Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is closely linked to gut microbial imbalance marked by loss of beneficial microbes and overgrowth of pathogens. Christensenella intestinihominis, a bacterium that associated with intestinal homeostasis, is depleted in patients with ulcerative colitis (UC), yet its therapeutic potential against this disease remains to be elucidated. Here we demonstrate that C. intestinihominis AF73-05CM02, a strain isolated from Chinese individual, alleviates colitis. In healthy human gut, C. intestinihominis co-occurs with beneficial microbes in strongly connected networks, while these interactions are disrupted in UC. We employ the dextran sulfate sodium (DSS)-induced murine colitis model, a widely recognized preclinical model for investigating intestinal inflammation. In this model, oral gavage with AF73-05CM02 mitigates weight loss, ameliorates colonic injury, improves intestinal health markers, and reverses colon damage. It exerts these effects by reducing harmful bacteria such as Helicobacter species and increasing beneficial taxa like Akkermansia, while enhancing the intestinal epithelial barrier integrity and regulating immune responses. These findings indicate AF73-05CM02 may aid in the treatment of inflammatory bowel disease by restoring a healthy gut microbial community.

Microbial fuel cell (MFC) coupling has shown considerable potential for alleviating bio-clogging in constructed wetlands (CW). However, the multi-scale mechanisms underlying circuit-dependent clogging control remain poorly understood. In this study, a conventional gravel-filled wetland (CK), an open-circuit microbial fuel cell-coupled wetland (MCO), and a closed-circuit microbial fuel cell-coupled wetland (MCC) were comparatively investigated. After four months of operation, the CK system exhibited hydraulic deterioration, with its hydraulic efficiency and effective volume ratio decreasing by 4.3 % and 8.8 %, respectively. In contrast, the MCC system demonstrated the most favorable hydraulic evolution, displaying an over four-fold increase in hydraulic efficiency alongside a slight 3.6 % increase in effective volume ratio. Analysis of the key component of bio-clogging materials, namely extracellular polymeric substances (EPS), revealed that total EPS accumulation followed the order CK > MCO > MCC. In the MCC system, polysaccharides and DNA in the soluble and tightly bound EPS fractions were selectively reduced, and the β‑polysaccharide‑associated structural EPS on electrode biofilms was also weakened, which together increased the hydrophilicity of the bio‑clogging substances. Multi-omics analysis revealed that MFC coupling reshaped both microbiota and metabolism along the clogging pathway. Closed-circuit operation reduced clogging-relevant functional carriers, limiting the flow of sugar and nucleotide-related resources into the PS- and DNA-rich scaffold. This ultimately weaken the structural matrix, reducing the tendency for dense, clogged deposits to form. This study provides important implications for designing more stable MFC coupled CW for long-term wastewater treatment.

Heavy metal toxicity is a severe global threat, adversely affecting environmental health, food safety, and human well-being. Microbial biosorbents are a renowned effective solution for environmental pollution; however, their success depends on the adsorption capacity of the microbes. Metallothionein (MT) proteins are high in cysteine content and have a strong affinity to bind divalent metal ions. Thus, deliberately increasing cysteine content in bacterial MTs might hold promise in enhancing their metal-binding capacity. However, expressing these MTs in bacterial hosts is challenging due to many genetic constraints. In this study, we applied sequence-based protein design to generate three novel synthetic MT proteins (M_MT01, M_MT02, and M_MT03) with 32–38

Wheat (Triticum aestivum L.) quality is a major focus of wheat breeding that is influenced by multiple factors. The Huang-Huai wheat region is one of the main wheat-producing areas in China, and it has favorable conditions for cultivating wheat cultivars with strong-gluten and medium-strong-gluten. In this study, a systematic assessment of seven crucial quality traits and two important genetic loci (Glu-1 and Sec-1) in 436 wheat cultivars in the Huang-Huai wheat region of China by principal component analysis (PCA) and fuzzy comprehensive evaluation (FCE) methods identified the stability time (ST), stretch area (SA), and maximum resistance (MAXR) as three key factors which significantly influence wheat quality. Glu-1 and Sec-1 primarily impacted these three traits and subsequently influenced wheat quality. Compared to Glu-A1 and Glu-B1, Glu-D1 has a more significant impact on the comprehensive evaluation value D, principal components PC1-PC3, and the main traits ST, SA and MAXR of PC1. Wheat cultivars carrying the high-molecular-weight glutenin subunit (HMW-GS) Dx5+Dy10 exhibited notable improvements in the ST, SA, and MAXR traits compared with those carrying HMW-GS Dx2+Dy12, suggesting that Dx5+Dy10 may enhance wheat quality by improving those traits. By combining the results of the D value, genotype by yield & times;trait (GYT) index, and HMW-GS score, 20 high-quality and high yielding wheat cultivars were identified, which can be used as elite parents for wheat quality breeding.

Microbial metal resistance, a trait that enables microorganisms to withstand high levels of toxic metals, has been studied for over a century. The significance of uncovering these mechanisms goes beyond basic science as they have implications for human health through their connection to microbial pathogenesis, metal bioremediation, and biomining. Recent advances in analytical chemistry and molecular biology have accelerated the discovery and understanding of genetic mechanisms underlying microbial metal resistance, identifying specific metal resistance genes and their operons. The emergence of omics tools has further propelled research towards a comprehensive understanding of how cells respond to metal stress at the systemic level, revealing the complex regulatory networks and evolutionary dynamics that drive microbial adaptation to metal-rich environments. In this article, we present a historical overview of the evolving understanding of the genetic determinants of metal resistance in microbes. Through multiple narrative threads, we illustrate how our knowledge of microbial metal resistance and genetics has interacted with genetic tools and concept development. This review also discusses how our understanding of microbial metal resistance has progressed from the Mendelian perspective to the current systems biology viewpoint, particularly as omics approaches have considerably enhanced our understanding. This system-level understanding has opened new possibilities for genetically engineered microorganisms to regulate metal homeostasis.

In the past decade, third-generation sequencing technologies (such as PacBio (Pacific Biosciences) and Nanopore) have become gradually matured and are widely used for microbial taxonomy and quantification. Compared with Illumina sequencing, PacBio or Nanopore has advantages with long reads and high resolution in taxonomic classification. However, there is currently a lack of an easy-to-use, reproducible, and community-supported pipeline for PacBio or Nanopore amplicon sequencing data analysis. To address this shortcoming, the highly cited EasyAmplicon is updated to version 2, a pipeline fully supporting third-generation full-length amplicon data. EasyAmplicon 2 is a user-friendly pipeline that embraces data analysis and visualization options for data obtained from various sequencing technologies (Illumina, BGI (Beijing Genomics Institution), PacBio, Nanopore or Qitan). It integrates popular tools such as DADA2 and Emu, and provides a workflow from raw data to publication-ready visualizations. EasyAmplicon 2 inherits the advantages of the previous version and further optimizes the visualization part. The updated version of the pipeline includes data preprocessing, annotation, and quantification of amplicon sequence variants, intergroup comparison, and visualization for third-generation sequencing. EasyAmplicon 2 provides a simple and easy-to-use analysis environment for long-read amplicon sequencing data analysis. It is available for free on GitHub (https://github.com/YongxinLiu/EasyAmplicon).

The diversity and functions of metallothioneins (MTs) in Archaea remain poorly understood. This study identifies 180 archaeal MTs from 406 genomes, revealing distinct evolutionary lineages and structural diversity. Phylogenetic analysis suggests a novel class with divergent ancestry. AlphaFold3-based modeling highlights conserved Cys-rich motifs and irregular structures, potentially enhancing adaptation to extreme environments. Functional assays show that four MTs (MT334126, MT382228, MT114104, and MT282443) increase cadmium resistance, while MT334126 and MT382228 also enhance copper resistance. Targeted mutations at key sites boost metal adsorption, validated by structural modeling. This work provides the first comprehensive insight into archaeal MTs, laying the foundation for environmental and biotechnological applications.

Thermophilic microorganisms offer a favorable solution to accelerate thermophilic composting; however, the details of the microbial community responsible for compost production have only emerged recently. In this study, we reported a detailed study of fungal succession during thermophilic composting and identified key thermophilic fungi capable of enhancing the biological process of compost humification. Through high-throughput sequencing, a total of 238 fungal species were identified with beta-diversity of the fungal community significantly changing during the thermophilic phase and then maintained a relatively stable composition. The Class of Eurotiomycetes played an important role in the Thermophilic and Maturation process and became the center of fungal community network. Functional prediction revealed that fungal groups with cellulose/xylandegrading activities were significantly more abundant during the thermophilic phase compared to the initial stage. Subsequently, a total of 16 fungi were isolated in situ, and their phylogeny and degradation capabilities were determined. Two fungal strains were reintroduced into the compost, resulting in a shortened composting time from 5 days to 3 days, an improved germination index, and enhanced compost quality, particularly promoting wheat growth. The findings of this study contribute to the development of fungal inocula for accelerating composting and providing new strategies for the efficient utilization of agricultural waste. This research holds significant importance for the increasing utilization of agricultural waste.

Grain cadmium (Cd) contamination threatens global food safety. Addressing the scarcity of genetic targets for low-Cd crops, this study reveals a critical role for the transcription factor GT-2 LIKE 1 (GTL1) in regulating Cd accumulation. In Arabidopsis, AtGTL1 expression decreased under prolonged Cd stress. The gtl1 knockout mutants exhibited significantly reduced sensitivity to Cd and accumulated less of the metal in roots, leaves, and seeds compared to wild-type plants. Mechanistically, AtGTL1 directly binds the promoter of AtHIPP6 and represses its transcription. Consistent with this, hipp6 mutants showed increased Cd accumulation in leaves and enhanced root-to-shoot translocation, while AtHIPP6 overexpression reduced Cd accumulation. Notably, AtHIPP6's function in Cd regulation is independent of membrane association. Crucially, targeting the rice homolog OsGTL1 via CRISPR/Cas9 knockout dramatically decreased Cd content by up to 80.3 % in leaves and 60.6 % in grains. This work identifies GTL1 as a key regulator of Cd accumulation through repression of HIPP6 and demonstrates its high potential as a genetic target for engineering low-Cd crops in major cereals like rice.

The extraction and processing of ores from lead-zinc mines, coupled with the disposal of tailings, often result in severe environmental contamination that poses significant ecological and public health risks, demanding urgent attention and action. In this study, field investigations and analyses were performed to evaluate the state of heavy metal pollution and microbial diversity in the soil around Qixia Mountain lead-zinc mine in Nanjing, China. The effect of plant-/microorganism-induced mineralization on the remediation of the contaminated soil was studied via pot experiments. Results indicated serious soil pollution around the mine, and dominant bacterial species (e.g. Sphingomonas) in different soil environments exhibited high resistance to heavy metals. Pot experiments showed that amaranth-/Bacillus velezensis-induced mineralization can significantly reduce the heavy metal pollution levels (Nemerow pollution index decreased from 4.5 to about 1.0) in soil. This study reveals the profound impacts of mining activities on soil ecology and human health, providing a theoretical basis for the prevention and control of soil pollution in farmlands surrounding lead-zinc mines.

Yeast has been extensively studied and engineered due to its genetic amenability. Projects like Sc2.0 and Sc3.0 have demonstrated the feasibility of constructing synthetic yeast genomes, yielding promising results in both research and industrial applications. In contrast, plant synthetic genomics has faced challenges due to the complexity of plant genomes. However, recent advancements of the project SynMoss, utilizing the model moss plant Physcomitrium patens, offer opportunities for plant synthetic genomics. The shared characteristics between P. patens and yeast, such as high homologous recombination rates and dominant haploid life cycle, enable researchers to manipulate P. patens genomes similarly, opening promising avenues for research and application in plant synthetic biology. In conclusion, harnessing insights from yeast synthetic genomics and applying them to plants, with P. patens as a breakthrough, shows great potential for revolutionizing plant synthetic genomics.

The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.

Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.

Cr(VI) is a major heavy metal contaminant that poses great threats to aquatic ecosystems and human health. To guarantee the safety of water quality, the development of in-situ and online sensors for monitoring Cr(VI) contamination events is crucial. In this work, sediment microbial fuel cell (SMFC) based sensors using floating cathode as sensing element were operated in outdoor environment for one year to monitor repeated Cr(VI) shocks in wetlands constructed with coastal alkaline soil (YC), paddy of acidic soil (YT), and paddy of neutral soil (NJ). K2CrO4 solutions were added to the cathode four times in January, March, June, and September, respectively. Results showed that each Cr(VI) addition triggered a voltage peak and the voltage increments were linearly correlated with Cr(VI) concentrations within the range of 5 to 120 mg L-1 Cr(VI). The highest sensitivity was observed for YC (1.2 mV L mg-1) and YT (1.4 mV L mg-1) in June and for NJ (1.2 mV L mg-1) in September. XPS analysis demonstrated the reduction reaction of Cr(VI) to Cr(III) on the cathode might contribute to the generation of voltage peaks. Despite repeated shocks, Cr(VI) was immobilized in the soil and completely reduced to low-toxic Cr(III) with the consumption of soil organic matter, and the diversity and abundance of exoelectrogenic bacteria-associated genera were not inhibited. As a result, stable operation of the SMFC sensors was ensured. The SMFC sensors exhibited great potential for in-situ and online monitoring of Cr(VI) contamination events across various wetlands.

A novel and facile electrospinning-electrospray (EE) method that based on electrospinning technique and simultaneous electrospray was proposed to anchor TiO2 (P25) nanoparticles on the surface of rice straw-derived cellulose acetate (CA) nanofiber, a series of EE-CA/P25 nanofibrous membranes with different P25 dosage were successfully fabricated, which were characterized in terms of SEM, TEM, FI-IR, XRD, DRS, PL, UV-vis and 3DEMMs, etc. Results confirmed that P25 nanoparticles were anchored on the surface of CA nanofiber. For different organic dyes of Methylene blue (MB), Rhodamine B (RhB) and Methyl orange (MO), EE-CA/P25(0.05) nanofibrous membrane toward MB dye showed the best photocatalytic degradation efficiency of 99.13 % after 30 min of light exposure. For the different antibiotics of Tetracycline (TC), Ciprofloxacin (CIP) and Sulfamethoxazole (SMX), EE-CA/P25(0.05) exhibited the best photocatalytic degradation efficiency of 83.59 % for TC after 30 min of light exposure. Moreover, EE-CA/P25(0.05) exhibited a good antimicrobial efficiency of 98.42 % for E. coli, and maintained 97.49 % after 5 cycles. The reactive radical trapping experiments revealed that h+, center dot O 2-, and center dot OH participated in the reaction, and h+ and center dot O 2- played a major role in the photocatalytic degradation process. Moreover, EE-CA/P25(0.05) flexible membrane was easy to recycle and transform rice straw waste into treasure.

The recognition of structure -induced interfacial activation in heterogenized molecule catalysts is essential to steer CO 2 value-added electroconversion but remains inadequate. Herein, through designing three congeneric Co -N 4 model molecules (Co-CPY, Co-TAA and Co-PHE) with recognizable steric configurations, we systematically investigated the impact of structure -induced interfacial activation on promoting CO 2 electroconversion. Concretely, the Co-CPY/CNTs, featuring highly planar and conjugated molecules immobilized onto CNTs, delivers an ultra -high current density and enables near -unity Faradaic efficiency for CO 2 electroconversion, exceeding the counterparts. The theoretical and spectrographic findings demonstrate that the Co-CPY/CNTs not only creates the adaptive interfaces with strong communication to greatly expedite electron transfer but also reconstructs the electronic structures of active Co -N 4 units to effectively promote the formation of intermediates. Furthermore, the electroconversion of CO 2 to dimethyl carbonate was reliably performed with a high yield of 96 mu mol cm -2 h -1 through paired tandem electrosynthesis, highlighting the superior expansibility of Co-CPY/CNTs.

Whether eukaryotic organisms can evolve for higher heavy metal resistance in laboratory conditions remains unknown. In this study, we challenged a macrofungi, Pleurotus ostreatus, in a designed microbial evolution and growth arena (MEGA)-plate with an extreme Cd gradient. Within months, the wild-type strain developed 10 mutants, exhibiting a maximum three-fold increase in Cd tolerance and slower growth rates. Genomic sequencing and re-sequencing of the wild-type and ten mutant strains generated about 51 GB data, allowing a comprehensive comparative genomics analysis. As a result, a total of 2512 common single nucleotide poly-morphisms, 70 inserts and deletes, 39 copy number variations and 21 structural variations were found in the 10 mutants. The mutant genes were primarily involved in substrate transport. In combination with transcriptome analysis, we discovered that the ten mutants had a distinct Cd-resistant mechanism compared to the wild-type strain. Genes involved in oxidation-reduction, ion transmembrane transport, and metal compartment/efflux are primarily responsible for the extreme Cd tolerance in the P. ostreatus mutants. Our findings contribute to the understanding of eukaryotic Cd resistance at the genome level and establish a foundation for developing bioremediation tools utilizing highly tolerant macrofungi.

The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.