Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting.

While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA. IMPORTANCE: The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.

Sunlight Significantly Enhances Soil Denitrification via an Interfacial Biophotoelectrochemical Pathway.

Denitrification is an essential step of the nitrogen cycle in soil. However, although sunlight is an important environmental factor for soil, the investigation of the influence of sunlight on soil denitrification is limited to plant photosynthesis-mediated processes. Herein, a new pathway, denoted as a biophotoelectrochemical process, which is induced by the direct photoexcitation of soil, was found to greatly enhance soil denitrification. Using red soil as the research object, the soil with irradiation showed nitrate reduction that was 2.6-4.7 times faster than that without irradiation. The irradiation of soil accelerated the reduction of nitrite and enhanced the conversion of nitrous oxide to nitrogen, indicating that more electron sources were generated. This resulted from the photoinduced generation of ferrous substrates and photoelectrons. The contribution of irradiation to soil denitrification was almost half (45.4%), of which 30.9% was from photoinduced ferrous substrates and 14.5% was from photoelectrons. Moreover, a designed biophotoelectrochemical cell provided solid evidence for direct photoelectron transfer from soil photosensitive substrates to microorganisms. Irradiation promoted the enrichment of Alicyclobacillus, which participates in iron oxidation and electroautotrophy. This finding reveals a role of sunlight in soil denitrification that has been thus seriously overlooked and provides solid evidence for the natural occurrence of photoelectrotrophic effects.

Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes.

Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to nontarget organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides-glyphosate, glufosinate, and dicamba-increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and ARGs. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across 11 provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.

Herbicide promotes the conjugative transfer of multi-resistance genes by facilitating cellular contact and plasmid transfer.

The global dissemination of antibiotic resistance genes (ARGs), especially via plasmid-mediated horizontal transfer, is becoming a pervasive health threat. While our previous study found that herbicides can accelerate the horizontal gene transfer (HGT) of ARGs in soil bacteria, the underlying mechanisms by which herbicides promote the HGT of ARGs across and within bacterial genera are still unclear. Here, the underlying mechanism associated with herbicide-promoted HGT was analyzed by detecting intracellular reactive oxygen species (ROS) production, extracellular polymeric substance composition, cell membrane integrity and proton motive force combined with genome-wide RNA sequencing. Exposure to herbicides induced a series of the above bacterial responses to promote HGT except for the ROS response, including compact cell-to-cell contact by enhancing pilus-encoded gene expression and decreasing cell surface charge, increasing cell membrane permeability, and enhancing the proton motive force, providing additional power for DNA uptake. This study provides a mechanistic understanding of the risk of bacterial resistance spread promoted by herbicides, which elucidates a new perspective on nonantibiotic agrochemical acceleration of the HGT of ARGs.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage.

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.

Hyperthermophilic Composting Accelerates the Removal of Antibiotic Resistance Genes and Mobile Genetic Elements in Sewage Sludge.

Composting is an efficient way to convert organic waste into fertilizers. However, waste materials often contain large amounts of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) that can reduce the efficacy of antibiotic treatments when transmitted to humans. Because conventional composting often fails to remove these compounds, we evaluated if hyperthermophilic composting with elevated temperature is more efficient at removing ARGs and MGEs and explored the underlying mechanisms of ARG removal of the two composting methods. We found that hyperthermophilic composting removed ARGs and MGEs more efficiently than conventional composting (89% and 49%, respectively). Furthermore, the half-lives of ARGs and MGEs were lower in hyperthermophilic compositing compared to conventional composting (67% and 58%, respectively). More-efficient removal of ARGs and MGEs was associated with a higher reduction in bacterial abundance and diversity of potential ARG hosts. Partial least-squares path modeling suggested that reduction of MGEs played a key role in ARG removal in hyperthermophilic composting, while ARG reduction was mainly driven by changes in bacterial community composition under conventional composting. Together these results suggest that hyperthermophilic composting can significantly enhance the removal of ARGs and MGEs and that the mechanisms of ARG and MGE removal can depend on composting temperature.

A new acidophilic thermostable endo-1,4-ß-mannanase from Penicillium oxalicum GZ-2: cloning, characterization and functional expression in Pichia pastoris.

BACKGROUND: Endo-1,4-ß-mannanase is an enzyme that can catalyze the random hydrolysis of ß-1, 4-mannosidic linkages in the main chain of mannans, glucomannans and galactomannans and has a number of applications in different biotechnology industries. Penicillium oxalicum is a powerful hemicellulase-producing fungus (Bioresour Technol 123:117-124, 2012); however, few previous studies have focused on the cloning and expression of the endo-1,4-ß-mannanase gene from Penicillium oxalicum. RESULTS: A gene encoding an acidophilic thermostable endo-1,4-ß-mannanase (E.C. 3.2.1.78) from Penicillium oxalicum GZ-2, which belongs to glycoside hydrolase family 5, was cloned and successfully expressed in Pichia pastoris GS115. A high enzyme activity (84.4 U mL(-1)) was detected in the culture supernatant. The recombinant endo-1,4-ß-mannanase (rPoMan5A) was tagged with 6 × His at its C-terminus and purified using a Ni-NTA Sepharose column to apparent homogeneity. The purified rPoMan5A showed a single band on SDS-PAGE with a molecular mass of approximately 61.6 kDa. The specific activity of the purified rPoMan5A was 420.9 U mg(-1) using locust bean gum as substrate. The optimal catalytic temperature (10 min assay) and pH value for rPoMan5A are 80 °C and pH 4.0, respectively. The rPoMan5A is highly thermostable with a half-life of approximately 58 h at 60 °C at pH 4.0. The K m and V max values for locust bean gum, konjac mannan, and guar gum are 7.6 mg mL(-1) and 1425.5 µmol min(-1) mg(-1), 2.1 mg mL(-1) and 154.8 µmol min(-1) mg(-1), and 2.3 mg mL(-1) and 18.9 µmol min(-1) mg(-1), respectively. The enzymatic activity of rPoMan5A was not significantly affected by an array of metal ions, but was inhibited by Fe(3+) and Hg(2+). Analytical results of hydrolytic products showed that rPoMan5A could hydrolyze various types of mannan polymers and released various mannose and manno-oligosaccharides, with the main products being mannobiose, mannotriose, and mannopentaose. CONCLUSION: Our study demonstrated that the high-efficient expression and secretion of acid stable and thermostable recombinant endo-1, 4-ß-mannanase in Pichia pastoris is suitable for various biotechnology applications.

A new acidophilic endo-ß-1,4-xylanase from Penicillium oxalicum: cloning, purification, and insights into the influence of metal ions on xylanase activity.

A new acidophilic xylanase (XYN11A) from Penicillium oxalicum GZ-2 has been purified, identified and characterized. Synchronized fluorescence spectroscopy was used for the first time to evaluate the influence of metal ions on xylanase activity. The purified enzyme was identified by MALDI TOF/TOF mass spectrometry, and its gene (xyn11A) was identified as an open reading frame of 706 bp with a 68 bp intron. This gene encodes a mature protein of 196 residues with a predicted molecular weight of 21.3 kDa that has the 100 % identity with the putative xylanase from the P. oxalicum 114-2. The enzyme shows a structure comprising a catalytic module family 10 (GH10) and no carbohydrate-binding module family. The specific activities were 150.2, 60.2, and 72.6 U/mg for beechwood xylan, birchwood xylan, and oat spelt xylan, respectively. XYN11A exhibited optimal activity at pH 4.0 and remarkable pH stability under extremely acidic condition (pH 3). The specific activity, K m and V max values were 150.2 U/mg, 30.7 mg/mL, and 403.9 µmol/min/mg for beechwood xylan, respectively. XYN11A is a endo-ß-1,4-xylanase since it release xylobiose and xylotriose as the main products by hydrolyzing xylans. The activity of XYN11A was enhanced 155 % by 1 mM Fe(2+) ions, but was inhibited strongly by Fe(3+). The reason of enhancing the xylanase activity of XYN11A with 1 mM Fe(2+) treatment may be responsible for the change of microenvironment of tryptophan residues studied by synchronous fluorescence spectrophotometry. Inhibition of the xylanase activity by Fe(3+) was first time demonstrated to associate tryptophan fluorescence quenching.

Phage lysate can regulate the humification process of composting.

Phages play a crucial role in orchestrating top-down control within microbial communities, influencing the dynamics of the composting process. Despite this, the impact of phage-induced thermophilic bacterial lysis on humification remains ambiguous. This study investigates the effects of phage lysate, derived explicitly from Geobacillus subterraneus, on simulated composting, employing ultrahigh-resolution mass spectrometry and 16S rRNA sequencing techniques. The results show the significant role of phage lysate in expediting humus formation over 40 days. Notably, the rapid transformation of protein-like precursors released from phage-induced lysis of the host bacterium resulted in a 14.8 % increase in the proportion of lignins/CRAM-like molecules. Furthermore, the phage lysate orchestrated a succession in bacterial communities, leading to the enrichment of core microbes, exemplified by the prevalence of Geobacillus. Through network analysis, it was revealed that these enriched microbes exhibit a capacity to convert protein and lignin into essential building blocks such as amino acids and phenols. Subsequently, these components were polymerized into humus, aligning with the phenol-protein theory. These findings enhance our understanding of the intricate microbial interactions during composting and provide a scientific foundation for developing engineering-ready composting humification regulation technologies.

Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study.

BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-ß-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context. METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli. FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids. INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.

Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages.

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.

Distinctive community assembly enhances the adaptation to extreme environments during hyperthermophilic composting.

Hyperthermophilic composting (hTC) is a promising technique for solid waste treatment due to its distinctive microbiomes. However, the assembly process of the hTC microbial community remains unclear. We investigated the assembly process of hTC and explored the underlying drivers influencing community assembly in this work by employing conventional thermophilic composting (cTC) as a comparison group. Our results showed that the two composting treatments have different community assembly processes. Especially for the initial and thermophilic phases, hTC is affected by homogeneous dispersal (48%) and homogeneous selection (44%), respectively, while cTC is controlled by undominant (38%) and homogeneous selection (92%), respectively. Furthermore, random forest models and network results suggested that different factors govern the community assembly in these two composting methods. Specifically, the hTC community increases the stability of the thermophilic community via enhancing the interactions of low-abundance taxa with other operational taxonomic units (OTUs) in community assembly. Our results suggested that the distinctive nature of hTC community assembly may be responsible for its adaptation to extreme environments.

Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting.

While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.

Auxin-producing bacteria promote barley rhizosheath formation.

The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.

Extensive production and evolution of free radicals during composting.

The production of free radicals has been widely documented in natural systems, where they play an important role in most organic matter and contaminants transformation. Here, the production and evolution of free radicals were systematically investigated during composting. Results indicated that multiple reactive oxygen species and environmentally persistent free radicals (G-factor 2.003-2.004) were generated with dynamic changes during composting. The ·OH yield fluctuated significantly with a maximum content of 365.7-1,262.3 µmol/kg at the thermophilic phase of composting, which was closely correlated with the changes of Fe (II) (Pearson's r = 0.928-0.932) and the electron-donating capacity of humus (Pearson's r = 0.958-0.896) during composting. Further investigation suggested that microorganisms driven iron/humus redox conversion could contribute to the production and dynamic changes of free radical during composting. These findings highlight the abiotic processes involving free radicals, and provide a new perspective for humification and contaminants removal during composting.

Isolation and Characterization of the Lytic Pseudoxanthomonas kaohsiungensi Phage PW916.

The emergence of multidrug-resistant bacterial pathogens poses a serious global health threat. While patient infections by the opportunistic human pathogen Pseudoxanthomonas spp. have been increasingly reported worldwide, no phage associated with this bacterial genus has yet been isolated and reported. In this study, we isolated and characterized the novel phage PW916 to subsequently be used to lyse the multidrug-resistant Pseudoxanthomonas kaohsiungensi which was isolated from soil samples obtained from Chongqing, China. We studied the morphological features, thermal stability, pH stability, optimal multiplicity of infection, and genomic sequence of phage PW916. Transmission electron microscopy revealed the morphology of PW916 and indicated it to belong to the Siphoviridae family, with the morphological characteristics of a rounded head and a long noncontractile tail. The optimal multiplicity of infection of PW916 was 0.1. Moreover, PW916 was found to be stable under a wide range of temperatures (4-60 °C), pH (4-11) as well as treatment with 1% (v/w) chloroform. The genome of PW916 was determined to be a circular double-stranded structure with a length of 47,760 bp, containing 64 open reading frames that encoded functional and structural proteins, while no antibiotic resistance nor virulence factor genes were detected. The genomic sequencing and phylogenetic tree analysis showed that PW916 was a novel phage belonging to the Siphoviridae family that was closely related to the Stenotrophomonas phage. This is the first study to identify a novel phage infecting the multidrug-resistant P. kaohsiungensi and the findings provide insight into the potential application of PW916 in future phage therapies.

Free radicals accelerate in situ ageing of microplastics during sludge composting.

Composting is the last "barrier" for microplastics (MPs) in the entry of organic solid wastes into the environment. The transformation of MPs is thought to be mainly driven by microorganisms during composting, whereas the contribution of abiotic processes that involve free radicals is often overlooked. Herein, we provide initial evidence for the generation of free radicals during sludge composting, including environmental persistent free radicals and reactive oxygen species, which accelerate the oxidative degradation of MPs. The ·OH yield of composting fluctuated greatly from 23.03 to 277.18 µmol/kg during composting, which was closely related to the dynamic changes in Fe(II) (R2 = 0.926). Analyses of the composted MPs physicochemical properties indicated that MPs were aged gradually with molecular weights decrease from 18% to 27% and carbonyl index value increase from 0.23 to 0.52. Further investigation suggested that the microbially-mediated redox transformation of iron oxides could occur on the MPs surface accompanied by the production of abundant free radicals, thereby leading to the damage of MPs during composting. These results reveal the critical role of free radicals in MPs ageing under oxic/anoxic alternation conditions of composting and provide new insights into the bio-chemical mechanism of contaminant removal or transformation during sludge composting.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying.

Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.

Enhanced in situ Pb(II) passivation by biotransformation into chloropyromorphite during sludge composting.

Composting is an effective technology for the disposal and utilization of solid biowastes. However, conventional composting is inefficient for the passivation of heavy metals in solid biowastes, thus limiting the applications of compost derived from solid biowaste. Here, a thermophilic biomineralization strategy was proposed and demonstrated during sludge composting for in situ heavy metals passivation via thermophiles inoculation. It was found that Thermus thermophilus could promote the transformation of Pb(II) into the most stable chloropyromorphite [Pb5(PO4)3Cl, Ksp = 10-84.4] during composting. After 40 days of composting with T. thermophilus FAFU013, the most insoluble residual fractions of Pb increased by 16.0% (from 76.5% to 92.5%), which was approximately 3 times higher than that of the uninoculated control. The DTPA-extractable Pb decreased to 11.5%, which was 14.4% less compared with the uninoculated control, indicating a significant Pb passivation by inoculation of T. thermophilus FAFU013. A series of batch experiments revealed that Pb(II) could be rapidly accumulated by selective biosorption and gradually transformed into chloropyromorphite through the biomineralization of T. thermophilus FAFU013. This study provides new insight into the mechanism of heavy metal passivation during composting and the problem associated with the disposal of Pb-contaminated solid biowastes through the biomineralization of thermophiles.

Linking microbial community structure with molecular composition of dissolved organic matter during an industrial-scale composting.

This study explored the interactions between dissolved organic matter (DOM) composition and microbial community structure during an industrial-scale composting by Fourier transform ion cyclotron resonance mass spectrometry and 16S rRNA sequencing analysis. The results revealed that DOM from matured compost contained primarily lignins/carboxylic-rich alicyclic molecules (73.6%), the higher double bond equivalent (5.97) and aromaticity index (0.18), indicating that the molecular composition of DOM had changed substantially. Drastic changes in microbial community structure were also observed along with the DOM transformation process of composting. Network analysis further indicated that Caldicoprobacter, Bacillus, and Dechloromonas were associated with the most DOM subcategories. Caldicoprobacter could degrade carbohydrates, Bacillus accelerated the humification by transforming N-containing compounds, and Dechloromonas could degrade polycyclic aromatic hydrocarbons distributed in low O/C. These findings are helpful for understanding the molecular mechanisms of DOM transformation and humification of sludge composting.