Search

Methanogens, which are found exclusively in the Archaea domain of life, have the potential to help solve future energy challenges by producing methane. As a result, their metabolism has attracted significant attention in recent years. Despite being unable to grow on sugars, they store glycogen, which raises intriguing questions about the role of this polymer in methanogen metabolism and the signals that trigger its degradation when methanogenic substrates are not available. Here, we examined genomic databases to identify the enzymes responsible for glycogen synthesis and degradation in methanogens and explored the critical role of glycogen when nutrients and methanogenic substrates are scarce. Additionally, we analyzed the metabolic pathways involved in glycogen metabolism and their connection to the various types of methanogenesis exhibited by these organisms. Potential regulatory steps are proposed based on the reported effectors. Also, by employing the Alphafold3 server, the structural location of these sites in the enzyme structure was predicted, highlighting the advantages and limitations of this tool. Analysis of the allosteric effectors involved in this regulation suggests that energy charge may be the signal that triggers the metabolic switch from gluconeogenesis and glycogen storage to glycolysis and methanogenesis., 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 Inc. All rights reserved.)

Dietary tannins can affect rumen microbiota and enteric fermentation to mitigate methane emissions, although such effects have not yet been fully elucidated. We tested two subunits of hydrolyzable tannins named gallic acid (GA) and ellagic acid (EA), alone (75 mg/g DM each) or combined (150 mg/g DM in total), using the Rusitec system. EA and EA+GA treatments decreased methane production, volatile fatty acids, nutrient degradation, relative abundance of Butyrivibrio fibrisolvens , Fibrobacter succinogenes , Ruminococcus flavefaciens but increased Selenomonas ruminantium . EA and EA+GA increased urolithins A and B. Also, EA and EA+GA reduced bacterial richness, with limited effects on archaeal richness. For bacteria, Megasphaera elsdenii was more abundant after EA and EA+GA, while Methanomethylophilaceae dominated archaea in all treatments. EA was more effective than GA in altering rumen microbiota and fermentation but GA did not reduce VFA and nutrient degradation. Thus, dietary supplementation of EA-plant extracts for ruminants may be considered to mitigate enteric methane, although a suitable dosage must be ensured to minimize the negative effects on fermentation.

The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. First discovered in archaea, this protein domain has evolved from RNA- to DNA-binding, with a concomitant expansion in the range of cellular processes that it regulates. Despite its widespread presence, the full extent of its sequence, structural, and functional diversity remains unexplored. In this study, we employed iterative searches in PSI-BLAST to identify 15,161 unique Alba domain-containing proteins from the NCBI non-redundant protein database. Sequence similarity network (SSN) analysis clustered them into 13 distinct subgroups, including the archaeal Alba and eukaryotic Rpp20/Pop7 and Rpp25/Pop6 groups, as well as novel fungal and Plasmodium-specific Albas. Sequence and structural conservation analysis of the subgroups indicated high preservation of the dimer interface, with Alba domains from unicellular eukaryotes notably exhibiting structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Arsenic (As) and antimony (Sb), two toxic metal(loid)s, behave similarly and commonly occur in mine tailings. Yet, responses of microbes to As and Sb co-contamination in tailings dam failure-affected area remain limited. Herein, soil microbiomes (archaea, bacteria and fungi) across two contrasting sites (tailing-contaminated farmland and nearby undisturbed forestland) at a Sb-Au mining district in Chizhou, China were investigated by high-throughput sequencing. Results showed that As and Sb occurred mainly in the residual form, accounting for 55.82 % and 52.04 %, respectively. The bioavailable form was 12.77 % and 10.39 % in contaminated farmland compared to 13.31 % and 11.66 % in undisturbed forestland, respectively. Contrary to archaea and fungi, bacterial alpha-diversity significantly increased in contaminated farmland. The taxa-taxa interactions in archaea were most robust, followed by bacteria; and fungi were the weakest, which was corresponding to the habitat niche breadth. Microbial communities were affected by the deterministic processes with a modified stochasticity ratio (MST) value of 36.36 %, whereas more stochasticity (MST = 49.71 %) was raised in contaminated farmland than in undisturbed forestland (MST = 36.98 %). The microbial function based on taxonomy-based inference indicated that nitrogen and carbon metabolisms associated with archaea and bacteria increased in contaminated farmland, as well as plant pathogen, wood saprotroph and endophyte related with fungi. The turnover of soil microbiomes was tightly correlated with As and Sb speciation. Collectively, this study reveals that the soil microbial survival strategies to As-Sb co-contamination after dam failure, providing guidance for the development of bioremediation and tailings management strategies., 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 B.V. All rights reserved.)

This study simulates a major environmental scenario involving "organic fertilizer source" plastics, by exploring the key factors influencing the changes in plastic-films during anaerobic digestion (AD), as well as the responses of the anaerobically digested plastics to ultraviolet (UV) radiation exposure. The results demonstrate that the degradation effect of AD on plastics is reflected by their yellowish and ruptured appearance, slightly worn surfaces, hardening and opacity, and fragmentation. AD significantly increases the content of oxygen-containing functional groups and the degree of unsaturation in plastic films, with thermophilic temperature processes proving more effective than those conducted at mesophilic temperatures. Exposure to UV light has been found to amplify the degradative effects, suggesting the potential cumulative impact of AD and UV. Both AD and UV irradiation reduced the hydrophilicity of plastics. In particular, the hydrophobicity of polylactic acid films was completely disrupted under overlay-exposure. Furthermore, microbial populations on plastic surfaces were mainly bacterial. These bacterial populations were primarily influenced by temperature, and moderately by the plastic types. In contrast, archaea were predominantly affected by both temperature and digested substrate. This study offers a theoretical foundation for strategies aimed at preventing and controlling plastic pollution derived from organic fertilizers., 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 B.V. All rights reserved.)

Anaerobic treatment of sulfur-rich wastewater is challenging because sulfide greatly inhibits the activity of anaerobic microorganisms, especially methanogenic archaea. We developed an internal phase-separated reactor (IPSR) that removed sulfide prior to methanogenesis by gas stripping using biogas produced in the reactor. The IPSR was fed with synthetic wastewater containing a very high sulfide concentration of up to 6,000 mg S L -1 with a chemical oxygen demand (COD) of 30,000 mg L -1 . The IPSR was operated at an organic loading rate of 5-12 kg COD m -3 day -1 at 35 °C. The results show that the sulfide concentration was reduced from 6,000 mg S L -1 in the influent to <700 mg S L -1 in the first-stage effluent. The second-stage effluent contained <400 mg S L -1 . As a result of effective sulfide removal by its gas stripping function, the IPSR had a COD removal efficiency of >90% over the entire experimental period. High-throughput 16S rRNA gene sequencing revealed that the major anaerobic archaea were Methanobacterium and Methanosaeta, which are frequently found in high-rate anaerobic reactors. Thus, the IPSR maintains these microorganisms and achieves high-process performance even when fed wastewater with very high sulfide concentrations ., Competing Interests: T.O. and K.S. have patent #Japanese Patent No. 6029081 issued to Licensee., (© 2024 The Authors This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (CC BY 4.0), which permits copying, adaptation and redistribution, provided the original work is properly cited (http://creativecommons.org/licenses/by/4.0/).)

Pyrolysis of lignocellulosic biomass commonly produces syngas, a mixture of gases such as CO, CO 2 and H 2 , as well as an aqueous solution generally rich in organic acids such as acetate. In this study, we evaluated the impact of increasing acetate shock loads during syngas co-fermentation with anaerobic microbiomes at different pH levels (6.7 and 5.5) and temperatures (37°C and 55°C) by assessing substrates consumption, metabolites production and microbial community composition. The anaerobic microbiomes revealed to be remarkably resilient and were capable of converting syngas even at high acetate concentrations of up to 64 g/L and pH 5.5. Modifying process parameters and acetate loads resulted in a shift of the product spectrum and microbiota composition. Specifically, a pH of 6.7 promoted methanogens such as Methanosarcina, whereas lowering the pH to 5.5 with lower acetate loads promoted the enrichment of syntrophic acetate oxidisers such as Syntrophaceticus, alongside hydrogenotrophic methanogens. Increasing acetate loads intensified the toxicity of undissociated acetic acid, thereby inhibiting methanogenic activity. Under non-methanogenic conditions, high acetate concentrations suppressed acetogenesis in favour of hydrogenogenesis and the production of various carboxylates, including valerate, with product profiles and production rates being contingent upon temperature. A possible candidate for valerate production was identified in Oscillibacter. Across all tested conditions, acetate supplementation provided additional carbon and energy to the mixed cultures and consistently increased carboxydotrophic conversion rates up to about 20-fold observed at pH 5.5, 55°C and 48 g/L acetate compared to control experiments. Species of Methanobacterium, Methanosarcina and Methanothermobacter may have been involved in CO biomethanation. Under non-methanogenic conditions, the bacterial species responsible for CO conversion remain unclear. These results offer promise for integrating process streams, such as syngas and wastewater, as substrates for mixed culture fermentation allowing for enhanced resource circularity, mitigation of environmental impacts and decreased dependence on fossil fuels., (© 2024 The Author(s). Microbial Biotechnology published by John Wiley & Sons Ltd.)

The genome of all organisms is spatially organized to function efficiently. The advent of genome-wide chromatin conformation capture (Hi-C) methods has revolutionized our ability to probe the three-dimensional (3D) organization of genomes across diverse species. In this Review, we compare 3D chromatin folding from bacteria and archaea to that in mammals and plants, focusing on topology at the level of gene regulatory domains. In doing so, we consider systematic similarities and differences that hint at the origin and evolution of spatial chromatin folding and its relation to gene activity. We discuss the universality of spatial chromatin domains in all kingdoms, each encompassing one to several genes. We also highlight differences between organisms and suggest that similar features in Hi-C matrices do not necessarily reflect the same biological process or function. Furthermore, we discuss the evolution of domain boundaries and boundary-forming proteins, which indicates that structural maintenance of chromosome (SMC) proteins and the transcription machinery are the ancestral sculptors of the genome. Architectural proteins such as CTCF serve as clade-specific determinants of genome organization. Finally, studies in many non-model organisms show that, despite the ancient origin of 3D chromatin folding and its intricate link to gene activity, evolution tolerates substantial changes in genome organization., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. Springer Nature America, Inc.)

Haloarchaea, known for their resilience to environmental fluctuations, require a minimum salt concentration of 10% (w/v) for growth and can survive up to 35% (w/v) salinity. In biotechnology, these halophiles have diverse industrial applications. This study investigates the tolerance responses of nine haloarchaea: Haloferax mediterranei, Haloferax volcanii, Haloferax gibbonsii, Halorubrum californiense, Halorubrum litoreum, Natrinema pellirubrum, Natrinema altunense, Haloterrigena thermotolerans and Haloarcula sinaiiensis, under various stressful conditions. All these archaea demonstrated the ability to thrive in the presence of toxic metals such as chromium, nickel, cobalt and arsenic, and their tolerance to significantly elevated lithium concentrations in the medium was remarkable. Among the studied haloarchaea, Hfx. mediterranei exhibited superior resilience, particularly against lithium, with an impressive minimum inhibitory concentration (MIC) of up to 4 M LiCl, even replacing NaCl entirely. Haloferax species showed specificity for conditions with maximal growth rates, while Htg. thermotolerans and Nnm. altunense displayed high resilience without losing growth throughout the ranges, although these were generally low. ICP-MS results highlighted the impressive intracellular lithium accumulation in Nnm. pellirubrum, emphasizing its potential significance in bioremediation. This research highlights a new characteristic of haloarchaea, their tolerance to high lithium concentrations and the potential for new applications in extreme industrial processes and bioremediation., (© 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)

Nitrification is the dominant process for nitrous oxide (N 2 O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N 2 O production in a range of unfertilized and fertilized paddy soils, using 13 CO 2 -DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C 2 H 2 ), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. 13 CO 2 -DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N 2 O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N 2 O emissions. Applying organic fertilizers significantly decreased the N 2 O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N 2 O production in other ecosystems than oligotrophic habitats., 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 B.V. All rights reserved.)

Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4-2.0 Ga) and several geological events in the "Boring Billion" (1.8-0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3-1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment., (Copyright © 2024 Elsevier Inc. All rights reserved.)

This study investigates the production of biomethane, and variation in microbial community and coal molecular structures using gas chromatography, 16S rRNA high-throughput sequencing and Fourier transform infrared spectroscopy. Additionally, the factors influencing microbial community structure at a molecular level are discussed. The results demonstrate that bituminous coal exhibits a higher biomethane yield than anthracite coal. In bituminous coal samples, Escherichia and Proteiniphilum are the predominant bacteria at day 0, while Macellibacteroides dominates from days 5 to 35. Methanofollis is the dominated archaea during days 0 to 15, followed by Methanosarcina on day 35. In anthracite coal samples, Soehngenia is the dominant bacterial genus at day 0; however, it transitions to mainly Soehngenia and Aminobacterium within days 5-15 before evolving into Acetomicrobium on day 35. Methanocorpusculum is predominantly found in archaeal communities during days 0-15 but shifts to Methanosarcina on day 35. Alpha diversity analysis reveals that bacterial communities have higher species abundance and diversity compared to archaeal communities. Redundancy analysis indicates a significant correlation between coal molecular structure and bacterial community composition (P value < 0.05), whereas no correlation exists with archaeal community composition (P value > 0.05). The research findings provide theoretical support for revealing the biological gasification mechanisms of coal., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Bioaugmentation regimes (i.e., dosage, repetition, and timing) in AD must be optimized to ensure their effectiveness. Although previous studies have investigated these aspects, most have focused exclusively on short-term effects, with some reporting conflicting conclusions. Here, AD experiments of three consecutive repeated batches were conducted to determine the effect of bioaugmentation regimes under ammonium/salt inhibition conditions. A positive correlation between reactor performance and inoculum dosage was confirmed in the first batch, which diminished in subsequent batches for both inhibitors. Moreover, a diminishing marginal effect was observed with repeated inoculum introduction. While the bacterial community largely influenced the reactor performance, the archaeal community exhibited only a minor impact. Prediction of the key enzyme abundances suggested an overall decline in different AD steps. Overall, repeated batch experiments revealed that a homogeneous bacterial community deteriorated the AD process during long-term operation. Thus, a balanced bacterial community is key for efficient methane production., 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.)

The slow stabilization process of landfill had brought obstacles to urbanization. The paper investigated the efficacy and mechanism of micro-aeration intensity for landfill stabilization. The micro-aeration intensity of 0.05 L/(h·kg) resulted in a significant increase of volatile fatty acids (VFAs) in the hydrolysis stage, and the NH 4 + -N concentration was reduced by 22.1 %. At the end of landfill, VFAs were rapidly degraded and organic matter was reduced from 36 % to 16 %, which was 55.5 % more efficient than the control group. In addition, the community succession and structure of bacteria and archaea were analyzed. The micro-aeration intensity of 0.05 L/(h·kg) increased the abundance of hydrolyzing functional bacteria such as Pseudomonas and Bacillus, and allowed methanogenic bacteria such as Methanobacterium and Methanothrix to gradually establish oxygen tolerance in the microaerobic environment. The appropriate micro-aeration intensity can accelerate the stabilization process of landfill, which has environmental and economic benefits., 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 demand for natural products has significantly increased, driving interest in carotenoids as bioactive compounds for both human and animal consumption. Carotenoids, natural pigments with several biological properties, like antioxidant and antimicrobial, are increasingly preferred over synthetic colorants by the consumers (chemophobia). The global carotenoid market is projected to reach US$ 2.45 billion by 2034, driven by consumer preferences for natural ingredients and regulatory restrictions on synthetic products. Among carotenoids, bacterioruberin (BR), a C 50 carotenoid naturally found in microbial hyperhalophilic archaea and in moderate halophilic archaea, stands out for its exceptional antioxidant capabilities, surpassing even well-known carotenoids like astaxanthin. BR's and its derivatives unique structure, with 13 conjugated double bonds and four -OH groups, contributes to its potent antioxidant activity and potential applications in food, feed, supplements, pharmaceuticals, and cosmeceuticals. This review explores BR's chemical and biological properties, upstream and downstream technologies, analytical techniques, market applications, and prospects in the colorants industry. While BR is not intended to replace existing carotenoids, its inclusion enriches the range of natural products available to meet the rising demand for natural alternatives. Furthermore, BR's promising antioxidant capacity positions it as a key player in the future carotenoid market, offering diverse industries a natural and potent alternative for several applications., Competing Interests: Declaration of competing interest There are no conflicts to declare., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

High-solid digestion (HSD) for biogas production is a resource-efficient and sustainable method to treat organic wastes with high total solids content and obtain renewable energy and an organic fertiliser, using a lower dilution rate than in the more common wet digestion process. This study examined the effect of reactor type on the performance of an HSD process, comparing plug-flow (PFR) type reactors developed for continuous HSD processes, and completely stirred-tank reactors (CSTRs) commonly used for wet digestion. The HSD process was operated in thermophilic conditions (52 °C), with a mixture of household waste, garden waste and agricultural residues (total solids content 27-28 %). The PFRs showed slightly better performance, with higher specific methane production and nitrogen mineralisation than the CSTRs, while the reduction of volatile solids was the same in both reactor types. Results from 16S rRNA gene sequencing showed a significant difference in the microbial population, potentially related to large differences in stirring speed between the reactor types (1 rpm in PFRs and 70-150 rpm in CSTRs, respectively). The bacterial community was dominated by the genus Defluviitoga in the PFRs and order MBA03 in the CSTRs. For the archaeal community, there was a predominance of the genus Methanoculleus in the PFRs, and of the genera Methanosarcina and Methanothermobacter in the CSTRs. Despite these shifts in microbiology, the results showed that stable digestion of substrates with high total solids content can be achieved in both reactor types, indicating flexibility in the choice of technique for HSD processes., 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.)

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic., 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 B.V.)

Biotreatment of oily sludge and the involved microbial communities, particularly in saline environments, have been rarely investigated. We enriched a halophilic bacterial consortium (OS-100) from petroleum refining oily sludge, which degraded almost 86% of the aliphatic hydrocarbon (C 10 -C 30 ) fraction of the oily sludge within 7 days in the presence of 100 g/L NaCl. Two halophilic hydrocarbon-degrading bacteria related to the genera Chromohalobacter and Halomonas were isolated from the OS-100 consortium. Hydrocarbon degradation by the OS-100 consortium was relatively higher compared to the isolated bacteria, indicating potential synergistic interactions among the OS-100 community members. Exclusion of FeCl 2, MgCl 2 , CaCl 2 , trace elements, and vitamins from the culture medium did not significantly affect the hydrocarbon degradation efficiency of the OS-100 consortium. To the contrary, hydrocarbon biodegradation dropped from 94.1 to 54.4% and 5% when the OS-100 consortium was deprived from phosphate and nitrogen sources in the culture medium, respectively. Quantitative PCR revealed that alkB gene expression increased up to the 3rd day of incubation with 11.277-fold, consistent with the observed increments in hydrocarbon degradation. Illumina-MiSeq sequencing of 16 S rRNA gene fragments revealed that the OS-100 consortium was mainly composed of the genera Halomonas, Idiomarina, Alcanivorax and Chromohalobacter. This community structure changed depending on the culturing conditions. However, remarkable changes in the community structure were not always associated with remarkable shifts in the hydrocarbonoclastic activity and vice versa. The results show that probably synergistic interactions between community members and different subpopulations of the OS-100 consortium contributed to salinity tolerance and hydrocarbon degradation., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Archaea represents a significant population of up to 10% in soil microbial communities. The role of Archaea in soil is often overlooked mainly due to its unculturability. Among the three domains of life biological nitrogen fixation (BNF) is mainly a trait of Eubacteria and some Archaea. Archaea mediated processes like BNF may become even more important in the face of global Climate change. Although there are reports on nitrogen fixation by Archaea, to best of our knowledge there is no comprehensive report on BNF by Archaea under environmental stresses typical to climate change. Here we report a survey of literature and DNA database to study N 2 -fixation among Archaea. A total of 37 Archaea belonging to Methanogens of the phylum Euryarchaeota within the class Methanococcus, Methanomicrobia Methanobacteria, and Methanotrophic ANME2 lineages either contain genes for BNF or are known to fix atmospheric N 2 . Archaea were found to have their nif genes arranged as clusters of 6-8 genes in a single operon. The genes code for commonly found Mo-nitrogenase while in some archaea the genes for alternative metal nitrogenases like vnf were also found. The nifHDK gene similarity matrices show that Archaea shared the highest similarity with the nifHDK gene of anaerobic Clostridium beijerinckii. Although there are various theories about the origin of N 2 -fixation in Archaea, the most acceptable is the origin of N 2 -fixation first in bacteria and its subsequent transfer to Archaea. Since Archaea can survive under extreme environmental conditions their role in BNF should be studied especially in soil under environmental stress., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water., Results: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles., Conclusions: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology., Results: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions., Conclusions: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

The rise in global energy demand has prompted research on developing strategies for transforming conventional nonrenewable sources to cleaner fuels. Biogenic methane production is a promising source that caters to increasing energy demands. Therefore, research to enhance their production is of great importance. Implementation of successful enhancement strategies requires knowledge of the factors impacting coalbed methane production. The microbial diversity of the formation water in coal seams is the crucial parameter influencing biomethane production. This study explores microbial diversity in the Producing and Marginal wells of Bokaro, India, intending to understand the potential application of microbial-enhanced coalbed methane technology in the marginal wells of this reservoir. The high throughput sequencing analysis revealed the presence of both archaeal and bacterial groups in both well types. The result showed significant differences in the diversity of the samples from the two well groups, suggesting the immense role played by the microbes in producing methane gas. Random forest analysis shows genera Gelria, Methanothermobacter, Thaurea, Youngiibacter, and Proteiniclasticum in the Producing wells while Roseomonas, Rhodobacter, Mycobacterium, Methylobacter, and Bosea in the Marginal wells as the significant contributor in differentiating the overall diversity between the wells of Bokaro. The current study is the first to show microbial uniqueness in coalbed methane wells based on gas production efficiency. It also explores the role of physicochemical factors in framing microbial community structure in the wells. The results provide salient information that will help better understand the impact of microbial diversity on the production of coalbed methane wells of studied coal seams. This knowledge will further aid in exploring the prospects of microbial-enhanced methane in the Marginal wells., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO 3 - &#95;N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems., Competing Interests: Declarations. Competing Interests: The authors declare no competing interests., (© 2024. The Author(s).)

Cobamides (Cbas) are cobalt-containing cyclic tetrapyrroles used by cells from all domains of life as co-catalyst of diverse reactions. There are several structural features that distinguish Cbas from one another. The most relevant of those features discussed in this review is the lower ligand, which is the nucleobase of a ribotide located in the lower face of the cyclic tetrapyrrole ring. The above-mentioned ribotide is known as the nucleotide loop, which is attached to the ring by a short linker. In Cbas, the nucleobase of the ribotide can be benzimidazole or derivatives of it, purine or derivatives of it, or phenolic compounds. Given the importance of Cbas in prokaryotic metabolism, it is not surprising that prokaryotes have evolved enzymes that cleave part or the entire nucleotide loop. This function is advantageous when Cbas contain nucleobases that somehow interfere with the function of Cba-dependent enzymes in the organism. After cleavage, Cbas are rebuilt via the nucleotide loop assembly (NLA) pathway, which includes enzymes that activate the nucleobase and the ring intermediate, followed by condensation of activated intermediates and a final dephosphorylation reaction. This exchange of nucleobases is known as Cba remodeling. The NLA pathway is used to salvage Cba precursors from the environment., Competing Interests: The authors declare no conflict of interest.

Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification., Competing Interests: Declarations. Competing Interests: The authors declare no competing interests., (© 2024. The Author(s).)

Measurement of the adenosine triphosphate (ATP) concentration among different cells, tissues and organs and even across the phylogenetic tree ordinarily yields exceedingly high concentrations at the millimolar (mM) level. This represents a conundrum in that ATP-driven cellular functions only require micromolar (μM) values. Considering that nature is ordinarily conservative in the generation of high-energy phosphatic metabolites such as ATP, a potential major role for ATP has been completely overlooked and may be of paramount importance because ATP is a hydrotrope. In all phylogenetic domains, reports have established that the excessively high mM concentration of ATP is present in studies of eukaryotic cellular and tissue homogenates, living tissues, and a living organ as well as archaeotic and prokaryotic organisms. These ATP concentrations are also present in contemporary relatives of microorganisms having progenitors existing in the Precambrian Era. This feature is fundamental to cell biology across taxonomic domains. These features are interpreted as serving a foundational molecular function for maintaining organismal homeostasis. We hypothesize that ATP prevents pathological protein aggregation and maintains protein solubility through its hydrotropic feature in cells, tissues, and organs., (© 2024 The Author(s). Published by IMR Press.)

Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity., Competing Interests: Declarations Conflict of interest The authors declare no competing interests., (© 2024. The Author(s).)

Microbial communities are shaped by cell-cell interactions. Although archaea are often found in associations with other microorganisms, the mechanisms structuring these communities are poorly understood. Here, we report on the structure and function of haloarchaeal contractile injection systems (CISs). Using a combination of functional assays and time-lapse imaging, we show that Halogeometricum borinquense exhibits antagonism toward Haloferax volcanii by inducing cell lysis and inhibiting proliferation. This antagonism is contact-dependent and requires a functional CIS, which is encoded by a gene cluster that is associated with toxin-immunity pairs. Cryo-focused ion beam milling and imaging by cryo-electron tomography revealed that these CISs are bound to the cytoplasmic membrane, resembling the bacterial type six secretion systems (T6SSs). We show that related T6SS gene clusters are conserved and expressed in other haloarchaeal strains, which exhibit antagonistic behavior. Our data provide a mechanistic framework for understanding how archaea may shape microbial communities and affect the food webs they inhabit.

The wide utilization of poly dimethyl diallyl ammonium chloride (polyDADMAC) in industrial conditions leads to its accumulation in waste activated sludge (WAS), thereby affecting subsequent WAS treatment processes. This work investigated the interaction between polyDADMAC and WAS components from the perspective of anaerobic digestion (AD) performance and anaerobes adaptability variation. The results showed that polyDADMAC decreased the content of biodegradable organic substrates (i.e., soluble protein and carbohydrate) by binding with the functional groups and then settling to the solid phase, thus impeding the subsequent utilization. Higher concentrations of polyDADMAC prompted an initial protective response of excreting organic substrates into extracellular environment, but its toxicity to archaea was irreversible. Consequently, polyDADMAC inhibited the processes of AD and induced a 30 % reduction in methane production with 0.05 g polyDADMAC/g total suspended solid (TSS) addition. Changes in microbial community structure indicated that archaea involved in methane production (e.g., Anaerolineaceae sp. and Methanosaeta sp.) were inhibited when exposed to polyDADMAC. However, several adaptive bacteria with the ability of utilizing complex organics and participating in nitrogen cycle (e.g., Aminicenantales sp. and Ellin6067 sp.) were enriched with the above dosage. Specifically, the decreased abundance of genes relevant to methane metabolism pathway (i.e., mer and cdh) and increased abundance of genes involved in metabolism of cofactors and vitamins (e.g., nad and thi) indicated the toxicity of polyDADMAC and the irritant response of microflora. Moreover, polyDADMAC underwent degradation in AD system, resulting in a 12 % reduction in 15 days, accompanied by an increase in the -NO 2 functional group. In general, this study provided a thorough understanding of the interaction between polyDADMAC and WAS components, raising concerns regarding the elimination of endogenous pollutants during AD., 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.)

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems., 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 Authors. Published by Elsevier B.V. All rights reserved.)

Background: Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies., Results: Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination., Conclusions: Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus , which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems., Importance: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N 2 O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA., Competing Interests: The authors declare no conflict of interest.

Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO 2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs., (© 2024. The Author(s).)

Ribosome structure and activity are challenged at high temperatures, often demanding modifications to ribosomal RNAs (rRNAs) to retain translation fidelity. LC-MS/MS, bisulfite-sequencing, and high-resolution cryo-EM structures of the archaeal ribosome identified an RNA modification, N 4, N 4-dimethylcytidine (m 4 2 C), at the universally conserved C918 in the 16S rRNA helix 31 loop. Here, we characterize and structurally resolve a class of RNA methyltransferase that generates m 4 2 C whose function is critical for hyperthermophilic growth. m 4 2 C is synthesized by the activity of a unique family of RNA methyltransferase containing a Rossman-fold that targets only intact ribosomes. The phylogenetic distribution of the newly identified m 4 2 C synthase family implies that m 4 2 C is biologically relevant in each domain. Resistance of m 4 2 C to bisulfite-driven deamination suggests that efforts to capture m 5 C profiles via bisulfite sequencing are also capturing m 4 2 C., Competing Interests: Competing interests statement:K.A.F., P.S.H., V.T., L.E., J.S., H.P.F., R.C., and T.J.S. do not have any competing financial interests nor conflicts of interest to report. N.D., E.J.W., R.T.F., Y.-L.T., G.B.R., and I.R.C. are employed and funded by New England Biolabs, Inc., a manufacturer and vendor of molecular biology reagents, including nucleic acid modifying and synthesis enzymes. The authors state that this affiliation does not affect their impartiality, objectivity of data generation or interpretation, adherence to journal standards and policies, or availability of data.

The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds ( Ascophyllum nodosum , Asparagopsis taxiformis , and Fucus vesiculosus ) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus , both harvested in Scotland and A. taxiformis , with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" ( M. smithii, M. gottschalkii, M. millerae or M. thaueri ; high methane yield) to "RO" ( M. ruminantium and M. olleyae ; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased., Importance: The application of A. taxiformis significantly reduced methane production in vitro . We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus , obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not., Competing Interests: The authors declare no conflict of interest.

Wastewater discharge is a global threat to freshwater resources. Streams, in particular, are receiving waterbodies that are directly impacted chemically and biologically due to effluent discharge. However, it is largely unknown how wastewater serves as a subsidy or a stressor to aquatic biodiversity, particularly microbiota, over space. Nutrient-diffusing substrata (NDS) were deployed; NDS release nutrients through diffusion into the water column into a wastewater-dependent stream across three reaches. We used N, P, and N + P treatments for the measurement of single nutrient and co-nutrient limitation, and a no-nutrient control. Both algal and total biofilm biomass was measured and the 16S ribosomal RNA genes via targeted amplicon sequencing was used to assess bacterial/archaeal community diversity. Data indicated that total organic matter in biofilms differs spatially with the greatest organic matter (OM) concentrations in the confluence downstream of wastewater inputs. Biofilm OM concentrations were greatest in P and N + P treatments in the confluence site relative to control or N-only treatments. This indicates heterotrophic microbial communities-likely bacteria that dominate stream biofilms-are P-limited in this ecosystem even with upstream wastewater inputs. In conjunction, bacteria/archaeal communities differed the greatest among nutrient treatments versus spatially and had several indicator taxa belonging to Flavobacterium spp. in N treatments relative to controls. Collectively with historical water quality data, we conclude that this wastewater-fed stream is primarily N-enriched but potentially P-limited, which results in significant shifts in biofilm bacterial communities and likely their overall biomass in this urban watershed., Importance: Streams in arid and semi-arid biomes are often dependent on their flow from municipal sources, such as wastewater effluent. However, wastewater has been shown to contain high concentrations of nutrients and chemical pollutants that can potentially harm aquatic ecosystems and their biota. Understanding if and the type of microorganisms that respond to pollution sources, specifically effluent from wastewater treatment facilities, in regions where flow is predominantly from treatment facilities, is critical for developing a predictive monitoring approach for eutrophication or other ecological degradation states for freshwaters., Competing Interests: The authors declare no conflict of interest.

Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N 2 O/H 2 S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance., 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. Declaration of Competing Interest The authors declare no competing interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Prokaryotes play crucial roles in hydrothermal vent ecosystems, yet their interactions with heavy metals are not well understood. This study explored the diversity of prokaryotic communities and their correlations with heavy metals and nutrient elements in hydrothermal sediments from Okinawa Trough. A total of 117 bacterial genera in 26 bacterial phyla and 10 archaeal classes in 3 archaeal phyla were identified, including dominant prokaryotic phyla Planctomycetes, Acidobacteria, Verrucomicrobia, and Euryarchaeota. Furthermore, Fe (39.61 mg/g), Mn (2.84 mg/g) and Ba (0.36 mg/g) were found to be the most abundant heavy metals in the Okinawa hydrothermal sediments. Notably, the concentrations of Zn, Ba, Mn, total organic carbon, and total nitrogen significantly increased, whereas the total sulfur concentration distinctively decreased at sampling sites farther from hydrothermal vents. These changes corresponded with reductions in prokaryotic abundance and diversity. Most heavy metals, including Mn, Fe, Co, Cu and As, presented significant positive correlations with a number of prokaryotic genera in the nearby sediment samples. In contrast, both positive and negative correlations with prokaryotes were observed in remote sediment. The keystone taxa include Magnetospirillum, GOUTA19, Lysobacter, Kaistobacter, Treponema, and Clostridium were detected through prokaryote interspecies interactions. The functional predictions revealed significant genes involved in carbon fixation, nitrogen/sulfur cycling, heat shock protein, and metal resistance pathways. Structural equation modeling confirmed that metal and nutrient elements directly influence the composition of prokaryotic communities, which in turn affects the relative abundance of functional genes., 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 B.V. All rights reserved.)

Grasslands are estimated to cover about 40% of the earth's land area and are primarily used for grazing. Despite their importance globally, there is a paucity of information on long-term grazing effects on the soil microbiome. We used a 68-year-old grazing experiment to determine differences in the soil permanganate-oxidizable C (POXC), microbial biomass C (MBC), the soil prokaryotic (bacterial and archaeal) community composition and enzyme activities between no-grazing, light grazing and heavy grazing, i.e. 0, 1.2 and 2.4 animal unit months (AUM) ha -1 . The grazing effects were determined in spring and fall grazing. Light grazing had little effect on soil MBC and the composition and diversity of prokaryotic communities in either grazing season, but the effects of heavy grazing depended on the grazing season. In spring, heavy grazing increased the relative abundances of copiotrophic phyla Actinomycetota, Bacillota and Nitrososphaerota , along with soil POXC contents but decreased those of oligotrophic phyla Acidobacteriota, Verrucomicrobiota and Nitrospirota . This difference in responses was not observed in fall, when grazing reduced soil POXC, MBC and the relative abundances of most phyla. The β -diversity analysis showed that the prokaryotic community structure under heavy grazing was different from those in the control and light grazing treatments, and α -diversity indices (except the Shannon index) were highest under heavy grazing in both grazing seasons. The activities of P-mobilizing and S-mobilizing soil enzymes decreased with increasing cattle stocking rate in both seasons, but the activities of the enzymes that mediate C and N cycling decreased only in the fall. The genus RB41 (phylum Acidobacteriota ) was one of two core bacterial genera, and its relative abundance was positively correlated with the activity of the S-mobilizing enzyme. Therefore, light grazing is recommended to reduce negative effects on the grassland soil microbiome and its activity, and the grazing season should be considered when evaluating such grazing effects.

Anaerobic ammonium oxidation (anammox) poses an emerging research field as it can outstand previous processes of biological wastewater treatment in terms of efficiency and costs. Anammox bacteria have the ability to metabolise NH 4 + and NO 2 - to produce N 2 under anaerobic conditions. Despite numerous studies, there is a lack of research on the co-occurrence and interrelationship of the predominant microbes that inhabit anammox-related processes. This systematic literature review follows the PSALSAR approach to assess metagenomic data on anammox bacteria and functional microbes in upstream reactors. Essential information on the physiology, metabolic pathways and inhibitory effects of anammox bacteria are reviewed and functional bacteria such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), ammonia-oxidising Archaea (AOA) and denitrifying bacteria are identified. Candidatus Kuenenia and Candidatus Brocadia were the most frequently sequenced genera in the observed literature. Pseudomonadota, Chloroflexota and Bacteroidota were prevalent regardless of crucial operational parameters and configurations that affect the microbial community. Interrelationship analysis revealed a positive association between the versatility of a phylum's metabolism and its presence in the observed wastewater treatment literature. Several groups, such as Calditrichota, Myxococcota and Deinococcota are highly underrepresented, a finding that should be investigated in more detail. No evidence was found to suggest that high anammox ratios are correlated with high nitrogen removal efficiencies, as some studies found high efficiency despite low anammox abundance (<1%)., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Philipp Witkabel reports financial support was provided by German Federal Ministry for Economic Affairs and Climate Action (grant number 16KN07012B). The work was developed in the frame of a research project, which includes further project partners. However, these partners have not contributed to this work, and they don't see a potential conflict of interest either. Apart from this, there are no other activities, which merit disclosure. If there are other authors, they 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 Authors. Published by Elsevier Ltd.. All rights reserved.)

Spirulina powder emerged as a novel and suitable co-metabolism substance significantly enhancing the anaerobic degradation of specific nitrogen heterocyclic compounds. On the addition of 1.0 mg/L of Spirulina powder, the reactor demonstrated optimal degradation efficiency for quinoline and indole, achieving ratios of 99.77 ± 1.83% and 99.57 ± 1.98%, respectively. Moreover, the incorporation of Spirulina powder resulted in increased concentrations of mixed liquor suspended solids, mixed liquor volatile suspended solids, proteins, and polysaccharides in anaerobic sludge. In addition, Spirulina powder led to reduced levels of Acinetobacter and enriched Aminicenantes genera incertae sedis , Levilinea , and Longilinea . The analysis of the archaeal community structure confirmed that the addition of Spirulina powder increased archaeal sequences, fostering greater richness and diversity in the archaeal community.

Methane-dependent complete denitrification primarily involves nitrate reduction to nitrite by ANME-2d archaea and nitrite reduction to dinitrogen by Methylomirabilis bacteria. 'Candidatus Methylomirabilis sinica' integrates the divisional labor. Physiological traits of this bacterium potentially enable the simultaneous reduction of N 2 O and CH 4 emissions. This forum article explores these traits and possible microbial mechanisms for co-reduction, providing guidance for greenhouse gas management strategies., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Pentachlorophenol (PCP) is a highly toxic and carcinogenic compound with significant environmental impact, necessitating effective treatment technologies. This study evaluates PCP removal mechanisms, including adsorption and biodegradation, during the startup of a horizontal-flow anaerobic immobilized biomass reactor (HAIB), and examines the impact of PCP concentration on microbial diversity using denaturing gradient gel electrophoresis (DGGE). The primary mechanism for PCP removal in the HAIB was adsorption, effectively described by the Freundlich isotherm model. Adsorption efficiency ranged from 86 to 104% for PCP concentrations between 0.2 and 5.0 mg/L, and 46% to 64% for concentrations between 0.098 and 0.05 mg/L. Additionally, PCP degradation intermediates such as 2,3-DCP and 2,6-DCP were detected, indicating that biodegradation also occurred in the HAIB. Organic matter degradation averaged 81 ± 9%, and methane content in the biogas averaged 46 ± 9%, confirming the anaerobic process. No inhibition of microbial activity was observed due to PCP toxicity, even at a PCP load of 5 mg PCP/g STV per day. While the archaeal community showed only slight changes, with similarity coefficients ranging from 88 to 95%, the bacterial community was significantly affected by PCP, with similarity coefficients ranging from 18 to 50%. Bacterial groups were responsible for the initial PCP degradation, while the archaeal community was involved in metabolizing the resulting byproducts. The use of indigenous inoculum from the Santos-São Vicente estuary demonstrated its potential for effective PCP removal. Polyurethane foam proved to be an effective support material, enhancing the adsorption process and reducing PCP toxicity to the microbial consortium. This study provides valuable insights into PCP adsorption and biodegradation mechanisms in HAIB, highlighting the effectiveness of indigenous inoculum and polyurethane foam for PCP removal., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Anaerobic digestion is one of the most promising options for the disposal of biodegradable food waste. However, the relatively high content of oil in food waste inhibits the conversion efficiency of anaerobic digestion because of the accumulation of long-chain fatty acids (LCFAs). In this study, activated anaerobic sludge was acclimated to accommodate high-oil conditions. The methane yield of high-oil food waste digested by the acclimated sludge increased by 24.9% compared to that digested by the raw sludge. To determine the internal changes in the acclimated sludge, the shifts in the microbial communities during the acclimation period were investigated via high-throughput sequencing (HTS) based on the 16 S rRNA gene. The results indicated that Bacteroidetes, Firmicutes, Chloroflexi and Proteobacteria were the dominant bacteria at the phylum level. The acclimation time allows some functional bacterial taxa to proliferate, such as Clostridium and Longilinea, which are able to degrade LCFAs and turn them into small organic molecules that also have nutrient value for other bacteria. Among the archaeal communities, the hydrogenotrophic methanogen Methanobacterium nearly supplanted the acetotrophic methanogen Methanosaeta. The time profiles of volatile fatty acids (VFAs) and pH during this period provided additional evidence for the success of the acclimation. This study demonstrated the effectiveness of acclimation and the dynamic of microbial communities, which further contributed to the management and resource utilization of high-oil food waste., (© 2024. The Author(s).)

Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Mondal 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.)

Biological N 2 fixation (BNF) is traced to the Archean. The nitrogen isotopic fractionation composition (δ 15 N) of sedimentary rocks is commonly used to reconstruct the presence of ancient diazotrophic ecosystems. While δ 15 N has been validated mostly using organisms grown under present-day conditions; it has not under the pre-Cambrian conditions, when atmospheric p O 2 was lower and p CO 2 was higher. Here, we explore δ 15 N signatures under three atmospheres with (i) elevated CO 2 and no O 2 (Archean), (ii) present-day CO 2 , and O 2 and (iii) future elevated CO 2 , in marine and freshwater, heterocytous cyanobacteria. Additionally, we augment our data set from literature for more generalized dependencies of δ 15 N and the associated fractionation factor epsilon ( ε = δ 15 N biomass - δ 15 N N2 ) during BNF in Archaea and Bacteria, including cyanobacteria, and habitats. The ε ranges between 3.70‰ and -4.96‰ with a mean ε value of -1.38 ± 0.95‰, for all bacteria, including cyanobacteria, across all tested conditions. The expanded data set revealed correlations of isotopic fractionation of BNF with CO 2 concentrations, toxin production, and light, although within 1‰. Moreover, correlation showed significant dependency of ε to species type, C/N ratios and toxin production in cyanobacteria, albeit it within a small range (-1.44 ± 0.89‰). We therefore conclude that δ 15 N is likely robust when applied to the pre-Cambrian-like atmosphere, stressing the strong cyanobacterial bias. Interestingly, the increased fractionation (lower ε ) observed in the toxin-producing Nodularia and Nostoc spp. suggests a heretofore unknown role of toxins in modulating nitrogen isotopic signals that warrants further investigation.IMPORTANCENitrogen is an essential element of life on Earth; however, despite its abundance, it is not biologically accessible. Biological nitrogen fixation is an essential process whereby microbes fix N 2 into biologically usable NH 3 . During this process, the enzyme nitrogenase preferentially uses light 14 N, resulting in 15 N depleted biomass. This signature can be traced back in time in sediments on Earth, and possibly other planets. In this paper, we explore the influence of p O 2 and p CO 2 on this fractionation signal. We find the signal is stable, especially for the primary producers, cyanobacteria, with correlations to CO 2 , light, and toxin-producing status, within a small range. Unexpectedly, we identified higher fractionation signals in toxin-producing Nodularia and Nostoc species that offer insight into why some organisms produce these N-rich toxic secondary metabolites., Competing Interests: The authors declare no conflict of interest.

Climate change and anthropogenic activities have significantly contributed to the degradation of wet meadows on the Qinghai-Tibet Plateau (QTP). Soil nitrogen (N) availability is a crucial determinant of the productivity of wet meadow vegetation. Furthermore, soil microbial nitrogen functional genes (NFGs) are critical in the transformation of soil N. Nevertheless, the dynamics of NFGs in response to vegetation degradation, as well as the underlying drivers, remain poorly understood. In this study, wet meadows at varying levels of vegetation degradation on the QTP, categorized as non-degraded (ND), slightly degraded (SD), moderately degraded (MD), and heavily degraded (HD), were examined. Soil samples from depths of 0 to 10 cm and 10 to 20 cm were collected during different growth cycles (June 2020, August 2020, and May 2021). The analysis focused on NFGs involved in organic nitrogen fixation ( nifH ), archaeal and bacterial ammonia oxidation ( amoA-AOA and amoA-AOB , respectively), and nitrite reduction ( nirK ), utilizing real-time fluorescence quantitative PCR. Our findings indicate a significant decline in the abundance of NFGs with intensified vegetation degradation, exhibiting notable spatial and temporal fluctuations. Specifically, the relative NFGs followed the pattern: nirK > amoA- AOA > amoA- AOB > nifH . Redundancy analysis revealed that vegetation cover was the primary regulator of NFGs abundance, accounting for 56.1%-57% of the variation. Additionally, soil total nitrogen, pH, and total phosphorus content were responsible for 38.5%, 28.2%, and 7% of the variability in NFGs, respectively. The ( amoA-AOA + amoA-AOB + nirK ) ratios associated with effective N transformation indicated that the vegetation degradation process moderately increased the nitrification potential., Importance: Our research investigates how the degradation of meadows affects the tiny organisms in soil that help plants use nitrogen, which is essential for their growth. In the Qinghai-Tibet Plateau, a region known for its unique ecosystems, we found that as meadows deteriorate-due to climate change and human activities-the number of these beneficial organisms significantly decreases. This decline could reduce soil fertility, impacting plant life and the overall health of the ecosystem. Understanding these changes helps us grasp how environmental pressures influence soil and plant health. Such knowledge is crucial for developing strategies to preserve these vulnerable ecosystems and ensure they continue to sustain biodiversity and provide resources for local communities., Competing Interests: The authors declare no conflict of interest.

Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes., Importance: Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide., Competing Interests: The authors declare no conflict of interest.

The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO 2 -forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO 2 -generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F 420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F 420 reductase. Accordingly, both systems exhibit robust coupled F 420 -reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F 420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F 420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy., (© 2024. The Author(s).)

The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important group of organic matter in the deep marine sediments, are primarily derived from bacterial peptidoglycan decomposition. Archaea are abundant in the deep ocean microbiome, yet their role in DAA metabolism remains poorly studied. Here, we report bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in DAA metabolism. Our analyses suggest that a variety of archaea, particularly the Candidatus Bathyarchaeota and the Candidatus Lokiarchaeaota, can metabolize DAAs. DAAs are converted into L-amino acids via amino acid racemases (Ala racemase, Asp racemase and broad substrate specificity amino acid racemase), and converted into α-keto acid via d-serine ammonia-lyase, whereas DAA-containing di-/tri-muropeptides can be hydrolyzed by peptidases (dipeptidase and D-aminopeptidase). Overall, this study reveals the identity and activity of deep marine sedimentary archaea involved in DAA metabolism, shedding light on the mineralization and biogeochemical cycling of DAAs in the deep marine sediments., 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. Published by Elsevier B.V.)