Search

The coupling of microscale zero-valent iron (mZVI) and anaerobic bacteria (AB) has gained increasing attention due to its ability to enhance dechlorination efficiency by combining the advantages of chemical and microbial reduction. However, the implementation of these coupling technologies at the field scale is challenging in terms of sustainability goals due to the coexistence of various natural electron acceptors in groundwater, which leads to limited electron selectivity and increased secondary risk. Therefore, this study used trichloroethylene (TCE) as a probe contaminant and nitrate (NO 3 - ) as a typical co-occurring natural electron acceptor to optimize the overall sustainable remediation performance of an mZVI/AB coupled system by adjusting the mZVI particle size and dosage. Results revealed that mZVI particles of different sizes exhibit different microorganism activation capabilities. In contrast to its 2 μm and 7 μm counterparts, the 30 μm mZVI/AB system demonstrated a strong dosage-dependency in TCE removal and its product selectivity. Finally, multi-criteria analysis (MCA) methods were established to comprehensively rank the alternatives, and 30 μm mZVI (15 g/L dosage) was determined to be the best remediation strategy with the highest total sustainability score under all studied hydro-chemical conditions when equal weights were applied to technical, environmental, and economic indicators. Our work provides a paradigm for comprehensively assessing the sustainable remediation performance of chlorinated aliphatic hydrocarbons polluted groundwater in practical applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Cotreatment, mechanical disruption of lignocellulosic biomass during microbial fermentation, is a potential alternative to thermochemical pretreatment as a means of increasing the accessibility of lignocellulose to biological attack. Successful implementation of cotreatment requires microbes that can withstand milling, while solubilizing and utilizing carbohydrates from lignocellulose. In this context, cotreatment with thermophilic, lignocellulose-fermenting bacteria has been successfully evaluated for a number of lignocellulosic feedstocks. Here, cotreatment was applied to sugarcane bagasse using monocultures of the cellulose-fermenting Clostridium thermocellum and cocultures with the hemicellulose-fermenting Thermoanaerobacterium thermosaccharolyticum. This resulted in 76 % carbohydrate solubilization (a 1.8-fold increase over non-cotreated controls) on 10 g/L solids loading, having greater effect on the hemicellulose fraction. With cotreatment, fermentation by wild-type cultures at low substrate concentrations increased cumulative product formation by 45 % for the monoculture and 32 % for the coculture. These findings highlight the potential of cotreatment for enhancing deconstruction of sugarcane bagasse using thermophilic bacteria., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Lee R. Lynd is a shareholder in a start-up company focusing on cellulosic biofuel production and conversion. The authors declare that they have no other competing financial interest or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Mechanistic investigation of host-microbe interactions in the human gut are hindered by difficulty of co-culturing microbes with intestinal epithelial cells. On one hand the gut bacteria are a mix of facultative, aerotolerant or obligate anaerobes, while the intestinal epithelium requires oxygen for growth and function. Thus, a coculture system that can recreate these contrasting oxygen requirements is critical step towards our understanding microbial-host interactions in the human gut. Here, we demonstrate Intestinal Organoid Physoxic Coculture (IOPC) system, a simple and cost-effective method for coculturing anaerobic intestinal bacteria with human intestinal organoids (HIOs). Using commensal anaerobes with varying degrees of oxygen tolerance, such as nano-aerobe Bacteroides thetaiotaomicron and strict anaerobe Blautia sp., we demonstrate that IOPC can successfully support 24-48 hours HIO-microbe coculture. The IOPC recapitulates the contrasting oxygen conditions across the intestinal epithelium seen in vivo. The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Fofanova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

The application of ANAMMOX technology is constrained by sluggish growth and difficulty in enriching ANAMMOX bacteria. Long-term starvation of functioning bacteria due to limited substrate supply makes the steady operation of ANAMMOX reactors more difficult. Re-examining the start-up and recovery performance of the ANAMMOX reactor and identifying its resistance mechanism are important from the standpoint of long-term starvation. By inoculating nitrifying and denitrifying sludge under various operating circumstances, the ANAMMOX reactors were successfully started. Under various start-up procedures, the tolerance mechanism and recovery performance were examined. The outcomes demonstrated that the denitrifying sludge-inoculated reactor operated steadily with a high substrate concentration and low flow rate. After 85 days of operation, the removal efficiencies of NH 4 + -N, NO 2 - -N, and total nitrogen reached 98.7%, 99.3%, and 89.3%, respectively. After 144 days of starvation and 30 days of recovery, the better nitrogen removal performance was achieved at a low substrate concentration and high flow rate, and the removal efficiencies were 99.8% （NH 4 + -N）, 99.8% （NO 2 - -N）, and 93.6% （total nitrogen）. During the starvation, extracellular polymeric substances wrapped the ANAMMOX bacteria and kept them intact to resist long-term starvation stress. The expression of nirS , hzsA , and hdh genes ensured the synthesis of nitrite/nitric oxide oxidoreductase, hydrazine synthase, and hydrazine dehydrogenase to maintain ANAMMOX activity. There was no significant difference in the relative abundance of ANAMMOX bacteria before and after starvation recovery. Candidatus Kuenenia had better anti-hunger ability, and the relative abundance increased by more than 86% after 30 days of recovery, confirming its tolerance to long-term starvation.

Co-aggregation of anaerobic microorganisms into suspended microbial biofilms (aggregates) serves ecological and biotechnological functions. Tightly packed aggregates of metabolically interdependent bacteria and archaea play key roles in cycling of carbon and nitrogen. Additionally, in biotechnological applications, such as wastewater treatment, microbial aggregates provide a complete metabolic network to convert complex organic material. Currently, experimental data explaining the mechanisms behind microbial co-aggregation in anoxic environments is scarce and scattered across the literature. To what extent does this process resemble co-aggregation in aerobic environments? Does the limited availability of terminal electron acceptors drive mutualistic microbial relationships, contrary to the commensal relationships observed in oxygen-rich environments? And do co-aggregating bacteria and archaea, which depend on each other to harvest the bare minimum Gibbs energy from energy-poor substrates, use similar cellular mechanisms as those used by pathogenic bacteria that form biofilms? Here, we provide an overview of the current understanding of why and how mixed anaerobic microbial communities co-aggregate and discuss potential future scientific advancements that could improve the study of anaerobic suspended aggregates. KEY POINTS: • Metabolic dependency promotes aggregation of anaerobic bacteria and archaea • Flagella, pili, and adhesins play a role in the formation of anaerobic aggregates • Cyclic di-GMP/AMP signaling may trigger the polysaccharides production in anaerobes., (© 2024. The Author(s).)

Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of Desulfatibacillum alkenivorans strain PF2803 T , a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen- and sulfur-containing polar head groups, moving beyond a reliance on conventional nonphospholipid types., Competing Interests: Competing interests statement:The authors declare no competing interest.

Background: Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea., Results: We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1 T and A2), Spirochaetota (strains M1 T , M2, and S2), Bacteroidota (strains B1 T , B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3 T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea., Conclusions: This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract., (© 2024. The Author(s).)

In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH 4 ), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H 2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na + -dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H 2 produced to reduce NAD(P) + to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment., Competing Interests: The authors declare no conflict of interest.

Nitrite-dependent anaerobic methane oxidation (n-DAMO) is a novel denitrification process that simultaneously further removes and utilizes methane from anaerobic effluent from wastewater treatment plants. However, the metabolic activity of n-DAMO bacteria is relative low for practical application. In this study, conductive magnetite was added into lab-scale sequencing batch reactor inoculated with n-DAMO bacteria to study the influence on n-DAMO process. With magnetite amendment, the nitrogen removal rate could reach 34.9 mg N·L -1 d -1 , nearly 2.5 times more than that of control group. Magnetite significantly facilitated the interspecies electron transfer and built electrically connected community with high capacitance. Enzymatic activities of electron transport chain were significantly elevated. Functional gene expression and enzyme activities associated with nitrogen and methane metabolism had been highly up-regulated. These results not only propose a useful strategy in n-DAMO application but also provide insights into the stimulating mechanism of magnetite in n-DAMO process., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C 1 -metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO 2 -fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential., (© 2023 Wiley Periodicals LLC.)

Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The emerging fluoroquinolone antibiotics (FQs) are highly influential in nitrogen removal from livestock wastewater. However, beyond the capability of nitrogen removal, little is known about the molecular mechanisms (e.g., shift of core metabolism and energy allocation) of different anaerobic ammonium-oxidizing bacteria (AnAOB) under continuous FQ stress. This study investigated the effects of ciprofloxacin, ofloxacin and their mixture at concentrations detected in livestock wastewater on two key anammox species in membrane bioreactors. It was found 20 μg/L FQs promoted nitrogen removal efficiency and community stability, and42-51 % of FQs were removed simultaneously. Integrated meta-omics analysis revealed varied gene expression patterns between the two dominant AnAOB, Candidatus Brocadia sapporoensis (B AnAOB) and Candidatus Kuenenia stuttgartiensis (K AnAOB). The nitrogen metabolic processes were bolstered in B AnAOB, while those involved in anammox pathway of K AnAOB were inhibited. This difference was tentatively attributed to the up-regulation of reactive oxygen species scavenger genes (ccp and dxf) and FQ resistance gene (qnrB72) in B AnAOB. Importantly, most enhanced core biosynthesis/metabolism of AnAOB and close cross-feeding with accompanying bacteria were also likely to contribute to their higher levels of biomass yield and metabolism activity under FQ stress. This finding suggests that B AnAOB has the advantage of higher nitrogen metabolism capacity over K AnAOB in livestock wastewater containing FQs, which is helpful for efficient and stable nitrogen removal by the functional anammox species., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Effects of short hydraulic retention time (HRT) in wet weather and long HRT in dry weather on sludge properties, microbial community, and metabolomic of anammox granular system were studied. Results showed under equal nitrogen loading rate (0.4 kg N/(m 3 · d)) conditions, an HRT of 4.41 h was beneficial for total nitrogen removal efficiency (78.9 %). The shorter the HRT, the lower the particle density (1.01±0.34 g/cm 3 ), the lower the settling performance (1.18±0.28 cm/s), and the worse the biomass retention (1.04±0.18 g/L), but the higher the mechanical strength (85.22 Pa). Properly decreasing HRT could increase the permeability of anammox granules, ensuring their activity. Metabolomics analysis indicated that the activity of anaerobic ammonium oxidizing bacteria was promoted by stimulating the metabolic pathways of amino acids and glycerophospholipids. In summary, this research clarified the effect of wet/dry weather on anammox granular system and provided theoretical guidance for the application in engineering., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes - Verrucomicrobia - Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2 T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2 T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2 T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases ( nifDKH ) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2 T (= DSM 113125 T = MCCC 1K08672 T ) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2 T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal., Competing Interests: The authors declare no conflict of interest.

Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH 4 . In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics. In addition to the reported SAOB classified in the genera Tepidanaerobacter , Desulfotomaculum , and Thermodesulfovibrio , we identified a number of potential SAOB that are affiliated with Clostridia , Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. The potential SAOB possessing the glycine-mediated acetate oxidation pathway dominates SAOB communities. Moreover, formate appeared to be the main product of the acetate degradation by the most active potential SAOB. We identified the methanogen partner of these potential SAOB in the acetate-fed chemostat as Methanosarcina thermophila . The dominated potential SAOB in each chemostat had similar metabolic characteristics, even though they were in different fatty-acid-fed chemostats. These novel syntrophic lineages are prevalent and may play critical roles in thermophilic methanogenic reactors. This study expands our understanding of the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders and presents novel insights into how they interact with methanogens.IMPORTANCECombining reactor operation with omics provides insights into novel uncultured syntrophic acetate degraders and how they perform in thermophilic anaerobic digesters. This improves our understanding of syntrophic acetate degradation and contributes to the background knowledge necessary to better control and optimize anaerobic digestion processes., Competing Interests: The authors declare no conflict of interest.

Wastes recycling and reutilization technique could simultaneously fulfill waste control and energy recovery sustainably, which has attracted increasing attention. This work proposed a novel waste reuse technology utilizing ceramsite and amended Fe 2 O 3 -ceramsite made from waste activated sludge (WAS) as additives to promote the yield of methane from WAS anaerobic digestion (AD). Experimental results demonstrated that compared to the control (85.05 ± 0.2 mL CH 4 /g-VS), the cumulative methane yield was effectively enhanced by 14% and 40% when ceramsite and Fe 2 O 3 -ceramsite were added. Further investigation revealed that ceramsite, especially the Fe 2 O 3 -ceramsite, enriched the populations of key anaerobes involved in hydrolysis, acidification, and methanogenesis. Meanwhile, potential syntrophic metabolisms between syntrophic bacteria and methanogens were confirmed in the Fe 2 O 3 -ceramsite AD system. Mechanisms studies exhibited that ceramsite and Fe 2 O 3 -ceramsite reinforced intermediate processes for methane production. The favorable pore structure, enhanced Fe (III) reduction capacity and conductivity also contributed a lot to the AD process., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Importance: Respiration is a fundamental and complex process that bacteria use to produce energy. Despite aerobic respiration being the most common, some bacteria make use of a mode of respiration in the absence of oxygen, called anaerobic respiration, which can yield advantages in adaptation to various environmental conditions. Denitrification is part of this respiratory process ensuring higher respiratory flexibility under oxygen depletion. Here, we report for the first time the evidence of anaerobic growth of Brucella spp. under denitrifying conditions, which implies that this genus should be reconsidered as facultative anaerobic. Our study further describes that efficient denitrification is not equally found within the Brucella genus, with atypical species showing a greater ability to denitrify, correlated with higher expression of the genes involved, as compared to classical species., Competing Interests: The authors declare no conflict of interest.

The human gut microbiome modulates physiological functions and pathologies; however, a mechanistic understanding of microbe-host and microbe-microbe interactions remains elusive owing to a lack of suitable approaches to monitor obligate anaerobic bacterial populations. Common genetically encoded fluorescent protein reporters, derived from the green fluorescent protein, require an oxidation step for fluorescent light emission and therefore are not suitable for use in anaerobic microbes residing in the intestine. Fluorescence in situ hybridization is a useful alternative to visualize bacterial communities in their natural niche; however, it requires tissue fixation. We therefore developed an approach for the real-time detection and monitoring of live communities of anaerobic gut commensals in their natural environment. We leverage the bacterial cells' reliance on sugars for macromolecule synthesis in combinatorial click chemistry labeling, where the addition of azide-modified sugars to the culturing media enables the fluorescence labeling of newly synthesized molecules via the addition of combinations of exogenous fluorophores conjugated to cyclooctynes. This process is suitable for labeling communities of live anaerobic gut bacteria with combinations of fluorophores that do not require oxygen to mature and fluoresce, and that can be detected over time in their natural environments. The labeling procedure requires 4-9 d, depending on the varying growth rates of different bacterial strains, and an additional 1-2 d for the detection and monitoring steps. The protocol can be completed by users with basic expertise in bacterial culturing., (© 2023. Springer Nature Limited.)

The sludge fermentation-driven biological nitrogen removal (SFBNR) has garnered increasing attention due to its efficient carbon resource utilization from waste activated sludge (WAS). This study successfully extended the application of this technique to a 38 m 3 reactor, facilitating a daily ultra-low carbon to nitrogen ratio (<1) wastewater treatment capacity of 16 tons and a WAS capacity of 500 L. After 185-days operation, the system demonstrated commendable performance with a denitrification efficiency (DNE) of 93.22 % and a sludge reduction efficiency (SRE) of 72.07 %. To better understand the potential mechanisms, various functional bacteria interactions were revealed by co-occurrence network analysis. The results unveiled module hubs (e.g., Anaerolineaceae, Denitratisoma, and Candidatus Brocadia) and connectors (e.g., Tuaera and Candidatus Alysiosphaera) in the network exhibited synergistic relationships facilitated by carbon metabolism and nitrogen cycling. Furthermore, the interaction between biofilm sludge (BS) and suspended sludge (SS) contributed to the in-situ enrichment of anaerobic ammonium oxidizing bacteria (AnAOB), whose abundance in BS reached 1.8 % (200-times higher than in SS) after six months, and the suspend-biofilm interface served as a hotspot for anammox activity., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (Se IV RB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative Se IV RB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative Se IV RB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Polyphenols are abundant in nature, and their anaerobic biodegradation by gut and soil bacteria is a topic of great interest. The O 2 requirement of phenol oxidases is thought to explain the microbial inertness of phenolic compounds in anoxic environments, such as peatlands, termed the enzyme latch hypothesis. A caveat of this model is that certain phenols are known to be degraded by strict anaerobic bacteria, although the biochemical basis for this process is incompletely understood. Here, we report the discovery and characterization of a gene cluster in the environmental bacterium Clostridium scatologenes for the degradation phloroglucinol (1,3,5-trihydroxybenzene), a key intermediate in the anaerobic degradation of flavonoids and tannins, which constitute the most abundant polyphenols in nature. The gene cluster encodes the key C-C cleavage enzyme dihydrophloroglucinol cyclohydrolase, as well as ( S )-3-hydroxy-5-oxo-hexanoate dehydrogenase and triacetate acetoacetate-lyase, which enable phloroglucinol to be utilized as a carbon and energy source. Bioinformatics studies revealed the presence of this gene cluster in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on human health and carbon preservation in peat soils and other anaerobic environmental niches. IMPORTANCE This study provides novel insights into the microbiota's anaerobic metabolism of phloroglucinol, a critical intermediate in the degradation of polyphenols in plants. Elucidation of this anaerobic pathway reveals enzymatic mechanisms for the degradation of phloroglucinol into short-chain fatty acids and acetyl-CoA, which are used as a carbon and energy source for bacterium growth. Bioinformatics studies suggested the prevalence of this pathway in phylogenetically and metabolically diverse gut and environmental bacteria, with potential impacts on carbon preservation in peat soils and human gut health., Competing Interests: The authors declare no conflict of interest.

1 The combination of carbonaceous materials and microbial degradation is an attractive measure in improving the removal efficiency of organic pollutants in water environment. In this study, the anaerobic dechlorination in a coupled system of ball-milled plastic chars (BMPCs) and the microbial consortium were investigated. The anaerobic microorganism cultured from raw sludge (CAM) contributed to the dechlorination of the 2,4,6-trichlorophenol (2,4,6-TCP) into 4-chlorophenol (4-CP) as the final product via ortho-dechlorination in all testing groups. The dechlorination rate was accelerated in different BMBC plus CAM groups than that in only CAM group (0.048 d -1 ), of which, it was greater in BMPC-500 plus CAM group (0.375 d -1 ) than that in BMPC-700 plus CAM group (0.171 d -1 ). The electron exchange capacity (EEC) of BMPCs decreased with the increase of pyrolysis temperature (0.053 mmol e - /g for BMPC-500 and 0.037 mmol e - /g for BMPC-700), which directly affected anaerobic dechlorination. Direct interspecies electron transfer (DIET) of BMPCs also boosted the biogas yield by 1.5 times compared to that without BMPCs. Microbial community analysis illustrated that BMPCs helped to enrich the putative dechlorinating bacteria. The abundance of Clostridium&#95;aenus&#95;stricto&#95;12, as a dominant dechlorinator, significantly increased from 0.02 % to 11.3 % (without BMPCs), 39.76 % (BMPC-500) and 9.3 % (BMPC-700), and followed by， Prevotella and Megaspheara, which was reported to take part in anaerobic dechlorination and digestion as H 2 producers, also increased in the presence of BMPC. This study contributes to the realization of 2,4,6-TCP in-situ reduction technology and provides a scientific reference for anaerobic dechlorination by cultured anaerobes combined with BMPCs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

H 2 -producing microorganisms are a promising source of sustainable biohydrogen. However, most H 2 -producing microorganisms are anaerobes, which are difficult to cultivate and characterize. While several methods for measuring H 2 exist, common H 2 sensors often require oxygen, making them unsuitable for anaerobic processes. Other sensors can often not be operated at high gas humidity. Thus, we applied thermal conductivity (TC) sensors and developed a parallelized, online H 2 monitoring for time-efficient characterization of H 2 production by anaerobes. Since TC sensors are nonspecific for H 2 , the cross-sensitivity of the sensors was evaluated regarding temperature, gas humidity, and CO 2 concentrations. The systems' measurement range was validated with two anaerobes: a high H 2 -producer (Clostridium pasteurianum) and a low H 2 -producer (Phocaeicola vulgatus). Online monitoring of H 2 production in shake flask cultivations was demonstrated, and H 2 transfer rates were derived. Combined with online CO 2 and pressure measurements, molar gas balances of the cultivations were closed, and an anaerobic respiration quotient was calculated. Thus, insight into the effect of medium components and inhibitory cultivation conditions on H 2 production with the model anaerobes was gained. The presented online H 2 monitoring method can accelerate the characterization of anaerobes for biohydrogen production and reveal metabolic changes without expensive equipment and offline analysis., (© 2023 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals LLC.)

Ketone bodies, including acetoacetate, 3-hydroxybutyrate, and acetone, are produced in the liver of animals during glucose starvation. Enzymes for the metabolism of ( R )-3-hydroxybutyrate have been extensively studied, but little is known about the metabolism of its enantiomer ( S )-3-hydroxybutyrate. Here, we report the characterization of a novel pathway for the degradation of ( S )-3-hydroxybutyrate in anaerobic bacteria. We identify and characterize a stereospecific ( S )-3-hydroxylbutyrate dehydrogenase (3SHBDH) from Desulfotomaculum ruminis, which catalyzes the reversible NAD(P)H-dependent reduction of acetoacetate to form ( S )-3-hydroxybutyrate. 3SHBDH also catalyzes oxidation of d-threonine (2 R , 3 S ) and l-allo-threonine (2 S , 3 S ), consistent with its specificity for β-(3 S )-hydroxy acids. Isothermal calorimetry experiments support a sequential mechanism involving binding of NADH prior to ( S )-3-hydroxybutyrate. Homologs of 3SHBDH are present in anaerobic fermenting and sulfite-reducing bacteria, and experiments with Clostridium pasteurianum showed that 3SHBDH, acetate CoA-transferase (YdiF), and ( S )-3-hydroxybutyryl-CoA dehydrogenase (Hbd) are involved together in the degradation of ( S )-3-hydroxybutyrate as a carbon and energy source for growth. ( S )-3-hydroxybutyrate is a human metabolic marker and a chiral precursor for chemical synthesis, suggesting potential applications of 3SHBDH in diagnostics or the chemicals industry. IMPORTANCE ( R )-3-hydroxybutyrate is well studied as a component of ketone bodies produced by the liver and of bacterial polyesters. However, the biochemistry of its enantiomer ( S )-3-hydroxybutyrate is poorly understood. This study describes the identification and characterization of a stereospecific ( S )-3-hydroxylbutyrate dehydrogenase and its function in a metabolic pathway for the degradation of ( S )-3-hydroxybutyrate as a carbon and energy source in anaerobic bacteria. ( S )-3-hydroxybutyrate is a mammalian metabolic marker and a precursor for chemical synthesis and bioplastics, suggesting potential applications of these enzymes in diagnostics and biotechnology., Competing Interests: The authors declare no conflict of interest.

Prokaryotes that can oxidize carbon monoxide (CO oxidizers) can use this gas as a source of carbon or energy. They oxidize carbon monoxide with carbon monoxide dehydrogenases (CODHs): these are divided into nickel-containing CODH (Ni-CODH), which are sensitive to O 2 , and molybdenum-containing CODH (Mo-CODH), which can function aerobically. The oxygen conditions required for CO oxidizers to oxidize CO may be limited, as those which have been isolated and characterized so far contain either Ni- or Mo-CODH. Here, we report a novel CO oxidizer, Parageobacillus sp. G301, which is capable of CO oxidation using both types of CODH based on genomic and physiological characterization. This thermophilic, facultatively anaerobic Bacillota bacterium was isolated from the sediments of a freshwater lake. Genomic analyses revealed that strain G301 possessed both Ni-CODH and Mo-CODH. Genome-based reconstruction of its respiratory machinery and physiological investigations indicated that CO oxidation by Ni-CODH was coupled with H 2 production (proton reduction), whereas CO oxidation by Mo-CODH was coupled with O 2 reduction under aerobic conditions and nitrate reduction under anaerobic conditions. G301 would thus be able to thrive via CO oxidation under a wide range of conditions, from aerobic environments to anaerobic environments, even with no terminal electron acceptors other than protons. Comparative genome analyses revealed no significant differences in genome structures and encoded cellular functions, except for CO oxidation between CO oxidizers and non-CO oxidizers in the genus Parageobacillus ; CO oxidation genes are retained exclusively for CO metabolism and related respiration. IMPORTANCE Microbial CO oxidation has received much attention because it contributes to global carbon cycling in addition to functioning as a remover of CO, which is toxic to many organisms. Some microbial CO oxidizers, including both bacteria and archaea, exhibit sister relationships with non-CO oxidizers even in genus-level monophyletic groups. In this study, we demonstrated that a new isolate, Parageobacillus sp. G301, is capable of both anaerobic (hydrogenogenic) and aerobic CO oxidation, which has not been previously reported. The discovery of this new isolate, which is versatile in CO metabolism, will accelerate research on CO oxidizers with diverse CO metabolisms, expanding our understanding of microbial diversity. Through comparative genomic analyses, we propose that CO oxidation genes are not essential genetic elements in the genus Parageobacillus , providing insights into the factors which shape the punctate distribution of CO oxidizers in the prokaryote tree, even in genus-level monophyletic groups., Competing Interests: The authors declare no conflict of interest.

The sole H 2 and O 2 usually promote chlorinated hydrocarbons (CHCs) biotransformation by several mechanisms, including reductive dechlorination and aerobic oxidation. However, the mechanism of the CHCs transformation in joint H 2 and O 2 system (H 2 /O 2 system) is still unclear. In this study, the degradation kinetics of trichloroethene (TCE) were investigated and DNA stable isotope probing (DNA-SIP) were used to explore the synergistic mechanism of functional microorganisms on TCE degradation under the condition of H 2 /O 2 coexistence. In the H 2 /O 2 microcosm, TCE was significantly removed by 13.00 μM within 40 days, much higher than N 2 , H 2 and O 2 microcosms, and 1,1-DCE was detected as an intermediate. DNA-SIP technology identified three anaerobic TCE metabolizers, five aerobic TCE metabolizers, nine hydrogen-oxidizing bacteria (HOB), some TCE metabolizers utilizing limited O 2 , and some anaerobic dechlorinating bacteria reductively using H 2 to dechlorinate TCE. It is also confirmed for the first time that 3 OUTs belonging to Methyloversatilis and SH-PL14 can simultaneously utilize H 2 and O 2 as energy sources to grow and metabolize TCE or 1,1-DCE. HOB may provide carbon sources or electron acceptors or donors for TCE biotransformation. These findings confirm the coexistence of anaerobic and aerobic TCE metabolizers and degraders, which synergistically promoted the conversion of TCE in the joint H 2 /O 2 system. Our results provide more information about the functional microbe resources and synergetic mechanisms for TCE degradation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Dosing zero valent iron (ZVI) or sodium hydroxide (NaOH) is the common method of addressing acidification in anaerobic digestion (AD) systems; however, few studies have discussed and compared their effects on microbial metabolism. In the present study, microbial syntrophy and metabolic pathways under ZVI and NaOH regulation are comparatively analyzed through microbial network analysis and metagenomic/metaproteomic analyses. CH 4 yield in the ZVI reactor was 414 mL/gVS, an increase of 23% when compared with that in the reactor with NaOH dosing (336 mL/gVS). The methanogenesis recovery period in the ZVI reactor (37 days) was shorter than that in the NaOH reactor (48 days). Co-occurrence networks indicated that ZVI promoted Methanoculleus and Methanosarcina to establish a complex syntrophic association with SAO bacteria (Syntrophaceticus and Aminobacterium) and syntrophic acetogens (Syntrophomonas), strengthening SAO-hydrogenotrophic methanogenesis (HM) and acetoclastic methanogenesis (AM) pathways simultaneously. Metagenomic analysis showed that the relative abundance of mcrA and fwdB in the ZVI reactor was higher 27% than that in the NaOH reactor. Furthermore, through metaproteomics analysis, much more enzymes related to glucose degradation, bioconversion of butyric acid and pyruvate, conversion of formate and acetate to CO 2 , and production of CH 4 from acetate and CO 2 were significantly upregulated under ZVI regulation than under NaOH regulation (fold change relative to control [FC] > 1.5, p < 0.05). The results of the present study enhance our understanding of methanogenic mechanisms under the regulation of ZVI, providing a theoretical basis for its practical application in AD systems experiencing VFA suppression., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Fats, oil and grease, and their hydrolyzed counterparts-long chain fatty acids (LCFA) make up a large fraction of numerous wastewaters and are challenging to degrade anaerobically, more so, in low temperature anaerobic digestion (LtAD) systems. Herein, we perform a comparative analysis of publicly available Illumina 16S rRNA datasets generated from LCFA-degrading anaerobic microbiomes at low temperatures (10 and 20 °C) to comprehend the factors affecting microbial community dynamics. The various factors considered were the inoculum, substrate and operational characteristics, the reactor operation mode and reactor configuration, and the type of nucleic acid sequenced. We found that LCFA-degrading anaerobic microbiomes were differentiated primarily by inoculum characteristics (inoculum source and morphology) in comparison to the other factors tested. Inoculum characteristics prominently shaped the species richness, species evenness and beta-diversity patterns in the microbiomes even after long term operation of continuous reactors up to 150 days, implying the choice of inoculum needs careful consideration. The generalised additive models represented through beta diversity contour plots revealed that psychrophilic bacteria RBG-13-54-9 from family Anaerolineae, and taxa WCHB1-41 and Williamwhitmania were highly abundant in LCFA-fed microbial niches, suggesting their role in anaerobic treatment of LCFAs at low temperatures of 10-20 °C. Overall, we showed that the following bacterial genera: uncultured Propionibacteriaceae, Longilinea, Christensenellaceae R7 group, Lactivibrio, candidatus Caldatribacterium, Aminicenantales, Syntrophus, Syntrophomonas, Smithella, RBG-13-54-9, WCHB1-41, Trichococcus, Proteiniclasticum, SBR1031, Lutibacter and Lentimicrobium have prominent roles in LtAD of LCFA-rich wastewaters at 10-20 °C. This study provides molecular insights of anaerobic LCFA degradation under low temperatures from collated datasets and will aid in improving LtAD systems for treating LCFA-rich wastewaters., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.

Nanoscale zero-valent iron (nZVI) has the potential to degrade a diversity of chlorinated compounds, and it is widely used for remediation of contaminated groundwaters. However, some frequently detected contaminants such as dichloromethane (DCM) and 1,2-dichloroethane (1,2-DCA) have shown nearly no reactivity with nZVI. Here, we tested the feasibility of combining anaerobic dechlorinating bacteria, Dehalobacterium and Dehalogenimonas, and nZVI as a treatment train to detoxify chlorinated methanes (i.e., chloroform-CF- and DCM), and 1,2-DCA. First, we showed that CF (500 μM) was fully degraded by 1 g/L nZVI to DCM as a major by-product, which was susceptible to fermentation by Dehalobacterium to innocuous products. Our results indicate that soluble compounds released by nZVI might cause an inhibitory impact on Dehalobacterium activity, avoiding DCM depletion. The DCM dechlorination activity was recovered when transferred to a fresh medium without nZVI. The increase in H 2 production and pH was discarded as potential inhibitors. Similarly, a Dehalogenimonas-containing culture was unable to dichloroeliminate 1,2-DCA when exposed to 1 g/L nZVI, but dechlorinating activity was also recovered when transferred to nZVI-free media. The recovery of the dechlorinating activity of Dehalobacterium and Dehalogenimonas suggests that combination of nZVI and bioremediation techniques can be feasible under field conditions where dilution processes can alleviate the impact of the potential inhibitory soluble compounds., (© 2023. The Author(s).)

Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N 2 . The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH 4 + -N/L/d and 62.61 ± 4.17 mgNO 3 - -N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH 4 /NO 3 - molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification., Competing Interests: Declaration of competing interest The authors declare no competing financial interest., (Copyright © 2022 Elsevier B.V. All rights reserved.)

In this research, a comprehensive study was carried out on the removal of carbon tetrachloride (CT) in the anaerobic co-metabolism (ACM) reactor. The experiments showed that when the hydraulic retention time (HRT) was 36 h, pH was 7, and influent CT was 2.5mg/L, the average removal efficiency reached 82.45 ± 2.56% in the glucose co-metabolism substrate reactor, exhibiting a dramatic excellent difference in reaction performance from the other two reactors (p < 0.05) and a favorable tolerance on the CT shock loading. The content of extracellular polymeric substances (EPS) and volatile fatty acids (VFA) demonstrated that glucose could supply more energy to protect the microorganisms, which was the appropriate external energy source. Moreover, microbial community structure and biostatistics analysis demonstrated that Pseudomonas was the most important dechlorination bacteria in ACM reactors, which might via dehalogenation process mediate the transformation of CT. The succession of methanogenic bacteria further demonstrated that CT degradation using co-digestion require to destroy hydrogenotrophic methane generation pathway and the external energy substances could make up the lack of hydrogen in the treatment of CT. The change of intermediate products hinted that anaerobic dechlorination process of CT in an ACM reactor was a sequential dechlorination process, and major transformation products measured were CF. Overall, this study has improved our understanding of the roles of CT degradation process in ACM reactors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Genomic analyses indicate that anaerobic bacteria represent a neglected source of natural products. Whereas a limited number of polyketides have been reported from anaerobes, products of type III polyketide synthases (PKSs) have remained unknown. We found a highly conserved biosynthetic gene cluster (BGC) comprising genes putatively encoding a type III PKS and a methyltransferase in genomes of the Negativicutes, strictly anaerobic, diderm bacteria. By in vivo and in vitro expression of a type III PKS gene, dquA from the oak-associated Dendrosporobacter quercicolus in E. coli we show production of long-chain alkylpyrones. Intriguingly, this BGC is specific for sporulating Sporomusaceae but absent in related Negativicutes that do not sporulate, thus suggesting a physiological role., (© 2022 The Authors. ChemBioChem published by Wiley-VCH GmbH.)

In the past 20 years, there has been a major stride in understanding the core mechanism of anaerobic ammonium-oxidizing (anammox) bacteria, but there are still several discussion points on their survival strategies. Here, we discovered a new genus of anammox bacteria in a full-scale wastewater-treating biofilm system, tentatively named "Candidatus Loosdrechtia aerotolerans". Next to genes of all core anammox metabolisms, it encoded and transcribed genes involved in the dissimilatory nitrate reduction to ammonium (DNRA), which coupled to oxidation of small organic acids, could be used to replenish ammonium and sustain their metabolism. Surprisingly, it uniquely harbored a new ferredoxin-dependent nitrate reductase, which has not yet been found in any other anammox genome and might confer a selective advantage to it in nitrate assimilation. Similar to many other microorganisms, superoxide dismutase and catalase related to oxidative stress resistance were encoded and transcribed by "Ca. Loosdrechtia aerotolerans". Interestingly, bilirubin oxidase (BOD), likely involved in oxygen resistance of anammox bacteria under fluctuating oxygen concentrations, was identified in "Ca. Loosdrechtia aerotolerans" and four Ca. Brocadia genomes, and its activity was demonstrated using purified heterologously expressed proteins. A following survey of oxygen-active proteins in anammox bacteria revealed the presence of other previously undetected oxygen defense systems. The novel cbb3-type cytochrome c oxidase and bifunctional catalase-peroxidase may confer a selective advantage to Ca. Kuenenia and Ca. Scalindua that face frequent changes in oxygen concentrations. The discovery of this new genus significantly broadens our understanding of the ecophysiology of anammox bacteria. Furthermore, the diverse oxygen tolerance strategies employed by distinct anammox bacteria advance our understanding of their niche adaptability and provide valuable insight for the operation of anammox-based wastewater treatment systems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier Ltd.)

The combination of microbial reductive dechlorination and aerobic oxidation (RD-AO) process was proposed to be a promising strategy for extensive bioremediation of highly chlorinated polychlorinated biphenyls (PCBs). Nonetheless, experimental evidence on the impact of the RD on subsequent AO in anaerobic-aerobic two-stage treatment remains scarce. The present study applied stable-isotope probing (SIP) to explore the RD-AO mediated degradation of PCBs in an e-waste-contaminated soil. The RD-AO treatment resulted in 37.1 % and 48.2 % degradation of PCB180 and PCB9, respectively, while the PCB9 degradation efficiency decreased compared to the sole AO (81.2 %). The inhibition of PCB aerobic degradation might be caused by the alteration of aerobic bacterial community, which was proved by a higher abundance of anaerobic bacteria and a lower abundance of aerobic bacteria being observed in the aerobic stage of RD-AO. Further evidence was obtained using DNA-SIP that the anaerobic stage altered the PCB degraders' community structures and changed three of the five degraders. There were four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) identified as PCB degraders for the first time. Interestingly, three of them were found in RD-AO microcosm, suggesting that anaerobic-aerobic two-stage treatment can recruit novel bacteria involved in PCBs aerobic degradation. The present study provided novel insight into the synergistic integration of anaerobic and aerobic processes for extensive degradation of highly chlorinated PCBs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Biomethanization of crude rice straw (RS) was enhanced by a coupled effectiveness of sulphonated graphene (SGR) with sludge rich anaerobes (SRA). A reduction of 19.2 ± 1.32% for cellulose, 40.8 ± 3.7% for hemicellulose and 30.8 ± 2.4% for lignin was achieved with addition of SRA after fermentation of 60 days. The abundance of hydrolytic microbes in SRA i.e. Acidobacteria, Bacteroidetes, Chloroflexi and Proteobacteria caused RS structure liquefaction and dissolution. The reduction of cellulose, hemicellulose and lignin boosted to 92.3 ± 1.5, 84.9 ± 3.5 and 97.0 ± 1.8% respectively with SGR catalyst addition of 100 mg/gVS. Reducing sugars, phenols and volatile fatty acids (VFAs) were subsequently utilized by bacteria and archaea species of Methanosphaera, Methanocella, Candidatus Methanoregula, Methanolinea and Methanosaeta. The biogas yield was 92 ± 3.1 mL/gRS and methane content amounted to 68 ± 4.6% % at SGR catalyst of 80 mg/gVS. These findings show the potential of using SRA/SGR to improve the RS fermentation with a novel application for biogas productivity., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

In this study, single-chamber three-electrode electrochemical sequencing batch reactor (ESBR) was set up to investigate the impact of applying potential on denitrifying anaerobic methane oxidation (DAMO) process. When the applied potential was +0.8 V, the conversion rate of nitrite to nitrogen was superior to those of other potentials. With the optimal potential of +0.8 V for 60 days, the nitrite removal rate of ESBR could reach 3.34 ± 0.28 mg N/L/d, which was 4.5 times more than that of the non-current control (0.74 ± 0.16 mg N/L/d). The DAMO functional bacteria Candidatus Methylomirabilis exhibited noticeable enrichment under applying potential, and its functional gene of pmoA was significantly expressed. Through untargeted LC-MS metabolomics analysis, applied potential was shown to affect the regulation of prior metabolites including spermidine, spermine and glycerophosphocholine that were related to the metabolic pathways of glycerophospholipid metabolism and arginine and proline metabolism, which had positive effects on DAMO process. These results show that applying electric potential could be a useful strategy in DAMO process used for methane and nitrogen removal., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Colorectal cancer (CRC) is one of the most common malignant diseases. Generally, stoma construction is performed following surgery for the resection of the primary tumor in patients with CRC. The association of CRC with the gut microbiota has been widely reported, and the gut microbiota is known to play an important role in the carcinogenesis, progression, and treatment of CRC. In this study, we compared the microbiota of patients with CRC between with and without a stoma using fecal metagenomic sequencing data from SCRUM-Japan MONSTAR-SCREEN, a joint industry-academia cancer research project in Japan. We found that the composition of anaerobes was reduced in patients with a stoma. In particular, the abundance of Alistipes , Akkermansia , Intestinimonas , and methane-producing archaea decreased. We also compared gene function (e.g., KEGG Orthology and KEGG pathway) and found that gene function for methane and short-chain fatty acids (SCFAs) production was underrepresented in patients with a stoma. Furthermore, a stoma decreased Shannon diversity based on taxonomic composition but increased that of the KEGG pathway. These results suggest that the feces of patients with a stoma have a reduced abundance of favorable microbes for cancer immunotherapy. In conclusion, we showed that a stoma alters the taxonomic and functional profiles in feces and may be a confounding factor in fecal microbiota analysis., Competing Interests: SK reports honoraria from Eli Lilly, Taiho, Ono, Bristol-Myers Squibb, Chugai, Bayer, Merck Serono, Daiichi Sankyo, Eisai; and research funding from Taiho, Eli Lilly, MSD, Chugai, Nobelpharma, Ono, Daiichi Sankyo, and Yansen.TD reports honoraria from Sawai Pharmaceutical; speakers’ bureau from Sysmex; and research funding from MSD and Ono Pharmaceutical. HY reports honoraria from Taiho Pharmaceutical, Chugai, Bristol-Myers Squibb, Daiichi-Sankyo, Terumo, Eli Lilly Japan, Merck Biopharma, Yakult Honsha, and Bayer Yakuhin; and research funding from MSD, Daiichi-Sankyo, and Ono Pharmaceutical. MG reports honoraria from Yakult Honsha, Taiho Pharmaceutical, Daiichi-Sankyo, Eisai, and Ono Pharmaceutical; and research funding from Chugai, Taiho Pharmaceutical, Nippon Kayaku, Ono Pharmaceutical, and Eli Lilly. YK reports honoraria from Asahi Kasei Pharma, Bayer Yakuhin, Bristol-Myers Squibb., Chugai, Daiichi-Sankyo, Eli Lilly, Kyowa Kirin, Medical Review, Merck Biopharma, Mitsubishi Tanabe Pharma, Moroo, Nipro, Ono Pharmaceutical, Pfizer Japan, Sanofi, Shire Japan, and Taiho Pharmaceutical; and research funding from A2 Healthcare, Asahi Kasei Pharma, Astellas Pharma, Bayer Yakuhin, Daiichi-Sankyo, Sumitomo Dainippon Pharma, Eisai, Mediscience Planning, NanoCarrier, Ono Pharmaceutical, Parexel International, Sanofi-aventis, Shionogi & Co., Ltd., Taiho Pharmaceutical, Yakult Honsha, Incyte, IQVIA, MSD, Nippon Zoki Pharmaceutical, Syneos Health Clinical, and Sysmex. YN reports research grants from Taiho Pharmaceutical, Chugai Pharmaceutical, Guardant Health, Genomedia, Daiichi Sankyo, Seagen, and Roche Diagnostics. HB reports honoraria from Taiho Pharmaceutical, Lilly Japan, Takeda Pharmaceutical, Chugai, Sanofi, and Yakult Honsha: and research funding from AstraZeneca and Sysmex. TY reports honoraria from Taiho Pharmaceutical, Chugai Pharmaceutical, Eli Lilly, Merck Biopharma, Bayer Yakuhin, Ono Pharmaceutical, and MSD; and research funding from Ono Pharmaceutical, Sanofi, Daiichi Sankyo, PAREXEL International, Pfizer Japan, Taiho Pharmaceutical, MSD, Amgen, Genomedia, Sysmex, Chugai Pharmaceutical, and Nippon Boehringer Ingelheim KT reports honoraria from SRL Diagnostics, DNA Chip Research, Chugai, Novartis, Takeda, MSD, Sysmex, Nippon Kayaku, Illumina, Fujitsu, Varian Medical Systems, Miyarisan Pharmaceutical, Bristol-Myers Squibb, AstraZeneca, and Novartis. RY reports honoraria from Takeda Pharmaceutical. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be constructed as a potential conflict of interest., (Copyright © 2022 Sakai, Aoshima, Sawada, Horasawa, Yoshikawa, Fujisawa, Kadowaki, Denda, Matsuhashi, Yasui, Goto, Yamazaki, Komatsu, Nakanishi, Nakamura, Bando, Hamaya, Kageyama, Yoshino, Tsuchihara and Yamashita.)

A large amount of long-chain fatty acids (LCFA) are generated after lipids hydrolysis in anaerobic digestion (AD), and LCFA are difficult to be biodegraded. This study showed that hydrochar (HC), which was produced during the hydrothermal liquefaction of organic wastes, significantly increased the methane production rate (by 56.9%) of oleate, a typical refractory model LCFA. Genomic-centric metatranscriptomics analysis revealed that three novel microbes (Bin138 Spirochaetota sp., Bin35 Smithellaceae sp., and Bin54 Desulfomonilia sp.) that were capable of degrading LCFA were enriched by HC, which played an important role in the degradation of oleate. LCFA was degraded to acetate through the well-known LCFA β-oxidation pathway and the combined β-oxidation and butyrate oxidation pathway. In addition, it was found that HC promoted the direct interspecies electron transfer (DIET) between Methanothrix sp. and Bin54 Desulfomonilia sp. The enriched new types of LCFA-degrading bacteria and the promotion of DIET contributed to the improved methane production rate of oleate by HC. IMPORTANCE Long-chain fatty acids (LCFA) are difficult to be degraded in anaerobic digestion (AD), and the known LCFA degrading bacteria are only limited to the families Syntrophomonadaceae and Syntrophaceae . Here, we found that hydrochar effectively promoted AD of LCFA, and the new LCFA-degrading bacteria and a new metabolic pathway were also revealed based on genomic-centric metatranscriptomic analysis. This study provided a new method for enhancing the AD of organic wastes with high content of LCFA and increased the understanding of the microbes and their metabolic pathways involved in AD of LCFA.

Tetrabromobisphenol A (TBBPA) has extensive applications in various fields; its release into ecosystems and the potential toxic effects on organisms are becoming major concerns. Here, we investigated the effects of TBBPA on anaerobic digestion, whose process is closely related to the carbon cycles under anaerobic conditions. The results revealed that TBBPA exhibited dose-dependent hormesis-like effects on methane production from glucose, i.e., the presence of 0.1 mg/L TBBPA increased the methane production rate by 8.79%, but 1.0-4.0 mg/L TBBPA caused 3.45-28.98% of decrement. We found that TBBPA was bound by the tyrosine-like proteins of the extracellular polymeric substances of anaerobes and induced the increase of reactive oxygen species, whose slight accumulation stimulated the metabolism activities but high accumulation increased the apoptosis of anaerobes. Owing to the differences between individual anaerobes in tolerance, TBBPA at 0.1 mg/L stimulated the acidogenesis and hydrogenotrophic methanogenesis, whereas higher levels (i.e., 1.0-4.0 mg/L) severely restrained all of the processes of acidogenesis, acetogenesis, and methanogenesis. Along with the accumulation of bisphenol A (BPA) produced from TBBPA by Longilinea sp. and Pseudomonas sp., the methanogenic pathway was partly shifted from acetate-dependent to hydrogen-dependent direction, and the activities of carbon monoxide dehydrogenase and acetyl-CoA decarbonylase/synthase were inhibited, while acetate kinase and F420 were hormetically affected. These findings elucidated the mechanism of anaerobic syntrophic consortium responses to TBBPA, supplementing the potential environmental risks of brominated flame retardants.

The serious environmental problem caused by traditional plastics has stimulated the popularization of biodegradable plastics (BPs). However, the rigorous prerequisite for the efficient degradation of BPs has not eliminated its potential hazard to nature. In most biosystems exists the anaerobic environment, but it is still controversial whether BPs can be degraded under such condition. Therefore, this study systematically assessed the anaerobic degradation performance of ten common BPs under mesophilic and thermophilic conditions. Results showed that four BPs were degraded evidently under mesophilic condition with the biodegradability of 57.9%-84.6%, while during thermophilic condition, five BPs showed remarkable degradation performance with the biodegradability of 53.0% to 95.7%. According to morphological and micro-structural analysis, the biodegradation of the BPs probably proceeded via bulk and/or surface erosion. Under mesophilic condition, Anaerolineales, Bacteroidales, Clostridiales, SBR1031, and Synergistales appeared to play an important role. During thermophilic condition, the hydrolysis, acidogenesis, and methanogenesis of most BPs were mainly conducted by Coprothermobacter and the archaea Methanothermobacter. This work not only provides crucial data on the anaerobic biodigestibility of BPs but also enriches the understanding of the BPs degradation mechanisms, which are of great importance for future popularization of BP products and simultaneously relieving the environmental pollution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Why oxygen ceases the growth of strictly anaerobic bacteria is a longstanding question, yet the answer remains unclear. Studies have confirmed that the dehydratase-fumarase containing an iron-sulfur cluster ([4Fe-4S]) is inactivated upon exposure to oxygen in the intestinal obligate anaerobe, Bacteroides thetaiotaomicron (B. thetaiotaomicron); this blocks fumarate respiration, which is the essential energy-producing pathway in anaerobes. Here, we substituted the [4Fe-4S]-dependent fumarase in B. thetaiotaomicron with an iron-free isozyme from E. coli (Ec-FumC). Results show that Ec-FumC successfully performed the catalytic function of fumarase in B. thetaiotaomicron, as the fum-mutant strain that expressed Ec-FumC exhibited succinate-producing ability under anaerobic growth conditions. Ec-FumC is oxygen-resistant and remains active to produce fumarate upon aeration; however, B. thetaiotaomicron mutant that expressed Ec-FumC did not convert fumarate to succinate during air exposure. Biochemical assays of inverted membrane vesicles from wild-type B. thetaiotaomicron confirmed that the electron flux from NADH to fumarate was less efficient in the presence of air as compared to that without oxygen. Our findings suggest that the anaerobic fumarate respiration might be paralyzed due to electron dissipations upon aeration of the obligate anaerobe., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The bioconversion of waste activated sludge (WAS) into methane is usually limited by the poor hydrolysis of sludge and/or poor syntrophic methanogenesis during anaerobic digestion (AD). In this study, the underlying mechanism of MOF-808 enhancing hydrolysis and syntrophic methanogenesis during AD process of WAS was investigated. Experimentally, with the effects of MOF-808 (150 mg MOF-808/g Volatile Solid (VS)), the methane production and the proportion of methane in biogas increased by approximately 26.7% and 15.6%, respectively, and the lag phase of methanogenesis decreased by 50.8%, which indicate that MOF-808 enhanced the generation efficiency of methane. The changes in activities of main hydrolytic enzymes with and without MOF-808 (150 mg MOF-808/g VS) during AD process revealed that MOF-808 improved the enzymatic hydrolysis of sludge, and the abiotic hydrolysis of sludge extracellular organic substances by MOF-808 shows that the maximum proportion and the initial increasing rate of low-molecular weight fractions increased by 60% and 583.7%, respectively, indicating that MOF-808 can greatly enhance the hydrolysis degree and rate of sludge via abiotic effect. These demonstrate that MOF-808 enhanced both biological and abiotic hydrolysis of sludge during AD. In addition, changes in the concentrations of acetate kinase and volatile fatty acids (VFAs) with and without MOF-808 (150 mg MOF-808/g VS) during AD process showed that MOF-808 accelerated the bioconversion of VFAs to methane, suggesting MOF-808 has a positive effect on syntrophic metabolism for methanogenesis. Moreover, further analyses of the microbial community structure of sludge samples with and without MOF-808 (150 mg MOF-808/g VS) showed that MOF-808 enriched hydrogen-producing bacteria and mixotrophic methanogens (i.e. Methanosarcina), and changed the methanogenic pathway via accelerating proton transfer between syntrophic anaerobes, especially improving the reduction of CO 2 to methane, and resulting in highly efficient syntrophic methanogenesis. These findings, however, may provide an important reference for enhancing AD efficiency of WAS based on MOF-like materials., (Copyright © 2022. Published by Elsevier Ltd.)

Due to limited diffusion, active root respiration and intense microbial metabolism, rhizosphere and deeper layer of bulk soil often face hypoxic or anaerobic conditions. The majority of the data on plant growth promotion (PGP) and rhizoremediation have been obtained in aerobic conditions using aerobic or facultative anaerobic microbes neglecting anaerobes and actual soil oxygen conditions. Data obtained with a nutrient-rich medium from an aerobic condition do not exactly translate in oxygen-stressed oligotrophic environments of soil, leading to failure of hypothesis and microbial technology for PGP and pollutants remediation. Anaerobes are key players in the soil ecosystems and participate in the different biogeochemical processes of ecological and environmental significance. This Opinion article aims to divert the attention of agricultural and environmental Microbiologists towards neglected anaerobes and anaerobic processes to develop successful and sustainable PGP and pollutants removal by rhizospheric microorganisms., (© 2022 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Recent advances in understanding the association of gut microbiota with the host have shown evidence of certain bacterial therapeutic potentiality in preventing and treating metabolic diseases. Hyperoxaluria is a severe challenge in nephrology and has led to the novel gut eubiosis as current therapy. The human gut commensal, obligate anaerobic, and intestinal oxalate-degrading strains of Oxalobacter formigenes have drawn a promising significant interest for the next-generation probiotics (NGPs). This nonpathogenic, potential probiotic, and specialist oxalotrophic properties of O. formigenes give a new hope as a live biotherapeutic agent for calcium oxalate renal therapy. Numerous satisfactory outcomes of in vitro and in vivo studies were achieved on evaluating O. formigenes functionality, but the commercial production of this bacterium is yet to be achieved. This bacterium finds diverse application in dietary and endogenous oxalate degradation and the improvement of gut health, on which we concentrated our attention in this review. The relationship between good anaerobic gut bacterial dysbiosis and renal complications is comprehensively discussed to address the need for the development probiotic formulation. However, the commercial production of this bacteria on a broad scale is complex, with numerous obstacles, mainly because they are oxygen-sensitive and difficult to culture. This review will coherently present the current and available methodologies in producing, stabilizing, and delivering these NGPs to treat calcium stones. Moreover, the study presents the extensive work and key milestones achieved in the research on O. formigenes from tale to the truth., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Bacteria in the order 'Candidatus Brocadiales' within the phylum Planctomycetes (Planctomycetota) have the remarkable ability to perform anaerobic ammonium oxidation (anammox). Two families of anammox bacteria with different biogeographical distributions have been reported, marine Ca. Scalinduaceae and freshwater Ca. Brocadiaceae. Here we report evidence of three new species within a novel genus and family of anammox bacteria, which were discovered in biofilms of a subsea road tunnel under a fjord in Norway. In this particular ecosystem, the nitrogen cycle is likely fuelled by ammonia from organic matter degradation in the fjord sediments and the rock mass above the tunnel, resulting in the growth of biofilms where anammox bacteria can thrive under oxygen limitation. We resolved several metagenome-assembled genomes (MAGs) of anammox bacteria, including three Ca. Brocadiales MAGs that could not be classified at the family level. MAGs of this novel family had all the diagnostic genes for a full anaerobic ammonium oxidation pathway in which nitrite was probably reduced by a NirK-like reductase. A survey of published molecular data indicated that this new family of anammox bacteria occurs in many marine sediments, where its members presumably would contribute to nitrogen loss., (© 2022 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Degradation experiments are conducted to specifically compare the degradation of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) by aerobic and anaerobic strains isolated from real e-waste sites contaminated by BDE-47. The effect of carbon sources, inducers and surfactants on the degradation was examined to strengthen such a comparison. An aerobic strain, B. cereus S1, and an anaerobic strain, A. faecalis S4, were obtained. The results indicated that BDE-47 could be used as the sole carbon source by B. cereus S1 and A. faecalis S4 under aerobic and anaerobic conditions, respectively. The degradation of BDE-47 by B. cereus S1 and A. faecalis S4 was illustrated a first-order kinetics process obtaining a removal efficiency of 61.6% and 51.6% with a first-order rate constant of 0.0728 d -1 and 0.0514 d -1 , and corresponding half-life of 8.7 d and 13.5 d, respectively. The addition of carbon sources (yeast extract, glucose, acetic acid and ethanol) and inducers (2,4-dichlorophenol, bisphenol A and toluene) promoted BDE-47 degradation by both B. cereus S1 and A. faecalis S4 under aerobic and anaerobic conditions, while hydroquinone as the inducer inhibited the degradation. All of the surfactants tested (CTAB, Tween 80, Triton X-100, rhamnolipid and SDS) showed inhibitory effect. BDE-47 degradation by B. cereus S1 under aerobic condition was more efficient than A. faecalis S4 under anaerobic condition whether with or without the additives. The results of the study indicated that in the field sites contaminated by BDE-47, the aerobic condition can be more favorable for BDE-47 removal and the degradation can be further enhanced by applying suitable carbon sources and inducers., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Thiobencarb is a herbicide globally used in the agricultural sector, and its extensive application leads to severe environmental pollution. In this study, the thiobencarb supplementation caused a significant shift in the bacterial community in the sediment slurry. An analysis of the degradation metabolites of microorganisms from the sediment indicated that deschlorothiobencarb, S-4-chlorobenzyl ethylthiocarbamate, 4-chlorobenzyl mercaptan, 4-chlorobenzyl alcohol, 4-chlorobenzoic acid and chlorobenzene were the main intermediates. The degradation rates were significantly enhanced using a horizontal-flow anaerobic reactor with immobilized cells in polyurethane foam. The degradation rates at 2.6, 12.9 and 25.6 mg L-1 concentrations by suspended microorganisms from the sediment in the mineral medium supplemented with glucose were 0.085 ± 0.000, 0.383 ± 0.010 and 0.500 ± 0.045 mg day-1, respectively. The corresponding data for degradation in the reactor were 2.54 ± 0.03, 11.69 ± 0.72 and 18.58 ± 1.83 mg day-1 at the sixth operation period. Moreover, COD removal efficiencies were >90% achieved in the reactor. The proposed method facilitates degradation using a horizontal-flow anaerobic immobilized biomass bioreactor. Moreover, this study reveals the degradation of metabolites of thiobencarb under anaerobic conditions., (© The Author(s) 2022. Published by Oxford University Press on behalf of FEMS.)