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Root-associated microbial communities have been widely studied in the model plant Arabidopsis thaliana, but have been much less explored in agronomically important crops. Here, we used deep pyrosequencing of bacterial 16S rRNA to identify and characterize the root-associated microbial community of three traditional rice cultivars (representing indica and japonica subspecies and a hybrid) cultivated in typical paddy soils from China. We separated the root microbiota into endosphere and rhizosphere compartments, which were found to be the major determinant of variation in the total root microbial community. The microbial communities in each rhizocompartment were strongly influenced by soil type, while rice genotype exhibited a small but significant influence on both endosphere and rhizosphere microbiota. Pairwise comparisons showed that the endophytic bacterial community of indica rice differed significantly from that of japonica rice, while no remarkable differences were noted when comparing the community of indica vs. hybrid or japonica vs. hybrid. A core functional rice endophytic microbiota was identified, which accounted for relative abundances of up to 72.5% of the total microbial community. The 88 core root operational taxonomic units (OTUs) mainly belonged to the phylum Proteobacteria specifically Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria. These results clarify the rice root-associated microbial community assemblage and facilitate the construction of an artificial core root microbiota to promote plant growth and resistance.

Biochar - Solid Carbon for Sustainable Agriculture explores the potential of biochar, a form of charcoal produced from organic materials, to improve soil health, increase crop yields, and mitigate climate change. This book offers a comprehensive overview of biochar and its applications in sustainable agriculture. The book begins by introducing the concept of biochar and its historical use in agriculture. Next, the content deals with the production methods and properties of biochar, providing insights into its chemical composition and physical characteristics. Subsequent chapters explore the diverse applications of biochar in agriculture, including its role in soil fertility improvement, carbon sequestration, and pollution remediation. Case studies and practical examples illustrate the effectiveness of biochar across different agricultural settings. The authors also discuss the potential challenges and future directions of biochar research and application. This book is essential reading for agronomists, soil scientists, environmental scientists, farmers, policymakers, and anyone interested in sustainable agriculture and climate change mitigation strategies. Readership Agronomists, soil scientists, environmental scientists, farmers, policymakers, and anyone interested in sustainable agriculture and climate change initiatives.

An increasing number of studies indicate that microbial diversity plays a crucial role in the mediation of ecosystem multifunctionality (EMF) in natural ecosystems. However, this point remains mostly overlooked in managed ecosystems, especially in agriculture. Here, we compiled promising strategies for the targeted exploitation of the associations between microbial diversity and EMF of agricultural soils using samples from two long‐term (more than 30 years) experimental field sites in southern China. The two sites experienced a similar monsoon climate and fertilization management practices. We used high‐throughput amplicon sequencing, structural equation modelling and random forest analysis, to analyse our data and validate our hypotheses. We found that soil physiochemical properties and the C‐, N‐, P‐ and S‐cycle enzyme activities were increased with the increase in microbial diversity. Specifically, a positive linear relationship was observed between microbial diversity and EMF, which was mediated by long‐term fertilization management via changes in soil microbial communities and physiochemical properties. Random forest analysis and SEM showed that the important role of microbial diversity on EMF was maintained even when simultaneously taking multiple multifunctionality drivers (soil physiochemical properties, soil aggregation and enzymatic patterns) into account. In addition, microbial diversity, C‐cycle enzyme activity and pH value are feasible predictors of EMF; these factors were shown to be the main drivers of EMF of arable soils. Our findings suggest that there may be a limited degree of multifunctional redundancy in arable soils. The relationship we observed between microbial diversity and EMF suggests that management practices that foster more diverse soil microbial communities may have the potential to improve the functioning of agroecosystems. A plain language summary is available for this article. Plain Language Summary

The horizontal transfer of plasmids has been recognized as one of the key drivers for the worldwide spread of antimicrobial resistance (AMR) across bacterial pathogens. However, knowledge remain limited about the contribution made by environmental stress on the evolution of bacterial AMR by modulating horizontal acquisition of AMR plasmids and other mobile genetic elements. Here we combined experimental evolution, whole genome sequencing, reverse genetic engineering, and transcriptomics to examine if the evolution of chromosomal AMR to triclosan (TCS) disinfectant has correlated effects on modulating bacterial pathogen ( Klebsiella pneumoniae ) permissiveness to AMR plasmids and phage susceptibility. Herein, we show that TCS exposure increases the evolvability of K. pneumoniae to evolve TCS-resistant mutants (TRMs) by acquiring mutations and altered expression of several genes previously associated with TCS and antibiotic resistance. Notably, nsrR deletion increases conjugation permissiveness of K. pneumoniae to four AMR plasmids, and enhances susceptibility to various Klebsiella -specific phages through the downregulation of several bacterial defense systems and changes in membrane potential with altered reactive oxygen species response. Our findings suggest that unrestricted use of TCS disinfectant imposes a dual impact on bacterial antibiotic resistance by augmenting both chromosomally and horizontally acquired AMR mechanisms. In this work, Yang et al. provide evidence of triclosan exposure resulting in increased evolvability of K. pneumoniae in experimental evolution studies. They utilize sequencing and transcriptomics to explore the chromosomally and horizontally acquired antimicrobial resistance mechanisms.

The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters ( ugpB , ugpC , and ugpQ ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales . These contain ugp genes but no gcd , and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling. IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.

Background Arsenic is known as a toxic metalloid, which primarily exists in inorganic form [As(III) and As(V)] and can be transformed by microbial redox processes in the natural environment. As(III) is much more toxic and mobile than As(V), hence microbial arsenic redox transformation has a major impact on arsenic toxicity and mobility which can greatly influence the human health. Our main purpose was to investigate the distribution and diversity of microbial arsenite-resistant species in three different arsenic-contaminated soils, and further study the As(III) resistance levels and related functional genes of these species. Results A total of 58 arsenite-resistant bacteria were identified from soils with three different arsenic-contaminated levels. Highly arsenite-resistant bacteria (MIC > 20 mM) were only isolated from the highly arsenic-contaminated site and belonged to Acinetobacter , Agrobacterium , Arthrobacter , Comamonas , Rhodococcus , Stenotrophomonas and Pseudomonas . Five arsenite-oxidizing bacteria that belonged to Achromobacter , Agrobacterium and Pseudomonas were identified and displayed a higher average arsenite resistance level than the non-arsenite oxidizers. 5 aoxB genes encoding arsenite oxidase and 51 arsenite transporter genes [18 arsB , 12 ACR3 ( 1 ) and 21 ACR3 ( 2 )] were successfully amplified from these strains using PCR with degenerate primers. The aoxB genes were specific for the arsenite-oxidizing bacteria. Strains containing both an arsenite oxidase gene ( aoxB ) and an arsenite transporter gene ( ACR3 or arsB ) displayed a higher average arsenite resistance level than those possessing an arsenite transporter gene only. Horizontal transfer of ACR3 ( 2 ) and arsB appeared to have occurred in strains that were primarily isolated from the highly arsenic-contaminated soil. Conclusion Soils with long-term arsenic contamination may result in the evolution of highly diverse arsenite-resistant bacteria and such diversity was probably caused in part by horizontal gene transfer events. Bacteria capable of both arsenite oxidation and arsenite efflux mechanisms had an elevated arsenite resistance level.

RNA interference is an eco-friendly alternative to chemical pesticides, yet its efficacy in lepidopterans like Spodoptera frugiperda ( S. frugiperda ) is limited by poor uptake. Here, we report on ZIF-8 polydopamine nanoparticles that protect dsRNA against enzymatic degradation and active the endocytic/phagosome pathways for increased uptake. Furthermore, the uptake of nano-enabled dsRNA induces the overgrowth of Serratia marcescens , this reduces the S. frugiperda reactive oxygen species (ROS) immune response, increasing the effects of plant’s natural defenses, further inhibiting Enteroccous mundtii growth. This work shows the synergistic potential of nanoparticles for influencing the gut bacteria to prevent resistance mechanisms and for RNAi delivery for pest management. RNA interference therapy has huge potential in pesticide applications, however delivery and stability remain an issue. Here, the authors report on a metal-organic framework, polydopamine nanoparticle for increasing delivery and stability of RNA to plants. Demonstrating application in targeting the fall armyworm.

The application of biochar and plant‐growth‐promoting bacteria (PGPBs) in biocontrol soil‐borne pathogens has garnered worldwide interest recently. However, how agricultural replanting disease is alleviated by a combination of biochar and PGPBs treatment (SYBB) remains largely unexplored. In this study, we investigated the beneficial effects of single biochar addition and the combination of biochar and PGPBs on alleviating replanting disease by altering the rhizosphere microbiome and metabolites. Our field experiment showed that the SYBB treatment had a better alleviating effect on replanting disease than the single biochar addition. The study indicated the dominant effect of deterministic processes on the bacterial community and of stochastic processes on the fungal community under biochar and PGPBs treatment. The combination of biochar and PGPBs tended to convert the stochastic processes of fungal community assembly into deterministic processes. We found SYBB treatment increased the abundance of potentially beneficial Pseudomonas, Lysobacter, Gemmatimonadetes and Nitrospira, and decreasing the abundance of potentially pathogenic Fusarium, Talaromyces and Fusarium oxysporum. Moreover, the SYBB treatment increased the abundances of carbohydrates, fatty acids and plant hormones, and decreased the abundances of amino acids in the rhizosphere soil. Co‐occurrence network analysis indicated that SYBB treatment increased the connections within the microbial communities and drove the alteration of co‐occurrence network among the microbial communities and metabolites, which increased positive correlations in bacteria‐metabolite networks and decreased positive correlations in fungi‐metabolite networks. Spearman correlation analysis showed the abundances of beneficial Streptomyces, Pseudomonas and Lysobacter were significantly and positively correlated to the metabolites most increased under SYBB treatment. The combination of biochar and PGPBs alleviated replanting disease by mediating the change of rhizosphere soil metabolites, and stimulating the proliferation of indigenous and beneficial soil microbes. The research results are intended to provide the basis for new strategies for green and sustainable remediation of soil‐borne pathogens. The combination of biochar and plant‐growth‐promoting bacteria (PGPBs) treatment (SYBB) had a better alleviating effect on replanting disease than the single biochar addition. The study indicated the dominant effect of deterministic processes on the bacterial community and of stochastic processes on the fungal community under biochar and PGPBs treatment. The SYBB treatment was able to extend bacterial niche breadth and decrease fungal niche breadth. The combination of biochar and PGPBs stimulated the indigenous and beneficial soil microbes to suppress host‐specific pathogens by mediating an increase production of rhizosphere soil metabolites, further alleviating the serious replanting disease.

Conductive nanowires are thought to contribute to long-range electron transfer (LET) in Geobacter sulfurreducens anode biofilms. Three types of nanowires have been identified: pili, OmcS, and OmcZ. Previous studies highlighted their conductive function in anode biofilms, yet a structural function also has to be considered. We present here a comprehensive analysis of the function of nanowires in LET by inhibiting the expression of each nanowire. Meanwhile, flagella with poor conductivity were expressed to recover the structural function but not the conductive function of nanowires in the corresponding nanowire mutant strain. The results demonstrated that pili played a structural but not a conductive function in supporting biofilm formation. In contrast, the OmcS nanowire played a conductive but not a structural function in facilitating electron transfer in the biofilm. The OmcZ nanowire played both a structural and a conductive function to contribute to current generation. Expression of the poorly conductive flagellum was shown to enhance biofilm formation, subsequently increasing current generation. These data support a model in which multiheme cytochromes facilitate long-distance electron transfer in G. sulfurreducens biofilms. Our findings also suggest that the formation of a thicker biofilm, which contributed to a higher current generation by G. sulfurreducens, was confined by the biofilm formation deficiency, and this has applications in microbial electrochemical systems. The low power generation of microbial fuel cells limits their utility. Many factors can affect power generation, including inefficient electron transfer in the anode biofilm. Thus, understanding the mechanism(s) of electron transfer provides a pathway for increasing the power density of microbial fuel cells. Geobacter sulfurreducens was shown to form a thick biofilm on the anode. Cells far away from the anode reduce the anode through long-range electron transfer. Based on their conductive properties, three types of nanowires have been hypothesized to directly facilitate long-range electron transfer: pili, OmcS, and OmcZ nanowires. However, their structural contributions to electron transfer in anode biofilm have not been elucidated. Based on studies of mutants lacking one or more of these facilitators, our results support a cytochrome-mediated electron transfer process in biofilms and highlight the structural contribution of nanowires in anode biofilm formation, which contributes to biofilm formation and current generation, thereby providing a strategy to increase current generation.

Carbapenem-resistant Klebsiella pneumoniae represents one of the leading pathogens for infectious diseases. With traditional antibiotics often being ineffective, phage therapy has emerged as a promising alternative. However, phage predation imposes a strong evolutionary pressure on the rapid evolution of bacteria, challenging treatment efficacy. Our findings illustrate how co-evolution enhances phage lytic capabilities through accumulated mutations in the tail proteins gp12 and gp17, while simultaneously reducing bacterial virulence and antibiotic resistance. These insights advance our understanding of phage-host interactions in clinical settings, potentially inspiring new approaches akin to an “arms race” model to combat multidrug-resistant crises effectively.