Neorhizobium fuzhouense sp. nov. (type strain SGZ-381T=GDMCC1.4207T=JCM 36770T), Neotabrizicola paludis sp. nov. (type strain sgz301269T=MCCC 1K09178T=KCTC 8856T).

Bacterial Typing Techniques↗
PubMed2024

In-situ enrichment of ARGs and their carriers in soil by hydroxamate siderophore: A promising biocontrol approach for source reduction.

Pathogenic microorganisms with antibiotic resistance genes (ARGs) pose a serious threat to public health and soil ecology. Although new drugs and available antibacterial materials can kill ARG carriers but accidentally kill beneficial microorganisms. Therefore, the rapid enrichment and separation of ARGs and their carriers from soil is becoming an important strategy for controlling the diffusion of ARGs. Hydroxamate siderophore (HDS) has gained widespread attentions for its involvement in trace element transfer among microorganisms in the soil environment, we thus explored an in-situ trapping-enrichment method for ARGs and their carriers via a small molecular HDS secreted by Pseudomonas fluorescens HMP01. In this study, we demonstrate that HDS significantly in-situ traps and enriches certain ARGs, including chloramphenicol, MLS, rifamycin, and tetracycline resistance genes in the soil environment. The enrichment efficiencies were 1473-fold, 38-fold, 17-fold, and 5-fold, respectively, higher than those in the control group. Specifically, the primary enriched ARGs were rpoB, mphL, catB2, and tetA(60), and Bacillus, Rhizobium, Rossellomorea, and Agrobacterium were hosts for these ARGs. This enrichment was caused by the upregulation of chemotaxis genes (e.g., cheW, cheC, and cheD) and rapid biofilm formation within the enriched bacterial population. Notably, representative ARGs such as cat, macB, and rpoB were significantly reduced by 36%, 85.7%, and 72%, respectively, in the paddy soil after HDS enrichment. Our research sheds light on the potential application of siderophore as a rapping agent for the eco-friendly reduction of ARGs and their carriers in soil environments.

Soil Microbiology↗
PubMed2024

Transfer of antibiotic resistance genes from soil to rice in paddy field.

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Oryza↗
PubMed2026

An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.

Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.

Wetlands↗