Ab initio gene identification in metagenomic sequences

New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions

Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O₂ limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.

Natural mackinawite-based elimination of vanadium and ammonium from wastewater in autotrophic biosystem

Vanadium (V) production results in significant amounts of wastewater, which often co-contains considerable ammonium (NH4+) after being used as precipitants. Both pentavalent V [V(V)] and NH4+ can be removed independently through biological process. However, internal interactive biotechnology for one-step elimination of V(V) and NH4+ remains an enigma. In this study, we proposed biologically removing V(V) and NH4+ simultaneously with natural mineral mackinawite as electron donor and its oxidation products as electron acceptors. Our bioreactor achieved a V(V) removal efficiency of 99.5 ± 0.22 % and an NH4+-N removal capacity of 49.5 ± 0.40 g/m3·d. V(V) was reduced to tetravalent V precipitates, while mackinawite was bio-oxidized to Fe(III) and sulfate. Metagenomic binning analysis indicated Sulfurivermis sp. mediated mackinawite oxidation and V(V) reduction. Putative Pseudomonas sp. conducted NH4+ assimilation, anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox), and denitrification, achieving complete NH4+-N removal. Real-time qPCR validated the upregulation of functional genes involved in V(V) reduction and nitrogen metabolisms, with improved functional enzyme activities. Cytochrome c, nicotinamide adenine dinucleotide, and extracellular polymeric substances promoted electron transfer, facilitating the elimination of both V(V) and NH4+-N from wastewater. This study offers a novel and sustainable biological strategy for one-step treating V industrial wastewater.

Emission of CO2 enhanced by thiamethoxam and cadmium in agricultural soil

The coexistence of neonicotinoid insecticide thiamethoxam (TMX) and heavy metal cadmium (Cd) is quite common in agricultural soils, yet their effects on the emission of greenhouse gas CO2 remain insufficiently studied. To address this issue, microcosms spiked with singe or combined TMX (20 mg/kg) and Cd (20 mg/kg) in soil were studied for 90 days. It turned out that single TMX (+12.13 %) and Cd (+22.76 %) both stimulated the emission of CO2, and the combined TMX and Cd exhibited synergic effect (+51.00 %). The presence of Cd reduced the attenuation of TMX (-3.32 %), while the presence of TMX increased the attenuation of Cd (+3.11 %). The relative abundances of bacteria Sphingomonas, Devosia, Erythrobacter, Phaselicystis, Woeseia, FFCH7168, Rhizorhapis, Hamadaea and genes related to sugar metabolism, glycolysis and the TCA cycle were found positively correlated to CO2 emission in the studied microcosms (p < 0.05). Results from this study provide scientific basis for developing sound environmental policies that aim to reduce CO2 emission from agricultural soils.

Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China

Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.

Kinetic and Physiological Characterization of Acidophilic Nitrobacter spp. in a Nitrite-Oxidizing Culture

Novel acidophilic nitrite-oxidizing Nitrobacter spp. were enriched, with kinetic and physiological features characterized comprehensively. The acidophilic Nitrobacter enrichment culture was cultivated in a membrane bioreactor at pH 4.6-5.5 for 500 days, with a relative abundance of 16S rRNA genes of 17.9 ± 0.5% during the characterization experiments. Metagenomic analysis recovered 2 Nitrobacter genomes, which corresponded to previously unknown species within the Nitrobacter genus with average nucleotide identity (ANI) < 91% compared to the publicly available genomes. In contrast to the known NOB, the acidophilic Nitrobacter enrichment culture exhibited strong tolerance to environmental stress, including low pH and free nitrous acid (FNA), and have low affinity for oxygen. Moreover, the acidophilic Nitrobacter enrichment culture also exhibited a higher nitrite affinity (Km = 0.19 ± 0.03 mg NO2--N/L) than all currently characterized Nitrobacter cultures. These characteristics define acidophilic Nitrobacter as both a K-strategist and an adversity-strategist that tends to flourish in acidic activated sludge, where low pH (<5.5) and low nitrite levels suppress other nitrifiers. This study extends our understanding of nitrifiers growing in acidic environments and also provides a potential to remove nitrogen in acidic wastewater.

Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater

Excess manganese (Mn) and NH4+-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn2+ in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn4+ as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4+-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4+-N. NO3--N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.

Different effects of bio/non-degradable microplastics on sewage sludge compost performance: Focusing on antibiotic resistance genes, virulence factors and key metabolic functions

Microplastics (MP) have aroused increasing concern due to the negative environmental impact. However, the impact of bio/non-biodegradable MPs on the sludge composting process has not been thoroughly investigated. This study examined antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial community functions in sludge compost with the application of polylactic acid (PLA) and polypropylene (PP), using metagenomic sequencing. The findings indicated that both types of MPs could extend the thermophilic phase, enhance microbial activity, and inhibit the formation of humic acids. Compared to CK, the subtypes of ARGs decreased 4.22 % and 13.11 % in PLA and PP groups, respectively. But new ARGs emerged, particularly in the PLA group. The proportions of ARGs related to efflux and VFs associated with the adhesion system increased 1.62 %-2.27 % and 55.56 %-60.00 %, respectively, in MPs-added composts. The relative abundance of potential bacterial hosts (e.g., Psychrobacter) carrying multiple ARGs and VFs was much higher in PLA-added compost than in the other two. Moreover, PP facilitated denitrification process and PLA enhanced dissimilatory nitrate reduction to ammonium. Both types of MPs inhibited assimilatory nitrate reduction to ammonia but promoted inorganic nitrogen assimilation. This study broadens our understanding of the potential environmental risks posed by biodegradable and non-biodegradable microplastics on sludge compost and offers valuable insights for the management and application of compost products.

Metagenomic investigation of bacterial laccases in a straw-amended soil

Background

Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.

Methods

Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.

Results

A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.

Implications

These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.

Urban wild bee well-being revealed by gut metagenome data: A mason bee model

Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.

Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types

Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.

Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage

Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation.

Cryo-EM structures of a Xanthomonas phage: Insights into viral architecture and implications for the model phage HK97

Xanthomonas bacteria are responsible for disease outbreaks in several hundred plant species, causing significant economic losses. Xanthomonas phages have emerged as a promising biocontrol strategy in managing various important plant diseases caused by Xanthomonas bacteria. However, structural information for Xanthomonas phages has remained limited so far. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the Xanthomonas citri phage ΦXacJX1 from siphoviruses. These structures include atomic models for the head, head-to-tail connector and head-proximal portion of the tail. ΦXacJX1's head and head-to-tail connector components show significant protein sequence and structural homology with those of the model siphophage HK97. However, the in-situ structures of head-to-tail connector of phage HK97 remain unavailable. The presented structures of phage ΦXacJX1 enhance our understanding of Xanthomonas phages and the mature virion of phage HK97. They provide a valuable framework for future structural and functional studies on both Xanthomonas phages and phage HK97.

Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta

The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.

Decipher syntrophies and adaptive response towards enhancing conversion of propionate to methane under psychrophilic condition

Propionate is a key intermediate in anaerobic digestion (AD) under low operational temperatures, which can destabilize the process. In this study, the supplementation of syntrophic cold-tolerant consortia and trace elements significantly improved the performance of psychrophilic (20 °C) reactor, increasing methane production to 91 % of mesophilic reactor levels and reducing propionate concentrations to less than 2 % of those in untreated psychrophilic reactors. Multi-omics analyses revealed that psychrophilic conditions downregulated the methylmalonyl-CoA and aceticlastic methanogenesis pathways. Electron paramagnetic resonance analyses detected 2.6E-05mol/L reactive oxygen species as stress metabolites in the inhibited psychrophilic reactors. Conversely, supplementation with syntrophic cold-tolerant consortia and trace elements enhanced the abundance of Smithellaceae, Syntrophobacteraceae, and Methanothrix by fivefold in the bioenhanced reactors. This supplementation broadened the propionate degradation pathways from relying solely on the methylmalonyl-CoA pathway to also incorporating the dismutation pathway, while upregulating both pathways. These changes enhanced methanogenesis from propionate through improved activity of the syntrophic cold-tolerant consortia. Genome-centric metatranscriptomic analysis identified the upregulation of key antioxidant genes (sod, kat, grx), temperature regulation genes (cspA), and cryoprotective genes (pslF, pslH, cysE) within the syntrophic cold-tolerant consortia. Additionally, extracellular polymeric substance (EPS) yield per cell increased in the bioenhanced reactors by up to 1.07-fold compared to RC-P. These metabolic traits emphasize the critical roles in mitigating oxidative stress, adapting to low temperatures, and supporting efficient methanogenesis under psychrophilic conditions. These findings offer insights into the transcriptional responses and adaptive mechanisms of propionate-degrading consortia in response to psychrophilic stress.

Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation

The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.

Fully circular shapable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea

To mitigate marine pollution from single-use plastics, it is crucial to transition to next-generation commodity materials that are derived from biomass and are recyclable and marine biodegradable even at abyssal depths in case of the accidental release to the ocean. Here, we develop an optically transparent millimeter-thick paperboard called transparent paperboard (tPB) through dissolution and coagulation of cellulose. The tPB is made entirely of pristine cellulose and compositionally identical to paper. A cup-shaped tPB can hold just-boiled water without an internal film coating because of its high wet tensile properties and anisotropic thermal properties. In addition, the spent tPB is material recyclable in a closed system, where all chemicals and water are also recyclable. Furthermore, the marine biodegradability of tPB across shallow to abyssal depths is confirmed by on-site degradation tests and metagenomic analyses. Hence, tPB is expected to serve as a key fully circular commodity material in sustainable societies of the future.

Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis

The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.

Mitomycin C eliminates cyanobacterial transcription without detectable prophage induction in a Microcystis-dominated harmful algal bloom in Lake Erie

Although evidence indicates that viruses are important in the ecology of Microcystis spp., many questions remain. For example, how does Microcystis exist at high, bloom-associated cell concentrations in the presence of viruses that infect it? The phenomenon of lysogeny and associated homoimmunity offer possible explanations for this question. Virtually nothing is known about lysogeny in Microcystis, but a metatranscriptomic study suggests that widespread, transient lysogeny is active during blooms. These observations lead us to posit that lysogeny is important in modulating Microcystis blooms. Using a classic mitomycin C-based induction study, we tested for lysogeny in a Microcystis-dominated community in Lake Erie in 2019. Treated communities were incubated with 1 mg L-1 mitomycin C for 48 h alongside unamended controls. We compared direct counts of virus-like particles (VLPs) and examined community transcription for active infection by cyanophage. Mitomycin C treatment did not increase VLP count. Mitomycin C effectively eliminated transcription in the cyanobacterial community, while we detected no evidence of induction. Metatranscriptomic analysis demonstrated that the standard protocol of 1 mg L-1 was highly toxic to the cyanobacterial population, which likely inhibited induction of any prophage present. Follow-up lab studies indicated that 0.1 mg L-1 may be more appropriate for use in freshwater cyanobacterial studies. These findings will guide future efforts to detect lysogeny in Microcystis blooms.IMPORTANCEHarmful algal blooms dominated by Microcystis spp. occur throughout the world's freshwater ecosystems, leading to detrimental effects on ecosystem services that are well documented. After decades of research, the scientific community continues to struggle to understand the ecology of Microcystis blooms. The phenomenon of lysogeny offers an attractive potential explanation for several ecological questions surrounding blooms. However, almost nothing is known about lysogeny in Microcystis. We attempted to investigate lysogeny in a Microcystis bloom in Lake Erie and found that the standard protocols used to study lysogeny in aquatic communities are inappropriate for use in Microcystis studies, and perhaps freshwater cyanobacterial studies more broadly. This work can be used to design better methods to study the viral ecology of Microcystis blooms.

Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds

The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.

Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets

In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.

Impact of land use on antibiotic resistance genes and bacterial communities in rivers

River ecosystems support essential ecosystem functions and services, including supplying water for domestic, agricultural, and industrial activities, provisioning of hydropower and fisheries, supporting navigation and recreational activities, and regulating water quality. In recent decades, the presence and spread of antibiotic resistance genes (ARGs) have emerged as a key threat to ecosystem health and human well-being. Rivers that are surrounded by human-modified landscapes serve as primary repositories and sources of ARGs. However, our understanding of the relationship between the diversity of ARGs and land use remain limited. We collected 30 sediment samples from five rivers in Ningbo, China, and then classified the sampling sites into two groups (i.e., group A with low levels of human impacts and group B with intense human impact) based on land use in their upstream areas. In total, we found 31 types of ARGs and 148 phyla of bacteria in the samples. ARGs abundance had a positive relationship with the levels of anthropogenic activities, and exhibited significant difference between the two groups. Co-occurrence networks showed that the interrelationship between bacteria and ARGs was more complex in group B than in group A. Moreover, Structural Equation Modeling (SEM) revealed that anthropogenic activity not only posed direct effect on ARGs but also indirectly affected ARGs through bacteria. Our results underscore the profound impacts of land-use changes on the diversity of ARGs, bacteria communities, and their relationships, which highlight the need for integrating ARGs in river assessments in regions with human-dominated land use.

Simulated Discharge of Ballast Water Reveals Potential Contribution to Spread of Antibiotic Resistance Genes in Geographically Isolated Receiving Waters

Background/Objectives: The propagation of antibiotic resistance genes (ARGs) poses a huge threat to environmental and human health. The ballast water from ships has been recognized as an important vector of ARGs. However, little is known about how ballast water from geographically isolated water affects ARGs in receiving waters. Methods: Herein, we investigated the changes in ARGs in receiving water by microcosm experiments simulating the discharge of ballast water. Results: The simulated discharge of ballast water increased the abundances of target ARGs, which were 1.3-5.6-fold higher in the mixture of ballast water and receiving water (microcosm M) than in receiving water at the end of the experiment. The enrichment of target ARGs was significantly associated with MGEs. Moreover, the discharge of ballast water changed the microbial communities in receiving water. Further network analysis identified potential ARG hosts, such as Pseudohongiellaa and Amphritea, with the abundance in microcosm M (0.23% and 0.036%) being higher than in receiving water (0.09% and 0.006%), the changes of which might be responsible for ARG variations. Conclusions: Overall, our findings suggest the discharge of ballast water might promote the spread of ARGs in different geographical waters and the corresponding ecological risks should not be ignored.

Microbes drive more carbon dioxide and nitrous oxide emissions from wetland under long-term nitrogen enrichment

Wetlands are frequently regarded as weak carbon dioxide (CO2) sinks, the largest natural sources of methane (CH4), and weak sources of nitrous oxide (N2O). Anthropogenic activities and climate change-induced nitrogen (N) enrichment may affect wetland carbon (C) and N cycling via soil microbes, consequently modifying the original greenhouse gas (GHG) emissions. However, the effects and mechanisms of the duration and rate of N inputs on wetland GHG emissions remain uncertain and controversial. Therefore, this study conducted an in situ field experiment to investigate the effects and driving mechanisms of long-term N enrichment on wetland GHG emissions throughout the 2023 growing season by using the static opaque chambers method. Soil microbial composition and function were also analyzed through metagenomic sequencing. The results showed that N enrichment significantly increased wetland CO2 emissions, which were associated with the abundance of microbial C-fixing functional genes and the soil C content. Although nitrogen enrichment tended to suppress CH4 emissions, the effect was not significant. High N enrichment created a powerful wetland N2O source driven by the abundance of microbial nitrification function genes and microbial species. Vegetation influenced wetland GHG emissions by altering soil carbon content. This study elucidates the response mechanism of wetland GHG emissions to long-term nitrogen enrichment, thereby furnishing a theoretical basis for wetland conservation and nitrogen management.

Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights

Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.

Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms

BACKGROUND

The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").

RESULTS

The results demonstrated that annual cumulative N2O and CO2 fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH4 annual cumulative fluxes decreased from 12,669.45 ± 564.69 kg·ha- 1 to 8,238.40 ± 207.72 kg·ha- 1 in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50 ± 48.83 and 422.21 ± 73.59 mg·CO2-eq·m- 2·h- 1, respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH4 production. Functional genes related to CH4 oxidation (pmoA) and gene related to N2O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p < 0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH4 serving as an electron donor. This suggests that Dryland may act as a CH4 sink, despite the significant enhancement in CO2 and N2O fluxes.

CONCLUSIONS

In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.

Loss of Myostatin leads to low production of CH4 by altering rumen microbiota and metabolome in cattle

Myostatin (MSTN) is a protein that plays a crucial role in regulating skeletal muscle development. Despite the known benefits of MSTN mutant cattle for increasing beef production, their potential impact on CH4 emissions has not been quantified. The study comparing wild-type (WT) cattle to MSTN-knockout (MSTN-KO) cattle revealed that CH4 production was lower. Macrogenomic analysis revealed a significant decrease in rumen archaea, with reduced Richness indices (P = 0.036). The MSTN-KO cattle also showed altered archaea distribution and composition at different taxonomic levels. LEfSe results showed changes in 21 methanogenic archaea clades, with obligately hydrogen (H2)-dependent methylotrophs Candidatus Methanoplasma termitum species belonging to Methanomassiliicoccales order demonstrating the most significant decrease. Rumen metabolites revealed a decrease in the ratio of acetate to propionate, indicating a shift in rumen fermentation pattern towards propionate fermentation. Additionally, the changing trend of methanogenic archaea is consistent with the evolution of methanogens, and this is correlated with the higher levels of linoleic acid in the rumen of MSTN-KO cattle. Linoleic acid affects the utilization of H2 by methanogenic archaea, leading to a reduction in obligately H2-dependent methylotrophs. Our study suggests that MSTN-KO cattle have potential as an economically and ecologically benign breed for reducing methane emissions.

Behavioral alterations in antibiotic-treated mice associated with gut microbiota dysbiosis: insights from 16S rRNA and metabolomics

The gut and brain interact through various metabolic and signaling pathways, each of which influences mental health. Gut dysbiosis caused by antibiotics is a well-known phenomenon that has serious implications for gut microbiota-brain interactions. Although antibiotics disrupt the gut microbiota's fundamental structure, the mechanisms that modulate the response and their impact on brain function are still unclear. It is imperative to comprehend and investigate crucial regulators and factors that play important roles. We aimed to study the effect of long-term antibiotic-induced disruption of gut microbiota, host metabolomes, and brain function and, particularly, to determine the basic interactions between them by treating the C57BL/6 mice with two different, most commonly used antibiotics, ciprofloxacin and amoxicillin. Anxiety-like behavior was confirmed by the elevated plus-maze test and open field test. Gut microbes and their metabolite profiles in fecal, serum, and brain samples were determined by 16S rRNA sequencing and untargeted metabolomics. In our study, long-term antibiotic treatment exerted anxiety-like effects. The fecal microbiota and metabolite status revealed that the top five genera found were Lactobacillus, Bacteroides, Akkermansia, Ruminococcus_gnavus_group, and unclassified norank_f_Muribaculaceae. The concentration of serotonin, L-Tyrosine, 5-Hydroxy-L-tryptophan, L-Glutamic acid, L-Glutamate, 5-Hydroxyindole acetic acid, and dopaminergic synapsis was comparatively low, while adenosine was high in antibiotic-treated mice. The KEGG enrichment analysis of serum and brain samples showed that amino acid metabolism pathways, such as tryptophan metabolism, threonine metabolism, serotonergic synapsis, methionine metabolism, and neuroactive ligand-receptor interaction, were significantly decreased in antibiotic-treated mice. Our study demonstrates that long-term antibiotic use induces gut dysbiosis and alters metabolic responses, leading to the dysregulation of brain signaling molecules and anxiety-like behavior. These findings highlight the complex interactions between gut microbiota and metabolic functions, providing new insights into the influence of microbial communities on gut-brain communication.

Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems

Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.

Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al

Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.

Lysogen formation governs colonies while lytic infection is more prevalent in single cells of the bloom-forming cyanobacterium, Microcystis

While the bloom-forming cyanobacterium Microcystis can exist as free-living single cells or within dense mucilaginous colonies, the drivers and consequences of colony formation remain unclear. Here, we integrated metatranscriptomic datasets from two Microcystis bloom events in Lake Taihu, China, to analyze and validate the functional differences between colonial and single-cell Microcystis . Our results confirmed colony expression profiles were disproportionately enriched in Microcystis transcripts (and functions) compared to other prokaryotic taxa. Concomitantly, viral infection strategies diverged by Microcystis community morphology: colony-associated cells expressed lysogeny-associated genes, while single cells exhibited increased signatures of lytic infection. These data are consistent with the hypothesis that Microcystis colonies foster conditions favorable to lysogen formation-likely due to local high cell densities and the resulting advantage of superinfection immunity-whereas solitary cells experience stronger lytic pressure. On a broader scale, our findings refine the understanding of bloom dynamics by identifying how community morphological states coincide with distinct host-virus interactions. Cumulatively, this work underscores the importance of colony formation in shaping Microcystis ecology and highlights the need for mechanistic studies that disentangle the interplay between phage infection modes, colony formation, and microbial community structure.

Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety

Arabica coffee, one of the most valuable crop commodities, harbors diverse microbial communities with unique genetic and functional traits that influence bean safety and final coffee quality. In Ecuador, coffee production faces challenges due to the spread of pathogenic organisms across cultivars, leading to reduced yields and compromised quality. This study employed a shotgun metagenomic approach to characterize the indigenous microbial diversity present in the cell biomass of fermented coffee cherries from three Coffea arabica varieties: Typica (Group A), Yellow Caturra (Group B), and Red Caturra (Group C), originating from the Intag Valley in northern Ecuador, at two ripe stages: green (immature fruits) and ripe (red/yellow mature fruits). Gene prediction and functional annotation were performed using multiple databases, including EggNOG, COG, KEGG, CAZy, CARD, and BacMet, to explore the potential impact of microbial communities on bean quality and safety. Metagenomic sequencing generated over 416 million high-quality reads, averaging 66 million clean reads per sample and yielding a total of 47 Gbps of data. Analysis revealed distinct differences in species abundance based on the coffee variety and ripening stage. A total of 799,658 protein-coding sequences (CDSs) were predicted, of which 205,937 genes were annotated with EggNOG, 181,723 with COG, 155,220 with KEGG, and 10,473 with CAZy. Additionally, 432 antibiotic resistance genes (ARGs) were identified using CARD, and 8974 biocide and metal resistance genes (BMRGs) were annotated with BacMet. Immature cherries exhibited enriched pathways associated with resistance to antibiotics such as fluoroquinolones, penams, rifamycin, macrolides, carbapenems, and cephalosporins. The abundance of these pathways varied with the ripening stage and variety. Furthermore, green cherries showed a significant increase in BMRGs associated with resistance to substances including hydrochloric acid, copper, nickel, hydrogen peroxide, arsenic, and zinc. Among mature cherries, Typica and Red Caturra shared similar profiles, while Yellow Caturra displayed a divergent microbial and functional profile. These study findings emphasize the interplay between microbial diversity, ripening stages, and coffee varieties, providing a foundation for innovative approaches to enhance coffee quality through microbiome management.

The complete genome sequence of Penaeus vannamei nudivirus (previously Baculovirus penaei or P. vannamei singly enveloped nuclear polyhedrosis virus)

Penaeus vannamei singly enveloped nuclear polyhedrosis virus (PvSNPV), also known as Baculovirus penaei (BP), is the first viral pathogen of penaeid shrimp described in 1974. Although PvSNPV was discovered almost 50 years ago, the complete genome sequence has not been elucidated until now. We detected the virus in a quarantine stock of P. vannamei shrimp by light microscopy of faecal samples and by PCR screening of broodstock. Subsequently, next-generation sequencing was deployed to determine the complete genome sequence of PvSNPV. The PvSNPV genome is a circular, double-stranded DNA molecule of 119 883 bp in length encoding 101 ORFs. The deduced aa sequences from 28 ORFs were homologous to 28 core proteins from all identified nudiviruses. Phylogenetic analyses based on deduced aa sequences of the core genes and orthologous genes revealed that PvSNPV clusters with Penaeus monodon nudivirus. Therefore, we propose to rename BP/PvSNPV as P. vannamei nudivirus and re-assign the virus to the family Nudiviridae instead of Baculoviridae.

Effect of inoculated sludge concentration on start-up of anammox reactor: Nitrogen removal performance and metabolic pathways

The anammox process is efficient for nitrogen removal but faces challenges due to slow bacterial growth and limited inoculated sludge supply. This study examined the effects of different inoculated sludge concentrations (3.5, 7, and 14 g/L) on start-up and nitrogen metabolism in anammox reactors. Three identical reactors were operated under controlled conditions, with comprehensive analysis of nitrogen removal efficiency, sludge characteristics, and microbial community dynamics through metagenomic and transcriptomic approaches. Results demonstrated that higher inoculated sludge concentrations accelerated reactor start-up, with the 14 g/L reactor achieving stable operation in 13 days compared to 44 days for the 3.5 g/L reactor. However, the improvement in nitrogen removal rate showed a boundary effect, not proportional to the increase in sludge concentration. Notably, reactors with higher inoculated sludge concentrations exhibited lower sludge loads but higher sludge yield coefficients. Metagenomic analysis revealed Candidatus Kuenenia as the dominant anammox bacteria, with decreasing hydrazine dehydrogenase (hdh) gene expression levels observed at higher sludge concentrations, suggesting hydrazine synthesis as a potential rate-limiting step. This study provides novel insights into the optimal range of inoculated sludge concentration for anammox reactor start-up and elucidates the underlying metabolic mechanisms, offering valuable guidance for practical engineering applications.

Exploring the mechanism of Paotianxiong polysaccharide in the treatment of chronic kidney disease combining metabolomics and microbiomics technologies

A close relationship between the pathogenesis of chronic kidney disease (CKD) and abnormalities in the gut-kidney axis. Paotianxiong polysaccharides (PTXP) that have demonstrated therapeutic effects on CKD. However, the specific mechanism by which PTXP ameliorates CKD through the gut-kidney axis remains to be explored. In this study, the microbiomes and metabolomics were combined to investigate the impact of PTXP on intestinal flora structure and metabolism, further unveiling the relationship through correlation analysis. The results showed that PTXP intervention significantly modulated renal function abnormalities in CKD rats and significantly modulates gut microbial disorders, evidenced by an increased abundance of Lactobacillus murinus, Bacteroides fragilis, and a decreased abundance of Bifidobacterium pseudolongum. Furthermore, PTXP reversed the changes in intestinal metabolites, such as linoleic acid and docosahexaenoic acid, induced by CKD and identified unsaturated fatty acid metabolism as a key metabolic pathway. Correlation analyses also revealed associations among gut microorganisms, metabolites, and renal function indexes, confirming that PTXP alleviated CKD through the gut-kidney axis. Moreover, the above conclusions were verified by fecal bacteria transplantation experiments. These findings provide insights into the mechanism of PTXP for the treatment of CKD and provide new targets for the treatment of CKD.

Unraveling the microecological mechanisms of phosphate-solubilizing Pseudomonas asiatica JP233 through metagenomics: insights into the roles of rhizosphere microbiota and predatory bacteria

The effects of phosphate-solubilizing bacteria (PSB) on plant productivity are high variable under field conditions. Soil phosphorus (P) levels are proposed to impact PSB performance. Furthermore, the effect of exogenous PSB on rhizosphere microbial community and their functions are largely unexplored. Our study examined how different P background and fertilization affected the performance of PSB Pseudomonas asiatica JP233. We further conducted metagenomic sequencing to assess its impact on rhizosphere microbiota and functions, with a focus on genes related to soil P cycling. We found that JP233 could enhance P solubilization and tomato growth to different extent in both high and low P soils, irrespective of P fertilization. It was particularly effective in high P soil without extra fertilization. JP233 altered the rhizosphere microbial community, boosting taxa known for plant growth promotion. It also changed soil gene profiling, enriching pathways related to secondary metabolite biosynthesis, amino acids, carbon metabolism, and other key processes. Particularly, JP233 increased the abundance of most P cycle genes and strengthened their interconnections. Populations of certain predatory bacteria increased after JP233 inoculation. Our findings provide valuable insights into PSB's mechanisms for P solubilization and plant growth promotion, as well as potential adverse impacts of resident microbes on bioinoculants.

Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.

Multi-omics dataset of individual variations in growth performance of large yellow croaker

Large yellow croaker (Larimichthys crocea) is a highly economically important marine fish species in China. However, substantial individual variations in growth performance have emerged as a limiting factor for the sustainable development of the large yellow croaker industry. Gut microbiota plays a crucial role in fish growth and development by regulating metabolic processes. To explore these dynamics, we employed metagenomics, transcriptomics, and untargeted metabolomics to comprehensively analyze the structure of the intestinal microbiome and its relationship with intestinal metabolism and host gene expression. We constructed association models for "gut microbiota-differentially expressed genes", "differentially expressed genes-metabolites," and "gut microbiota-metabolites." Sequencing data and LC-MS/MS raw data have been deposited in NCBI and MetaboLights databases for public access. Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.

Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing

Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH andNH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition,NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.

Evaluation of Enrichment Approaches for the Study of the Viromes in Mollusk Species

Invasive alien species such as freshwater snails have significantly affected the food, environment, and the health of humans and animals, which have unfortunately received insufficient attention. To facilitate the study of viromes in snail species, we compared the enrichment effect of cesium chloride (CsCl) and sucrose density gradient ultracentrifugations in the recovery of diverse viruses in Pomacea canaliculata and Achatina fulica. First, we showed that CsCl-based ultracentrifugation enriched more virus contigs and reduced the nucleic acid background of the Pomacea canaliculata and was thus beneficial for virus recovery. Further studies comparing CsCl- and sucrose-based density gradient ultracentrifugations revealed that the former enriched more viral contigs and viral families of RNA viruses, while the latter yielded more DNA viruses from both Pomacea canaliculata and Achatina fulica. Certain RNA virus families, such as Rhabdoviridae, Arenaviridae, Hepeviridae, Astroviridae, and Alphatetraviridae, were exclusively enriched by CsCl-based ultracentrifugation. Conversely, several DNA virus families including Bacilladnaviridae, Nudiviridae, Malacoherpesviridae, and Adintoviridae were solely identified using the sucrose-based method. Therefore, the selection of viral enrichment technique (either CsCl or sucrose density gradient ultracentrifugation) should be carefully considered based on the specific virome (DNA or RNA viruses) being studied in mollusk species.

Non-adapted bacterial infection suppresses plant reproduction

Environmental stressors, including pathogens, substantially affect the growth of host plants. However, how non-adapted bacteria influence nonhost plants has not been reported. Here, we reveal that infection of Arabidopsis flowers by Xanthomonas oryzae pv. oryzae PXO99A, a bacterial pathogen causing rice blight disease, suppresses ovule initiation and reduces seed number without causing visible disease symptoms. TleB, secreted by the type VI secretion system (T6SS), interacts with plant E3 ligase PUB14 and disrupts the function of the PUB14-BZR1 module, leading to decreased ovule initiation and seed yield. On the other site, PUB14 concurrently promotes TleB's degradation. Our findings indicate that bacterial infections in nonhost plants directly repress offspring production. The regulatory mechanism by effectors PUB14-BZR1 is widely present, suggesting that plants may balance reproduction and defense and produce fewer offspring to conserve resources, thus enabling them to remain in a standby mode prepared for enhanced resistance.

A novel Alteromonas phage with tail fiber containing six potential iron-binding domains

Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.

Adaptive survival strategies of rumen microbiota with solid diet deficiency in early life cause epithelial mitochondrial dysfunction

With extreme nutritional substrate deficiency, the adaptive responses of the gastrointestinal microbiota and host metabolism are largely unknown. Here, we successfully established a microbial substrate deficiency model in the rumen without solid diet introduction in neonatal lambs. In the absence of solid diet, we observed a reduction in the Simpson Index of rumen bacteria, along with a marked decline in the abundance of keystone microorganisms such as Prevotella, Selenomonas, Megasphaera, and Succiniclasticum, indicating a simplified microbial interaction network. Additionally, more urea and NH3-N production facilitated microbial efficient nitrogen utilization to prioritize ammonia as a nitrogen source for survival, reallocating energy to overcome nutritional limitations and sustain their viability. In addition, enriched archaea (Methanosarcina, Methanomicrobium, Methanobrevibacter, and Methanobacterium) promoted hydrogen removal and the growth of nitrogen-producing microorganisms (Pecoramyces, Piromyces, Caecomyces, and Orpinomyces). It also reinforced the glutamate-glutamine pathway, as evidenced by the higher expression of glnA, GLUL, gdhA, and ureAB, suggesting enhanced internal cycling of nitrogen for microbial survival. This selfish microbial survival strategy deprived the host of adequate volatile fatty acids for energy metabolism, resulting in the downregulation of rumen epithelial cell cycle proteins (CCNB1, CCNE), abnormal mitochondrial morphology, and reduced mitochondrial deoxyribonucleic acid copy number and adenosine triphosphate production. Overall, these findings revealed the adaptive survival strategies of rumen microbiota with solid diet deficiency in early life, which caused alterations in epithelial cell mitochondrial function.

Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans

Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.

Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research

INTRODUCTION

The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS

In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS

The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.

Improvement of soil nutrient cycling by dominant plants in natural restoration of heavy metal polluted areas

Referring to the natural succession to restore polluted land is one of the most vital assignments to solving the environmental problems. However, there is little understanding of the natural restoration of nutrient biogeochemical cycles in abandoned land with severe metal pollution. To clarify the nutrient cycling process and the influence of organisms on it, we investigated the magnitude of rhizosphere effects on soil nitrogen (N), phosphorus (P) and sulphur (S) cycles in natural restoration of an abandoned metal mine, as well as the roles of plants and microorganisms in the nutrient cycles. Our data revealed that the rhizosphere had higher levels of ammoniation than non-rhizosphere soil at both stages of restoration. In the early stage, the rhizosphere had greater levels of inorganic phosphorus and organophosphorus solubilisation, as well as sulphite oxidation, compared to non-rhizosphere soil. The bacterial composition influenced the N and S cycles, while the fungal composition had the greatest effect on the P cycles. Furthermore, rhizosphere nutrition cycles and microbial communities altered according plant strategy. Overall, the plants that colonize the early stages of natural recovery demonstrate enhanced restoration of nutrient efficiency. These results contribute to further knowledge of nutrient recovery in mining areas, as well as suggestions for selecting remedial microorganisms and plants in metal-polluted environments.

Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA

RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for therapeutic applications. However, our ability to design new RNA structures remains limited by an incomplete understanding of their folding principles. While global metrics such as the minimum free energy are widely used, they are at odds with naturally occurring structures and incompatible with established design rules. Here, we introduce local stability compensation (LSC), a principle that RNA folding is governed by the local balance between destabilizing loops and their stabilizing adjacent stems, challenging the focus on global energetic optimization. Analysis of over 100,000 RNA structures revealed that LSC signatures are particularly pronounced in bulges and their adjacent stems, with distinct patterns across different RNA families that align with their biological functions. To validate LSC experimentally, we systematically analyzed thousands of RNA variants using DMS chemical mapping. Our results demonstrate that stem reactivity correlates strongly with LSC (R2 = 0.458 for hairpin loops) and that structural perturbations affect folding primarily within ~6 nucleotides from the loop. These findings establish LSC as a fundamental principle that could enhance the rational design of functional RNAs.

Diversity and Characteristics of the Oral Microbiome Associated with Self-Reported Ancestral/Ethnic Groups

Periodontitis disproportionately affects genetic ancestral/ethnic groups. To characterize the oral microbiome from different genetic ancestral/ethnic groups, we collected 161 dental plaque samples from self-identified African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. DNA was extracted from these samples, and then DNA libraries were prepared and sequenced using an Illumina NovaSeq high-throughput sequencer. We found significant differences in the diversity and abundance of microbial taxa among dental plaque samples of the AA, CA, and HA groups. We also identified unique microbial species in a self-reported ancestral/ethnic group. Moreover, we revealed variations in functional potentials of the oral microbiome among the three ancestral/ethnic groups, with greater diversity and abundance of antibiotic-resistant genes in the oral microbiome and significantly more genes involved in the modification of glycoconjugates and oligo- and polysaccharides in AAs than in CAs and HAs. Our observations suggest that the variations in the oral microbiome associated with ancestral/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. These finding can be a steppingstone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.

Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera)

Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.

Alterations in Gut Microbiota Correlate With Hematological Injuries Induced by Radiation in Beagles

Dynamics of gut microbiota and their associations with the corresponding hematological injuries postradiation remain to be elucidated. Using single whole-body exposure to 60Co-γ ray radiation at the sublethal dose of 2.5 Gy, we developed a beagle model of acute radiation syndrome (ARS) and then monitored the longitudinal changes of gut microbiome and hematology for 45 days. We found that the absolute counts of circulating lymphocytes, neutrophils, and platelets were sharply declined postradiation, accompanied by a largely shifted composition of gut microbiome that manifested as a significantly increased ratio of Firmicutes to Bacteroidetes. In irradiated beagles, alterations in hematological parameters reached a nadir on day 14, sustaining for 1 week, which were gradually returned to the normal levels thereafter. However, no structural recovery of gut microbiota was observed throughout the study. Fecal metagenomics revealed that irradiation increased the relative abundances of genus Streptococcus, species Lactobacillus animalis and Lactobacillus murinus, but decreased those of genera Prevotella and Bacteroides. Metagenomic functions prediction demonstrated that 26 altered KEGG pathways were significantly enriched on Day 14 and 35 postradiation. Furthermore, a total of 43 bacterial species were found to correlate well with hematological parameters by Spearman's analysis. Our results provide an insight into the longitudinal changes in intestinal microbiota at different clinical stages during ARS in canine. Several key microbes those tightly associated with the hematological alterations may serve as biomarkers to discriminate the different phases of host with ARS.