Industrial systems contribute approximately 30% of total anthropogenic CO2 emissions. Microalgal-based CO2 capture from industrial off-gases is a promising self-sustainable technology, but its efficacy is limited by the toxicity of high CO2, SOX, and NOX. Periphytic biofilms (PBs), composed of microalgae, bacteria, and abiotic components, can overcome these limitations through enhanced collective tolerance and CO2 fixation efficiency. This resilience arises from matrix-mediated physicochemical gradients and community-level adaptations, including metabolite exchange, horizontal gene transfer, and intercellular signaling. Translating PBs into a viable industrial technology requires a coordinated strategy encompassing advanced photobioreactor design, innovative material development, and microbial community regulation. Overcoming challenges related to biofilm stability, system scalability, and economic feasibility is crucial for advancing tailored PB systems for industrial carbon capture.

Polychlorinated biphenyls (PCBs) persist globally as legacy pollutants with a complex structural diversity that complicates the understanding of their microbial conversion processes and remediation. In this study, high-throughput enzymatic assays, quantum chemical calculations, and machine learning were integrated to elucidate the reductive dechlorination pathways and reactivity of all 209 PCB congeners. By coupling Hirshfeld charge analysis with empirically derived steric effects, 98.3% accuracy was achieved in predicting dechlorination pathways across diverse Dehalococcoides isolates and enrichment cultures containing distinct organohalide-respiring bacteria. Furthermore, XGBoost models incorporating electronic, steric, and physicochemical descriptors were developed to quantify the dechlorination reactivity of PCBs, revealing that the steric effect-corrected Hirshfeld charge and PCB solubility primarily control microbial reductive dechlorination potential. The model successfully captured the observed trends in the dechlorination reactivity of PCBs across multiple dechlorinating cultures and predicted that 11 of the 12 dioxin-like PCB congeners were susceptible to microbial reductive dechlorination, highlighting intrinsic microbial detoxification potential under anaerobic conditions. This integrative framework unveils the first full picture of microbial dechlorination pathways and reactivity for the entire PCB family, providing mechanistic insight into how molecular properties dictate halogen removal. The findings advance the predictive understanding of organohalide respiration and offer a roadmap for designing microbiome-based bioremediation strategies for persistent halogenated pollutants like PCBs.

Persistent 4%-22% gaps in nitrogen (N) mass balances have hindered sustainable N management in paddy agriculture. Periphyton are known N sinks, yet their role in paddies remains unclear. We used 15N tracing in 840 paddies across China to quantify periphyton-associated N pools and their fate. Periphyton captured 6%-24% (mean: 12%) of the applied N fertilizer (i.e. ∼0.8 Tg N yr-1 nationwide), effectively accounting for the missing N in previous budgets. Most of the sequestered N was stored as bioavailable ammonium. Partitioning analysis revealed that periphyton-mediated N was subsequently released into residual soil N (512-640 kt), denitrification (56-128 kt) and ammonia volatilization (64-232 kt). Thus, periphyton act as transient N reservoirs, immobilizing N fertilizer early in the growing season and gradually releasing it through biomass decay. This overlooked pathway closes a critical gap in agroecosystem N cycling and supports more precise N management in rice systems.

The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.

Anoxic soils store approximately one-third of the global terrestrial carbon. In anoxic soils, hydroxyl radicals (center dot OH) can replace the role of O2 in promoting the decomposition of organic matter, but how to enhance center dot OH generation under such conditions remains insufficiently investigated. Here we introduced two different forms of Fe(III), nano Fe-C3N4 and ionic Fe(III), to regulate center dot OH generation and evaluated their effects on organic matter decomposition. Compared to the Control, nano Fe-C3N4 increased straw decomposition by 9.3% while ionic Fe (III) reduced it by 13.3%. This contrast aligned with their respective effects on center dot OH generation: sustained promotion by Fe-C3N4 versus transient inhibition by ionic Fe(III). In depth analyses supported that the opening of the "enzyme latch" by center dot OH in our soils and the importance of electroactive microorganisms for center dot OH generation. Accordingly, we propose a three-step cyclic mechanism for anoxic organic matter decomposition: (i) Fe(III)/Fe (II) redox cycling generates center dot OH; (ii) center dot OH opens the "enzyme latch" and stimulates organic matter decomposition; (iii) electroactive microorganisms become enriched and sustain center dot OH generation, thereby closing the loop cycle. This center dot OH-mediated loop provides a novel perspective on center dot OH-microbe synergy in organic matter decomposition and advances biogeochemical C-Fe cycle knowledge in oxygen-limited soils.

The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.

Polychlorinated biphenyls (PCBs) are pervasive pollutants that pose risks to ecosystems and human health. Microbial reductive dehalogenation plays crucial roles in attenuating PCBs, but comprehensive insights into PCB dechlorination pathways, reactivity, and governing factors are limited by the vast number of congeners and costly experimental approaches. We address this challenge by establishing a high-throughput in vitro assay approach of reductive dehalogenation (HINVARD), which increases dechlorination test throughput by 30-fold and enhances reagents and cell utilization efficiency by over 10-fold compared to conventional assay methods. Using HINVARD, we screened 61 PCB congeners across 9 enrichment cultures and 3 Dehalococcoides isolates, identifying active dechlorination of 31-44 congeners. Results showed that PCB congener properties (chlorine substitution patterns, steric hindrance, and solubility) primarily determine the dechlorination potential, leading to consistent reactivity trends across cultures. In contrast, different organohalide-respiring bacteria catalyzed distinct dechlorination pathways, preferentially removing para- or meta-chlorines. Structural modeling of reductive dehalogenases revealed unique binding orientations governing substrate specificity, offering molecular insights into these pathways. This study provides a high-efficiency strategy for investigating microbial reductive dehalogenation, yielding the first comprehensive understanding of PCB dechlorination patterns and mechanisms. These findings guide the design of tailored microbial consortia for effective PCB bioremediation.

Soil microorganisms play globally vital roles in the environ-ment,ecology,and agriculture[1],and have become a research hotspot.Most research in these fields depends on microbial sequencing and analysis[2,3],which should ideally be conducted immediately after sample collection[4].However on-site DNA extraction and sequencing are often impractical.Therefore,freshly collected soil samples must be properly stored for transport before sequencing.While this sounds like a natural operation,proper transport of soil samples has been widely overlooked,challenging the accuracy of all related research.

Climate warming impacts agricultural ecosystems in an unpredictable manner. Below-ground microbes are pivotal for aboveground productivity, but their influences on crop productivity in a warming climate are unknown. We conducted a regional-scale field survey in 253 rice-wheat rotation systems using bacterial 16S amplicon sequencing and satellite-derived crop net primary productivity (NPP) data to investigate the relationships between soil bacteria and crop NPP under different temperatures. Actinobacteria were identified as the main driver of crop NPP, accounting for 4.2 % of the variation, with summer warming accounting for 11.9 % of the increase in their relative abundance. Summer warming resulted in an increase in antibiotic production genes within Actinobacteria, potentially reducing crop productivity by inhibiting seed germination and root elongation and by suppressing plant growth-promoting microorganisms. Taken together, our study indicates that warmer summers are expected to increase the relative abundance of soil Actinobacteria in rice-wheat rotation systems, which will negatively impact crop NPP due to their production of antibiotics that suppress beneficial plant microbes and/or inhibit crop seed germination and root elongation.

Most of the energy, nitrogen/N and phosphorus/P entering wastewater treatment plants (WWTPs) accumulates in waste activated sludge (WAS). While these resources are theoretically recoverable through anaerobic digestion (AD), conventional sludge AD faces long-standing challenges of low organic loading rate and limited N/P recovery. Here, building on an innovative sludge liquefaction and stratification technique, we present a novel process entitled SPREAD that boasts 10 times higher organic loading rates and recovers 5 folds of N/P resources, relative to conventional sludge AD. We develop an anaerobic digestion database (ADDB) for multi-omics analyses of digestion microbiomes, and pinpoint the mechanism underlying the exceptionally high organic loading rate and remarkable N/P recovery in SPREAD. Importantly, we identify a negative correlation between the Gibbs free energy (ΔG) and the relative abundance of methanogens, enabling identification of bottleneck steps for stimulation and augmentation of methanogenic digestion. Our study provides a game-changing technology for the treatment and resource recovery from WAS and opens a new avenue for sustainable management and carbon/energy-neutrality of WWTPs. ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of ChinaNational Natural Science Foundation of China, , 42161160306, 42177001 Natural Science Foundation of Guangdong ProvinceNatural Science Foundation of Guangdong Province, , 2018B030314012

Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)-resource acquisition (A)-stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial-/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.

Quorum sensing (QS) has important consequences for the productivity and stability of microbial communities, determining community function. Microbial communities in nature often exist in the pattern of multi-species microbial aggregates, but the ecological roles of QS in aggregates are poorly understood due to the aggregates' heterogeneity and complexity, in particular the entrapment of rare earth elements (REEs) from waste streams. Using periphytic biofilm (PB) as a microbial-aggregate model, we addressed how QS via acyl-homoserine-lactones (AHLs) regulated REEs entrapment. The REEs entrapment capacity of AHLs-enhanced PBs were improved by ∼ 2x compared to native PBs, with entrapment efficiencies up to ∼ 96 %, which was feasible in real-world waste streams including mine wastewater, e-waste and coal fly ash. AHLs promoted the synthesis and sharing of biopolymers, which facilitated REEs entrapment by electrostatic interaction, proton release and complex precipitation. AHLs addition optimized the acid-tolerant community and reduced the damage to PB caused by pH and REEs stress using the protective barrier mechanism of extracellular biopolymers. The successful field-scale implementation of this strategy provides a green and feasible path for a circular economy of REEs.

Plant residue decomposition is central to soil organic matter formation. Fungi, bacteria, and archaea are all well-known agents of residue decomposition. However, their relative taxonomic and functional contributions to plant residue decomposition in anoxic paddy soils are not well understood, and neither are the factors that govern these contributions. Here, a series of microcosms inoculated with two distinct paddy soils and amended with 13C-labeled rice straw was set up. DNA stable-isotope probing (DNA-SIP) based shotgun metagenomic sequencing was performed to reveal the relative contributions of bacteria, archaea, and fungi in rice straw degradation. Furthermore, the possible underlying mechanisms were investigated, focusing on microbial interspecies interference competition. We found that bacteria and archaea collectively accounted for 96.2∼99.5% (in CS anoxic paddy soil) and 81.7∼96.0% (in YT anoxic paddy soil) of the total abundance, while fungi accounted for only 0.5∼3.8% and 4.0∼18.3%, respectively. Phylogenetic distribution of functional genes encoding the carbohydrate-active enzyme (CAZyme) revealed that 87.7% (in CS anoxic paddy soil) and 80.9% (in YT anoxic paddy soil) of these genes were derived from bacteria and archaea, the remainder (12.3% and 19.1%) coming from fungi. The bacteria-fungi antagonism experiment indicated that fungal growth was indeed markedly inhibited by members of the two well-known antimicrobial compounds producing bacterial groups present, the Actinobacteria and the Bacilli. This study indicates that bacterial interference competition and environmental filtering (i.e., low redox/oxygen conditions) may reduce the contribution of fungi to plant residue decomposition in anoxic paddy field environments. These outcomes are important when constructing models to forecast and/or quantitative the microbial contributions to the global carbon dynamics in anoxic paddy soils.

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTPollutant Behavior at the Soil/Sediment–Water Interface: From Two to Multiple PhasesYing XuYing XuZigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, ChinaMore by Ying Xu, Yonghong Wu*Yonghong WuZigui Ecological Station for Three Gorges Dam Project, State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China*[email protected], (86)-25-8688 1330, (86)-25-8688 1000More by Yonghong WuView Biographyhttps://orcid.org/0000-0002-2985-219X, and Jan DolfingJan DolfingFaculty of Energy and Environment, Northumbria University, Newcastle upon Tyne NE1 8QH, U.K.More by Jan Dolfinghttps://orcid.org/0000-0002-7220-530XCite this: ACS EST Water 2024, 4, 4, 1180–1182Publication Date (Web):February 12, 2024Publication History Received13 January 2024Accepted6 February 2024Revised5 February 2024Published online12 February 2024Published inissue 12 April 2024https://pubs.acs.org/doi/10.1021/acsestwater.4c00032https://doi.org/10.1021/acsestwater.4c00032article-commentaryACS PublicationsCopyright © 2024 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views431Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (3 MB) Get e-AlertscloseSUBJECTS:Environmental pollution,Metals,Soil pollution,Water,Water pollution Get e-Alerts

Reduction potentials of the electron producing and electron consuming physiologies constrain the window of opportunity in direct interspecies electron transfer (DIET).

Terrestrial inputs and subsequent degradation of dissolved organic matter (DOM) in lake ecosystems can result in rapid depletion of dissolved oxygen (DO). Inputs of terrestrial DOM including organic acids can also lead to decreases in pH. However, to date, few studies have investigated the linkages between terrestrial DOM inputs, DO and pH levels in the water column, and carbon dioxide (CO2) emissions from lake ecosystems. Based on monthly field sampling campaigns across 100 sites in Lake Qiandao, a major man -made drinking water reservoir in China, from May 2020 to April 2021, we estimated an annual CO2 efflux (FCO2) of 37.2 +/- 29.0 gC m- 2 yr- 1, corresponding to 0.02 +/- 0.02 TgC yr- 1 from this lake. FCO2 increased significantly with decreasing DO, chlorophyll-a (Chl-a) and delta 2H-H2O, while FCO2 increased with increasing specific UV absorbance (SUVA254) and a terrestrial humic-like component (C2). We found that DO concentration and pH declined with increasing terrestrial DOM inputs, i.e. increased SUVA254 and terrestrial humic-like C2 levels. Vertical profile sampling revealed that the partial pressure of CO2 (pCO2) increased with increasing terrestrial DOM fluorescence (FDOM), while DO, pH, and delta 13C-CO2 declined with increasing terrestrial FDOM. These results highlight the importance of terrestrial DOM inputs in altering physico-chemical environments and fueling CO2 emissions from this lake and potentially other aquatic ecosystems.

Short-chain carboxylic acids (SCCAs) production from waste-streams is attractive due to the increasing market demand and wide range of applications. This study investigated the influence of pH on the performance of anaerobic SCCA-producing reactors treating fruit waste and employed metagenomics to unveil the shifts and metabolic pathways of functional acidogens. Results showed that high SCCA concentrations of 45.0-65.8 g chemical oxygen demand (COD)/L were maintained at each pH. The maximum concentrations of SCCAs obtained at pH 8 (63.8 g COD/L) under alkaline conditions and at pH 5 (65.8 g COD/L) under acidic conditions were similar, yet there was a pronounced effect of pH on SCCA distribution as acetate and butyrate were the primary products at pH 6, while lactate was dominant at pH 8-10 and at pH 5-4. Key populations involved in acidogenesis at different pHs included Bifidobacterium (acetate fermenter at pH 6-7), Corynebacterium (acetate and lactate fermenter at pH 8-10), Acidipropionibacterium (propionate fermenter at pH 7-10), Clostridium (acetate, propionate, and butyrate fermenter at pH 6-5), and Lactobacillus (lactate fermenter at pH 5). This study enhances our understanding of the underlying microbial mechanism governing SCCA production from fruit waste with pH regulation, and provides guidance for the development of production processes for waste-based metabolites useful for the chemical industry.

The nitrogen cycle plays a vital role in sustaining productive and healthy ecosystems,with the microbial nitrogen cycle being a focal point in agriculture and eco-environmental protection.Among these microbially mediated processes is ammonium(NH4)oxidation,the gatekeeper of the nitrogen cycle.Our under-standing of ammonium oxidation is continuously evolving,thanks to recent research breakthroughs like comammox,Feammox,and dirammox[1-6].The increasing complexity of ammonium oxida-tion necessitates more precise and well-focused research tools beyond those commonly used today.

Rivers receive, transport, and are reactors of terrestrial dissolved organic matter (DOM) and are highly influenced by changes in hydrological conditions and anthropogenic disturbances, but the effect of DOM composition on the dynamics of the bacterial community in rivers is poorly understood. We conducted a seasonal field sampling campaign at two eutrophic river mouth sites to examine how DOM composition influences the temporal dynamics of bacterial community networks, assembly processes, and DOM-bacteria associations. DOM composition and seasonal factors explained 34.7% of the variation in bacterial community composition, and 14.4% was explained purely by DOM composition where specific UV absorbance (SUVA254) as an indicator of aromaticity was the most important predictor. Significant correlations were observed between SUVA254 and the topological features of subnetworks of interspecies and DOM-bacteria associations, indicating that high DOM aromaticity results in more complex and connected networks of bacteria. The bipartite networks between bacterial taxa and DOM molecular formulae (identified by ultrahigh-resolution mass spectrometry) further revealed less specialized bacterial processing of DOM molecular formulae under the conditions of high water level and DOM aromaticity in summer than in winter. A shift in community assembly processes from stronger homogeneous selection in summer to higher stochasticity in winter correlated with changes in DOM composition, and more aromatic DOM was associated with greater similarity in bacterial community composition. Our results highlight the importance of DOM aromaticity as a predictor of the temporal dynamics of riverine bacterial community networks and assembly.