Biodiversity in mountain soils above the treeline

Biological diversity in mountain ecosystems has been increasingly studied over the last decade. This is also the case for mountain soils, but no study to date has provided an overall synthesis of the current state of knowledge. Here we fill this gap with a first global analysis of published research on cryptogams, microorganisms, and fauna in mountain soils above the treeline, and a structured synthesis of current knowledge. Based on a corpus of almost 1400 publications and the expertise of 37 mountain soil scientists worldwide, we summarise what is known about the diversity and distribution patterns of each of these organismal groups, specifically along elevation, and provide an overview of available knowledge on the drivers explaining these patterns and their changes. In particular, we document an elevation-dependent decrease in faunal diversity above the treeline, while for cryptogams there is an initial increase above the treeline, followed by a decrease towards the nival belt. Thus, our data confirm the key role that elevation plays in shaping the biodiversity and distribution of these organisms in mountain soils. The response of prokaryote diversity to elevation, in turn, was more diverse, whereas fungal diversity appeared to be substantially influenced by plants. As far as available, we describe key characteristics, adaptations, and functions of mountain soil species, and despite a lack of ecological information about the uncultivated majority of prokaryotes, fungi, and protists, we illustrate the remarkable and unique diversity of life forms and life histories encountered in alpine mountain soils. By applying rule- as well as pattern-based literature-mining approaches and semi-quantitative analyses, we identified hotspots of mountain soil research in the European Alps and Central Asia and revealed significant gaps in taxonomic coverage, particularly among biocrusts, soil protists, and soil fauna. We further report thematic priorities for research on mountain soil biodiversity above the treeline and identify unanswered research questions. Building upon the outcomes of this synthesis, we conclude with a set of research opportunities for mountain soil biodiversity research worldwide. Soils in mountain ecosystems above the treeline fulfil critical functions and make essential contributions to life on land. Accordingly, seizing these opportunities and closing knowledge gaps appears crucial to enable science-based decision making in mountain regions and formulating laws and guidelines in support of mountain soil biodiversity conservation targets.

Exploring prokaryotic diversity in permafrost-affected soils of Ladakh's Changthang region and its geochemical drivers

Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R2 = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).

Quantity Versus Quality: Links Between Soil Organic Matter and Bacterial Community Composition Along a Geoclimatic Gradient

Soil organic matter (SOM) quantity drives soil bacterial community composition from the regional to global scale. Qualitative characteristics of SOM are known to affect soil bacterial communities in manipulation experiments. However, it remains unresolved how strongly SOM characteristics affect soil bacterial community composition at the macroscale. Here, we investigated how quantity versus qualitative characteristics of SOM shape community composition along a biogeochemical gradient of grassland soils. We assessed relative abundance patterns of soil bacteria and characterised SOM based on scalable methods. Soils with higher SOM content (along a continuum between 0.6% and 18.7% SOC) and acidic pH (along a continuum between pH 4.1-6.7) hosted fewer narrowly distributed taxa (i.e., taxa occurring in few sites) and therefore had lower bacterial alpha diversity. We could explain a larger fraction of bacterial community composition (up to 59.6% of 16S rRNA reads) in these soils. Consequently, we understand community composition in low-SOM soils less than in high-SOM soils, because the drivers of narrowly distributed taxa remain poorly understood. Qualitative SOM characteristics did not strongly affect biogeographical patterns of widely distributed soil bacterial taxa. This suggests that broad aspects of SOM quality do not dominate soil bacterial community composition at the investigated macroscale.

Pyrrhotite promote aerobic granular sludge formation in dye wastewater: pH, interfacial free energy, and microbial community evolution

This study introduces a technique utilizing natural pyrrhotite powder as a nucleating agent in four sequencing batch reactors (SBRs) for the treatment of dye wastewater. Through analysis of various factors including pH, pyrrhotite surface free energy, sludge zeta potential, and shifts in microbial communities, the mechanism by which pyrrhotite facilitates the formation of aerobic granular sludge (AGS) is elucidated. Over 140 days of continuous operation under neutral conditions, natural pyrrhotite rapidly cultivated AGS under neutral conditions. The structure of the sludge was compact and the settling properties were satisfactory (SVI30/SVI5 close to 1). Reductions in both sludge zeta potential and interfacial free energy of pyrrhotite correlated with increased hydrophobicity of AGS, leading to enhanced sludge aggregation. Changes in pH, sludge interfacial free energy, and zeta potential were found to influence the microbial community composition and diversity within the sludge.This study provides a novel approach for dye wastewater treatment.

Trees shape the soil microbiome of a temperate agrosilvopastoral and syntropic agroforestry system

Agroforestry systems are multifunctional land-use systems that promote soil life. Despite their large potential spatio-temporal complexity, the majority of studies that investigated soil organisms in temperate cropland agroforestry systems focused on rather non-complex systems. Here, we investigated the topsoil and subsoil microbiome of two complex and innovative alley cropping systems: an agrosilvopastoral system combining poplar trees, crops, and livestock and a syntropic agroforestry system combining 35 tree and shrub species with forage crops. Increasing soil depth resulted in a decline of bacterial and fungal richness and a community shift towards oligotrophic taxa in both agroforestry systems, which we attribute to resource-deprived conditions in subsoil. At each soil depth, the microbiome of the tree rows was compositionally distinct from the crop rows. We detected a shift towards beneficial microorganisms as well as a decline in putative phytopathogens under the trees as compared to the crop rows. Finally, based on our results on community dissimilarity, we found that compared to an open cropland without trees, spatial heterogeneity introduced by the tree rows in the agrosilvopastoral system translated into a compositionally less homogeneous soil microbiome, highlighting the potential of agroforestry to counteract the homogenization of the soil microbiome through agriculture.

Gallic and Ellagic Acids Differentially Affect Microbial Community Structures and Methane Emission When Using a Rumen Simulation Technique

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.

Enhanced warming of European mountain permafrost in the early 21st century

Mountain permafrost, constituting 30% of the global permafrost area, is sensitive to climate change and strongly impacts mountain ecosystems and communities. This study examines 21st century permafrost warming in European mountains using decadal ground temperature data from sixty-four boreholes in the Alps, Scandinavia, Iceland, Sierra Nevada and Svalbard. During 2013-2022, warming rates at 10 metres depth exceed 1 °C dec-1 in cases, generally surpassing previous estimates because of accelerated warming and the use of a comprehensive data set. Substantial permafrost warming occurred at cold and ice-poor bedrock sites at high elevations and latitudes, at rates comparable to surface air temperature increase. In contrast, latent heat effects in ice-rich ground near 0 °C reduce warming rates and mask important changes of mountain permafrost substrates. The warming patterns observed are consistent across all sites, depths and time periods. For the coming decades, the propagation of permafrost warming to greater depths is largely predetermined already.

Strengthened plant-microorganism interaction after topsoil removal cause more deterministic microbial assembly processes and increased soil nitrogen mineralization

Topsoil removal, among other restoration measures, has been recognized as one of the most successful methods to restore biodiversity and ecosystem functioning in European grasslands. However, knowledge about how removal as well as other restoration methods influence interactions between plant and microbial communities is very limited. The aims of the current study were to understand the impact of topsoil removal on plant-microorganism interactions and on soil nitrogen (N) mineralization, as one example of ecosystem functioning. We examined how three different grassland restoration methods, namely 'Harvest only', 'Topsoil removal' and 'Topsoil removal + Propagules (plant seed addition)', affected i) the interactions between plants and soil microorganisms, ii) soil microbial community assembly processes, and iii) soil N mineralization. We compared the outcome of these three restoration methods to initial degraded and target semi-natural grasslands in the Canton of Zurich, Switzerland. We were able to show that 'Topsoil removal' and 'Topsoil removal + Propagules', but not 'Harvest only', reduced the soil total N pool and available N concentration, but increased soil N mineralization and strengthened the plant-microorganism interactions. Microbial community assembly processes shifted towards more deterministic after both topsoil removal treatments. These shifts could be attributed to an increase in dispersal limitation and selection due to stronger interactions between plants and soil microorganisms. The negative relationship between soil N mineralization and microbial community stochasticity indicated that microbial assembly processes, to some extent, can be incorporated into model predictions of soil functions. Overall, the results suggest that topsoil removal may change the microbial assembly processes and thus the functioning of grassland ecosystems by enhancing the interaction between plants and soil microorganisms.

Verrucomicrobia of the Family Chthoniobacteraceae Participate in Xylan Degradation in Boreal Peat Soils

The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type hemicelluloses represent one of the most actively decomposed peat constituents. The aim of this work was to characterize the microorganisms capable of hydrolyzing xylan under the anoxic conditions typical of peatland soils. The laboratory incubation of peat samples with xylan resulted in the pronounced enrichment of several phylotypes affiliated with the Verrucomicrobiota, Firmicutes, and Alphaproteobacteria. Sequencing of the metagenome of the enrichment culture allowed us to recover high-quality metagenome-assembled genomes (MAGs) assigned to the genera Caproiciproducens, Clostridium, Bacillus (Firmicutes), and Rhizomicrobium (Alphaproteobacteria), Cellulomonas (Actinobacteriota) and the uncultured genus-level lineage of the family Chthoniobacteraceae (Verrucomicrobiota). The latter bacterium, designated "Candidatus Chthoniomicrobium xylanophilum" SH-KS-3, dominated in the metagenome and its MAG was assembled as a complete closed chromosome. An analysis of the SH-KS-3 genome revealed potential endo-1,4-beta-xylanases, as well as xylan beta-1,4-xylosidases and other enzymes involved in xylan utilization. A genome analysis revealed the absence of aerobic respiration and predicted chemoheterotrophic metabolism with the capacity to utilize various carbohydrates, including cellulose, and to perform fermentation or nitrate reduction. An analysis of other MAGs suggested that Clostridium and Rhizomicrobium could play the role of primary xylan degraders while other community members probably took advantage of the availability of xylo-oligosaccharides and xylose or utilized low molecular weight organics.

Organic farming systems improve soil quality and shape microbial communities across a cotton-based crop rotation in an Indian Vertisol

The adverse effects of intensified cropland practices on soil quality and biodiversity become especially evident in India, where nearly 60% of land is dedicated to cultivation and almost 30% of soil is already degraded. Intensive agricultural practice significantly contributes to soil degradation, highlighting the crucial need for effective countermeasures to support sustainable development goals. A long-term experiment, established in the semi-arid Nimar Valley (India) in 2007, monitors the effect of organic and conventional management on the plant-soil system in a Vertisol. The focus of our study was to assess how organic and conventional farming systems affect biological and chemical soil quality indicators. Additionally, we followed the community structure of the soil microbiome throughout the vegetation phase under soya or cotton cultivation in the year 2019. We found that organic farming enhanced soil organic carbon and nitrogen content, increased microbial abundance and activity, and fostered distinct microbial communities associated with traits in nutrient mineralization. In contrast, conventional farming enhanced the abundance of bacteria involved in ammonium oxidation suggesting high nitrification and subsequent nitrogen losses with regular mineral fertilization. Our findings underscore the value of adopting organic farming approaches in semi-arid subtropical regions to rectify soil quality and minimize nitrogen losses.

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

Globally distributed marine Gemmatimonadota have unique genomic potentials

BACKGROUND

Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.

RESULTS

Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.

CONCLUSIONS

This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.

Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from an ∼1000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift, with the importance of drift decreasing but that of dispersal limitation increasing with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.

Linking the composition of cryoconite prokaryotic communities in the Arctic, Antarctic, and Central Caucasus with their chemical characteristics

Cryoconites are the deposits on the surface of glaciers that create specific ecological niches for the development of microorganism communities. The sediment material can vary in origin, structure, and nutrient content, creating local variations in the growth conditions. An additional factor of variability is the location of the glaciers, as they are found in different climatic zones in the high mountain regions and closer to the poles. Here, using the analysis of amplicon sequencing of the 16S rRNA gene, we studied the taxonomic composition of the prokaryotic communities from glaciers from remote regions, including the Arctic (Mushketova on the Severnaya Zemlya, IGAN in Polar Ural), Antarctic (Pimpirev on the Livingstone Island) and Central Caucasus (Skhelda and Garabashi) and connected it with the variation of the physicochemical characteristics of the substrate: pH, carbon, nitrogen, macro- and microelements. The cryoconite microbiomes were comprised of specific for this environment phyla (mostly Pseudomonadota, Cyanobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota), but each glacier had a unique taxonomic imprint. The core microbiome between regions was composed of only a few ASVs, among which the most likely globally distributed ones attributed to Polaromonas sp., Rhodoferax sp., Cryobacterium sp., and Hymenobacter frigidus. The WGSNA defined clusters of co-occurring ASVs between microbiomes, that significantly change their abundance corresponding with the variation of chemical parameters of cryoconites, but do not fully coincide with their regional separation. Thus, our work demonstrates that the chemical characteristics of the sediment material can explain the variation in the cryoconite prokaryotic community which is not always linked to geographic isolation.

A case study on the application of spore sampling for the monitoring of macrofungi

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.

Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach

Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.

Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity

Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.

Metagenomic insights into the wastewater resistome before and after purification at large‑scale wastewater treatment plants in the Moscow city

Wastewater treatment plants (WWTPs) are considered to be hotspots for the spread of antibiotic resistance genes (ARGs). We performed a metagenomic analysis of the raw wastewater, activated sludge and treated wastewater from two large WWTPs responsible for the treatment of urban wastewater in Moscow, Russia. In untreated wastewater, several hundred ARGs that could confer resistance to most commonly used classes of antibiotics were found. WWTPs employed a nitrification/denitrification or an anaerobic/anoxic/oxic process and enabled efficient removal of organic matter, nitrogen and phosphorus, as well as fecal microbiota. The resistome constituted about 0.05% of the whole metagenome, and after water treatment its share decreased by 3-4 times. The resistomes were dominated by ARGs encoding resistance to beta-lactams, macrolides, aminoglycosides, tetracyclines, quaternary ammonium compounds, and sulfonamides. ARGs for macrolides and tetracyclines were removed more efficiently than beta-lactamases, especially ampC, the most abundant ARG in the treated effluent. The removal efficiency of particular ARGs was impacted by the treatment technology. Metagenome-assembled genomes of multidrug-resistant strains were assembled both for the influent and the treated effluent. Ccomparison of resistomes from WWTPs in Moscow and around the world suggested that the abundance and content of ARGs depend on social, economic, medical, and environmental factors.

Selenium- and chitosan-modified biochars reduce methylmercury contents in rice seeds with recruiting Bacillus to inhibit methylmercury production

Biochar could reshape microbial communities, thereby altering methylmercury (MeHg) concentrations in rice rhizosphere and seeds. However, it remains unclear whether and how biochar amendment perturbs microbe-mediated MeHg production in mercury (Hg) contaminated paddy soil. Here, we used pinecone-derived biochar and its six modified biochars to reveal the disturbance. Results showed that selenium- and chitosan-modified biochar significantly reduced MeHg concentrations in the rhizosphere by 85.83% and 63.90%, thereby decreasing MeHg contents in seeds by 86.37% and 75.50%. The two modified bicohars increased the abundance of putative Hg-resistant microorganisms Bacillus, the dominant microbe in rhizosphere. These reductions about MeHg could be facilitated by biochar sensitive microbes such as Oxalobacteraceae and Subgroup_7. Pinecone-derived biochar increased MeHg concentration in rhizosphere but unimpacted MeHg content in seeds was observed. This biochar decreased the abundance in Bacillus but enhanced in putative Hg methylator Desulfovibrio. The increasing MeHg concentration in rhizosphere could be improved by biochar sensitive microbes such as Saccharimonadales and Clostridia. Network analysis showed that Saccharimonadales and Clostridia were the most prominent keystone taxa in rhizosphere, and the three biochars manipulated abundances of the microbes related to MeHg production in rhizosphere by those biochar sensitive microbes. Therefore, selenium- and chitosan-modified biochar could reduce soil MeHg production by these microorganisms, and is helpful in controlling MeHg contamination in rice.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

Opening Pandora's Box: Neglected Biochemical Potential of Permafrost-Associated Fungal Communities in a Warming Climate

Permafrost, a vast storage reservoir of frozen organic matter, is rapidly thawing due to climate change, releasing previously preserved carbon into the environment. This phenomenon has significant consequences for microbial communities, including fungi, inhabiting permafrost-associated regions. In this review, we delve into the intricate interplay between permafrost thawing and fungal diversity and functionality with an emphasis on thermokarst lakes. We explore how the release of organic carbon from thawing permafrost alters the composition and activities of fungal communities, emphasizing the potential for shifts in taxonomic diversity and functional gene expression. We discuss the formation of thermokarst lakes, as an example of permafrost thaw-induced ecological disruptions and their impact on fungal communities. Furthermore, we analyze the repercussions of these changes, including effects on nutrient cycling, plant productivity, and greenhouse gas (GHG) emissions. By elucidating the multifaceted relationship between permafrost thaw and aquatic fungi, this review provides valuable insights into the ecological consequences of ongoing climate change in permafrost-affected regions.

New insight into the granule formation in the reactor for enhanced biological phosphorus removal

While granulated activated sludge exhibits high productivity, the processes of granule formation are incompletely studied. The processes of granule formation and succession of communities were investigated in a laboratory sequencing batch reactor (SBR) under conditions for enhanced biological phosphorus removal (EBPR) using microbiological and molecular techniques. Active consumption of acetate, primarily by the phosphate-accumulating organisms (PAO), commenced at day 150 of cultivation. This was indicated by the high ratio of molar P-released/acetate uptake (0.73-0.77 P-mol/C-mol), characteristic of PAO. During this period, two types of granule-like aggregates formed spontaneously out of the activated sludge flocs. The aggregates differed in morphology and microbial taxonomic composition. While both aggregate types contained phosphorus-enriched bacterial cells, PAO prevailed in those of morphotype I, and glycogen-accumulating organisms (GAOs) were predominant in the aggregates of morphotype II. After 250 days, the elimination of the morphotype II aggregates from the reactor was observed. The subsequent selection of the community was associated with the development of the morphotype I aggregates, in which the relative abundance of PAO increased significantly, resulting in higher efficiency of phosphorus removal. Metagenomic analysis revealed a predominance of the organisms closely related to Candidatus Accumulibacter IС and IIС and of Ca. Accumulibacter IIB among the PAO. Based on the content of the genes of the key metabolic pathways, the genomes of potential PAO belonging to the genera Amaricoccus, Azonexus, Thauera, Zoogloea, Pinisolibacter, and Siculibacillus were selected. The patterns of physicochemical processes and the microbiome structure associated with granule formation and succession of the microbial communities were revealed.

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.

The Impact and Determinants of Mountainous Topographical Factors on Soil Microbial Community Characteristics

Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows.

Elevational changes in soil properties shaping fungal community assemblages in terrestrial forest

Environmental variables shifted by climate change act as driving factors in determining plant-associated microbial communities in terrestrial ecosystems. However, how elevation-induced changes in soil properties shape the microbial community in forest ecosystems remains less understood. Thus, the Pinus tabuliformis forests at elevations of 1500 m, 1900 m, and 2300 m above sea level were investigated to explore the effect of environmental factors on microbial assemblage. Significant changes in the soil physicochemical properties were found across the investigated elevations, such as soil moisture, temperature, pH, nitrogen (N), and phosphorus (P). Soil enzymatic activities, including soil sucrase, phosphatase, and dehydrogenase, were significantly affected by elevation, and sucrase showed a linear correlation with soil organic matter. Furthermore, the richness of fungal communities in the rhizosphere was decreased as elevation increased, while a humpback pattern was found for roots. Certain core microbiota members, such as Agaricomycetes, Leotiomycetes, and Pezizomycetes, were crucial in maintaining a stable ecological niche in both the root and rhizosphere. We also found that shifting of fungal communities in the rhizosphere were more related to physical properties (e.g., pH, soil moisture, and soil temperature), while changes in root fungal communities along elevation gradient were related mostly to soil nutrients (e.g., soil N and P). Overall, this study demonstrates that the assemblage of the root and rhizosphere fungal communities in P. tabuliformis forest primarily depends on elevation-induced changes in environmental variables and highlights the importance of predicting fungal responses to future climate change.

One Step Closer to Enigmatic USCα Methanotrophs: Isolation of a Methylocapsa-like Bacterium from a Subarctic Soil

The scavenging of atmospheric trace gases has been recognized as one of the lifestyle-defining capabilities of microorganisms in terrestrial polar ecosystems. Several metagenome-assembled genomes of as-yet-uncultivated methanotrophic bacteria, which consume atmospheric CH4 in these ecosystems, have been retrieved in cultivation-independent studies. In this study, we isolated and characterized a representative of these methanotrophs, strain D3K7, from a subarctic soil of northern Russia. Strain D3K7 grows on methane and methanol in a wide range of temperatures, between 5 and 30 °C. Weak growth was also observed on acetate. The presence of acetate in the culture medium stimulated growth at low CH4 concentrations (~100 p.p.m.v.). The finished genome sequence of strain D3K7 is 4.15 Mb in size and contains about 3700 protein-encoding genes. According to the result of phylogenomic analysis, this bacterium forms a common clade with metagenome-assembled genomes obtained from the active layer of a permafrost thaw gradient in Stordalen Mire, Abisco, Sweden, and the mineral cryosol at Axel Heiberg Island in the Canadian High Arctic. This clade occupies a phylogenetic position in between characterized Methylocapsa methanotrophs and representatives of the as-yet-uncultivated upland soil cluster alpha (USCα). As shown by the global distribution analysis, D3K7-like methanotrophs are not restricted to polar habitats but inhabit peatlands and soils of various climatic zones.

Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature

In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite-arsenopyrite concentrate at temperatures of 40-50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov.

Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.

Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production

The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm-3 day-1. Despite the ambient water temperature of ~ 10-20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm-3 day-1 at 55 °C. A novel moderately thermophilic "Desulforudis audaxviator"-clade SRP has been isolated in pure culture from the coal-bed water.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition

Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.

Metagenomics Revealed a New Genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species 'Candidatus Thiothrix putei' sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na+- and H+-Motive Energetics

Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1-55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.

The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm-3 day-1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.

Growing in Saltwater: Biotechnological Potential of Novel Methylotuvimicrobium- and Methylomarinum-like Methanotrophic Bacteria

Methanotrophic bacteria that possess a unique ability of using methane as a sole source of carbon and energy have attracted considerable attention as potential producers of a single-cell protein. So far, this biotechnology implied using freshwater methanotrophs, although many regions of the world have limited freshwater resources. This study aimed at searching for novel methanotrophs capable of fast growth in saltwater comparable in composition with seawater. A methane-oxidizing microbial consortium containing Methylomarinum- and Methylotuvimicrobium-like methanotrophs was enriched from sediment from the river Chernavka (water pH 7.5, total salt content 30 g L-1), a tributary river of the hypersaline Lake Elton, southern Russia. This microbial consortium, designated Ch1, demonstrated stable growth on natural gas in a bioreactor in media with a total salt content of 23 to 35.9 g L-1 at a dilution rate of 0.19-0.21 h-1. The highest biomass yield of 5.8 g cell dry weight (CDW)/L with a protein content of 63% was obtained during continuous cultivation of the consortium Ch1 in a medium with a total salt content of 29 g L-1. Isolation attempts resulted in obtaining a pure culture of methanotrophic bacteria, strain Ch1-1. The 16S rRNA gene sequence of strain Ch1-1 displayed 97.09-97.24% similarity to the corresponding gene fragments of characterized representatives of Methylomarinum vadi, methanotrophs isolated from marine habitats. The genome of strain Ch1-1 was 4.8 Mb in size and encoded 3 rRNA operons, and about 4400 proteins. The genome contained the gene cluster coding for ectoine biosynthesis, which explains the ability of strain Ch1-1 to tolerate high salt concentration.

New insights into enhanced biodegradation of 4-bromphenol in a nitrate-reducing system: Process performance and mechanism

Due to the recalcitrant nature of halogenated phenol, conventional anaerobic bioprocess is often limited by low removal efficiency and poor process stability. At the presence of electron acceptors such as nitrate, 4-bromophenol (4-BP) removal efficiency is significantly higher than that in the anaerobic control system, but the mechanism involved is still unclear. Therefore, an up-flow nitrate-reducing bioreactor (NRBR) was designed and consecutively performed for 215 days to explore the synergistic mechanism for BPs biodegradation and nitrate reduction. Complete 4-BP biodegradation could be obtained in NRBR at HRT and 4-BP loading rate of 24 h and 0.29 mol m - 3d - 1, while the TOC removal and nitrate reduction efficiencies were as high as 91.33±2.11% and 98.31±1.33%, respectively. Population evolution analyses revealed that the microorganisms involved in 4-BP debromination and biodegradation (Candidatus Peregrinibacteria, Denitratisoma, Anaerolineaceae and Ignavibacterium) as well as nitrate reduction (Denitratisoma, Anaerolineaceae, Limnobacter and Ignavibacterium) were significantly enriched in NRBR. Major intermediates during 4-BP biodegradation, including 4-bromocatechol, 4‑bromo-6-oxo-hexanoic acid and succinic acid were identified, while a distinct 4-BP biodegradation pathway via hydration, aromatic-ring cleavage, hydrolysis debromination and oxidation was expounded. Metagenomic analysis indicated that oxidation (had, pht4, boh, butA), hydrolysis debromination ((S)-2-haloacid dehalogenase) and bio-mineralization (gabD, sdhA) of 4-BP were largely enhanced in NRBR. Moreover, carbon, nitrogen, energy and amino acid metabolisms were significantly facilitated with the injection of nitrate in order to provide energy and electron, thus enhanced microbial activities and enzymatic reactions in NRBR. The proposed mechanism provides new insights into our mechanistic understanding of halogenated phenol biodegradation and the development of sustainable bioremediation strategies.

Fecal Microbiota and Diet Composition of Buryatian Horses Grazing Warm- and Cold-Season Grass Pastures

The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistological fecal studies of horse diet composition on steppe pasture. The alpha diversity analysis showed horses had a more abundant and diverse gut microbiota in summer. There were significant effects on the beta diversity of microbial families, which were clustered by the warm and cold season in a principal coordinate analysis (PCoA), with 45% of the variation explained by two principal coordinates. This clustering by season was further confirmed by the significant differences observed in the relative abundances of microbial families and genera. The obtained results can serve as an experimental substantiation for further study of the impact of pasture grasses, which have a pharmacological effect, on the diversity of the gut microbiome and horse health.

Unrecognized diversity and distribution of soil algae from Maritime Antarctica (Fildes Peninsula, King George Island)

Introduction

Eukaryotic algae in the top few centimeters of fellfield soils of ice-free Maritime Antarctica have many important effects on their habitat, such as being significant drivers of organic matter input into the soils and reducing the impact of wind erosion by soil aggregate formation. To better understand the diversity and distribution of Antarctic terrestrial algae, we performed a pilot study on the surface soils of Meseta, an ice-free plateau mountain crest of Fildes Peninsula, King George Island, being hardly influenced by the marine realm and anthropogenic disturbances. It is openly exposed to microbial colonization from outside Antarctica and connected to the much harsher and dryer ice-free zones of the continental Antarctic. A temperate reference site under mild land use, SchF, was included to further test for the Meseta algae distribution in a contrasting environment.

Methods

We employed a paired-end metabarcoding analysis based on amplicons of the highly variable nuclear-encoded ITS2 rDNA region, complemented by a clone library approach. It targeted the four algal classes, Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Xanthophyceae, representing key groups of cold-adapted soil algae.

Results

A surprisingly high diversity of 830 algal OTUs was revealed, assigned to 58 genera in the four targeted algal classes. Members of the green algal class Trebouxiophyceae predominated in the soil algae communities. The major part of the algal biodiversity, 86.1% of all algal OTUs, could not be identified at the species level due to insufficient representation in reference sequence databases. The classes Ulvophyceae and Xanthophyceae exhibited the most unknown species diversity. About 9% of the Meseta algae species diversity was shared with that of the temperate reference site in Germany.

Discussion

In the small portion of algal OTUs for which their distribution could be assessed, the entire ITS2 sequence identity with references shows that the soil algae likely have a wide distribution beyond the Polar regions. They probably originated from soil algae propagule banks in far southern regions, transported by aeolian transport over long distances. The dynamics and severity of environmental conditions at the soil surface, determined by high wind currents, and the soil algae's high adaptability to harsh environmental conditions may account for the high similarity of soil algal communities between the northern and southern parts of the Meseta.

Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes

BACKGROUND

Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze-thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found.

RESULTS

We observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming.

CONCLUSIONS

Our study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.

Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau

In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.

Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics

The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.

Effect of elevation on composition and diversity of fungi in the rhizosphere of a population of Deyeuxia angustifolia on Changbai Mountain, northeastern China

Soil fungi are a key component of terrestrial ecosystems and play a major role in soil biogeochemical cycling. Although the diversity and composition of fungal communities are regulated by many abiotic and biotic factors, the effect of elevation on soil fungal community diversity and composition remains largely unknown. In this study, the soil fungal composition and diversity in Deyeuxia angustifolia populations along an elevational gradient (1,690 m to 2020 m a.s.l.) were assessed, using Illumina MiSeq sequencing, on the north-facing slope of the Changbai Mountain, northeastern China. Our results showed that soil physicochemical parameters changed significantly along with the elevational gradients. The Ascomycota and Basidiomycota were the most dominant phyla along with the gradient. Alpha diversity of soil fungi decreased significantly with elevation. Soil nitrate nitrogen (NO₃^--N) was positively correlated with fungal richness and phylogenetic diversity (PD), indicating that soil nitrate nitrogen (NO₃^--N) is a key soil property determining fungal community diversity. In addition to soil nitrate content, soil pH and soil moisture were the most important environmental properties determining the soil fungal diversity. Our results suggest that the elevational changes in soil physicochemical properties play a key role in shaping the community composition and diversity of soil fungi. This study will allow us to better understand the biodiversity distribution patterns of soil microorganisms in mountain ecosystems.

Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns

Mat-forming fungi are common in forest and grassland soils across the world, where their activity contributes to important soil ecological processes. These fungi maintain dominance through aggressive and abundant hyphae that modify their internal physical and chemical environments and through these modifications select for what appears to be a suite of mycophilic bacteria. Here, the bacteria associated with the fungal mats of Leucopaxillus gentianeus and Leucopaxillus albissimus from western North America are compared to adjacent nonmat substrates. Within the mats, the bacterial richness and diversity were significantly reduced, and the community composition was significantly different. The bacterial community structure between the two fungal hosts was marginally significant and indicated a shared set of bacterial associates. The genera Burkholderia, Streptomyces, Bacillus, Paenibacillus, and Mycobacterium were significantly abundant within the fungal mats and represent core members of these hypha-rich environments. Comparison with the literature from fungal mat studies worldwide showed that these genera are common and often significantly found within fungal mats, further reinforcing the concept of a mycophilic bacterial guild. These genera are incorporated into a synthesis discussion in the context of our current understanding of the nature of fungal-bacterial interactions and the potential outcomes of these interactions in soil nutrient cycling, plant productivity, and human health. IMPORTANCE Fungi and bacteria are the most abundant and diverse organisms in soils (perhaps more so than any other habitat on earth), and together these microorganisms contribute to broad soil ecosystem processes. There is a suite of bacteria that appears consistently within the physical space called the hyphosphere, the area of influence surrounding fungal hyphae. How these bacteria are selected for, how they are maintained, and what broader ecological functions they perform are subjects of interest in this relatively new field-the cross-kingdom interactions between fungi and bacteria. Understanding their cooccurrence and their interactions can open new realms of understanding in soil ecological processes with global consequences.

Niche-mediated bacterial community composition in continental glacier alluvial valleys under cold and arid environments

Introduction

Bacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments.

Methods

Here, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics.

Results and discussion

The different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

Unboxing the black box-one step forward to understand the soil microbiome: A systematic review

Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.

Biogeochemical Activity of Methane-Related Microbial Communities in Bottom Sediments of Cold Seeps of the Laptev Sea

Bottom sediments at methane discharge sites of the Laptev Sea shelf were investigated. The rates of microbial methanogenesis and methane oxidation were measured, and the communities responsible for these processes were analyzed. Methane content in the sediments varied from 0.9 to 37 µmol CH₄ dm^-3. Methane carbon isotopic composition (δ¹³C-CH₄) varied from -98.9 to -77.6‱, indicating its biogenic origin. The rates of hydrogenotrophic methanogenesis were low (0.4-5.0 nmol dm^-3 day^-1). Methane oxidation rates varied from 0.4 to 1.2 µmol dm^-3 day^-1 at the seep stations. Four lineages of anaerobic methanotrophic archaea (ANME) (1, 2a-2b, 2c, and 3) were found in the deeper sediments at the seep stations along with sulfate-reducing Desulfobacteriota. The ANME-2a-2b clade was predominant among ANME. Aerobic ammonium-oxidizing Crenarchaeota (family Nitrosopumilaceae) predominated in the upper sediments along with heterotrophic Actinobacteriota and Bacteroidota, and mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae). Members of the genera Sulfurovum and Sulfurimonas occurred in the sediments of the seep stations. Mehtanotrophs of the classes Alphaproteobacteria (Methyloceanibacter) and Gammaproteobacteria (families Methylophilaceae and Methylomonadaceae) occurred in the sediments of all stations. The microbial community composition was similar to that of methane seep sediments from geographically remote areas of the global ocean.

A possible unique ecosystem in the endoglacial hypersaline brines in Antarctica

Here, we present the results related to a new unique terrestrial ecosystem found in an englacial hypersaline brine found in Northern Victoria Land (Antarctica). Both the geochemistry and microbial (prokaryotic and fungal) diversity revealed an unicity with respect to all the other known Antarctic brines and suggested a probable ancient origin mainly due a progressive cryoconcentration of seawater. The prokaryotic community presented some peculiarities, such as the occurrence of sequences of Patescibacteria (which can thrive in nutrient-limited water environments) or few Spirochaeta, and the presence of archaeal sequences of Methanomicrobia closely related to Methanoculleus, a methanogen commonly detected in marine and estuarine environments. The high percentage (35%) of unassigned fungal taxa suggested the presence of a high degree of undiscovered diversity within a structured fungal community (including both yeast and filamentous life forms) and reinforce the hypothesis of a high degree of biological uniqueness of the habitat under study.