Genome-centric view of carbon processing in thawing permafrost

Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data

Recovering genomes from shotgun metagenomic sequence data allows detailed taxonomic and functional characterization of individual species or strains in a microbial community. Retrieving these metagenome-assembled genomes (MAGs) involves seven stages. First, low-quality bases, along with adapter and host sequences, are removed. Second, overlapping sequences are assembled to create longer contiguous fragments. Third, these fragments are clustered based on sequence composition and abundance. Fourth, these sequence clusters, or bins, undergo rounds of quality assessment and refinement to yield MAGs. The optional fifth stage is dereplication of MAGs to select representatives. Next, each MAG is taxonomically classified. The optional seventh stage is assessing the fraction of diversity that has been recovered. The output of this protocol is draft genomes, which can provide invaluable clues about uncultured organisms. This protocol takes ~1 week to run, depending on computational resources available, and requires prior experience with high-performance computing, shell script programming and Python.

The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate

Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

High Diversity and Functional Potential of Undescribed "Acidobacteriota" in Danish Wastewater Treatment Plants

Microbial communities in water resource recovery facilities encompass a large diversity of poorly characterized lineages that could have undescribed process-critical functions. Recently, it was shown that taxa belonging to "Acidobacteriota" are abundant in Danish full-scale activated sludge wastewater treatment plants (WWTP), and here we investigated their diversity, distribution, and functional potential. "Acidobacteriota" taxa were identified using a comprehensive full-length 16S rRNA gene reference dataset and amplicon sequencing surveys across 37 WWTPs. Members of this phylum were diverse, belonging to 14 families, eight of which are completely uncharacterized and lack type strains. Several lineages were abundant, with relative abundances of up to 5% of the microbial community. Genome annotation and metabolic reconstruction of 50 high-quality "Acidobacteriota" metagenome-assembled genomes (MAGs) from 19 WWTPs showed high metabolic diversity and potential involvement in nitrogen and phosphorus removal and iron reduction. Fluorescence in situ hybridization (FISH) using newly-designed probes revealed cells with diverse morphologies, predominantly located inside activated sludge flocs. FISH in combination with Raman microspectroscopy revealed ecophysiological traits in probe-defined cells from the families Holophagaceae, Thermoanaerobaculaceae, and Vicinamibacteraceae, and families with the placeholder name of midas_f_502, midas_f_973, and midas_f_1548. Members of these lineages had the potential to be polyphosphate-accumulating organisms (PAOs) as intracellular storage was observed for the key compounds polyphosphate and glycogen.

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile-but to a greater extent in the subsoil-physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

A genomic catalog of Earth's microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance

The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Mechanisms controlling CO₂ and CH₄ production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO₂ and CH₄ dynamics.

Metagenomic tools in microbial ecology research

Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.

Genome-Resolved Metagenomics Is Essential for Unlocking the Microbial Black Box of the Soil

Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A recent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are now enabling a deeper investigation of the evolutionary and functional role of high-complex soil microbiomes, promoting new knowledge from the reuse and sharing of multi-omics data.

Altered microbial structure and function after thermokarst formation

Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.

Substrate availability drives mixed culture fermentation of glucose to lactate at steady state

Mixed-culture fermentation (MCF) enables carbon recycling from complex organic waste streams into valuable feedstock chemicals. Using complex microbial consortia, MCF systems can be tuned to produce a range of biochemicals to meet market demand. However, the metabolic mechanisms and community interactions which drive biochemical production changes under differing conditions are currently poorly understood. These mechanisms are critical to useful MCF production models. Furthermore, predictable product transitions are currently limited to pH-driven changes between butyrate and ethanol, and chain-elongation (fed by lactate, acetate, and ethanol) to butyrate, valerate, and hexanoate. Lactate, a high-value biopolymer feedstock chemical, has been observed in transition states, but sustained production has not been described. In this study, steady state lactate production was achieved by increasing the organic loading rate of a butyrate-producing system from limiting to nonlimiting conditions at pH 5.5. Crucially, butyrate production resumed upon return to substrate-limited conditions. 16S ribosomal DNA community profiling combined with metaproteomics demonstrated that the butyrate-producing lineage Megasphaera redirected carbon flow through the methylglyoxal bypass when substrate was nonlimiting, which altered the community structure and metabolic expression toward lactate production. This metabolic mechanism can be included in future MCF models to describe the changes in product generation in substrate nonlimiting conditions.

Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw

It has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments, and thus their stability and capacity to prevent carbon mobilization during permafrost thaw, is poorly understood. We have followed the dynamic interactions between iron and carbon using a space-for-time approach across a thaw gradient in Abisko (Sweden), where wetlands are expanding rapidly due to permafrost thaw. We show through bulk (selective extractions, EXAFS) and nanoscale analysis (correlative SEM and nanoSIMS) that organic carbon is bound to reactive Fe primarily in the transition between organic and mineral horizons in palsa underlain by intact permafrost (41.8 ± 10.8 mg carbon per g soil, 9.9 to 14.8% of total soil organic carbon). During permafrost thaw, water-logging and O₂ limitation lead to reducing conditions and an increase in abundance of Fe(III)-reducing bacteria which favor mineral dissolution and drive mobilization of both iron and carbon along the thaw gradient. By providing a terminal electron acceptor, this rusty carbon sink is effectively destroyed along the thaw gradient and cannot prevent carbon release with thaw.

Iron minerals trap carbon in permafrost, preventing microbial degradation and release to the atmosphere as CO₂, but the stability of this carbon as permafrost thaws is unclear. Here the authors use nanoscale analyses to show that thaw conditions stimulate Fe-reducing bacteria that trigger carbon release.

Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils

Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.

Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

Recent discoveries of mcr and mcr-like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high-quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. These findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

Permafrost underlies a large portion of the land in the Northern Hemisphere. It is proposed to be an extreme habitat and home for cold-adaptive microbial communities. Upon thaw permafrost is predicted to exacerbate increasing global temperature trend, where awakening microbes decompose millennia old carbon stocks. Yet our knowledge on composition, functional potential and variance of permafrost microbiome remains limited. In this study, we conducted a deep comparative metagenomic analysis through a 2 m permafrost core from Svalbard, Norway to determine key permafrost microbiome in this climate sensitive island ecosystem. To do so, we developed comparative metagenomics methods on metagenomic-assembled genomes (MAG). We found that community composition in Svalbard soil horizons shifted markedly with depth: the dominant phylum switched from Acidobacteria and Proteobacteria in top soils (active layer) to Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria in permafrost layers. Key metabolic potential propagated through permafrost depths revealed aerobic respiration and soil organic matter decomposition as key metabolic traits. We also found that Svalbard MAGs were enriched in genes involved in regulation of ammonium, sulfur and phosphate. Here, we provide a new perspective on how permafrost microbiome is shaped to acquire resources in competitive and limited resource conditions of deep Svalbard soils.

Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. Here we combined geophysical, geochemical, metagenomic and metabolomic measurements to profile microbial activities at a newly discovered cold seep in the deep sea. Metagenomic profiling revealed compositional and functional differentiation between near-surface sediments and deeper subsurface layers. In both sulfate-rich and sulfate-depleted depths, various archaeal and bacterial community members are actively oxidizing thermogenic hydrocarbons anaerobically. Depth distributions of hydrocarbon-oxidizing archaea revealed that they are not necessarily associated with sulfate reduction, which is especially surprising for anaerobic ethane and butane oxidizers. Overall, these findings link subseafloor microbiomes to various biochemical mechanisms for the anaerobic degradation of deeply-sourced thermogenic hydrocarbons.

Effects of set cathode potentials on microbial electrosynthesis system performance and biocathode methanogen function at a metatranscriptional level

Microbial electrosynthesis exploits the catalytic activity of microorganisms to utilize a cathode as an electron donor for reducing waste CO2 to valuable fuels and chemicals. Electromethanogenesis is the process of CO2 reduction to CH4 catalyzed by methanogens using the cathode directly as a source of electrons or indirectly via H2. Understanding the effects of different set cathode potentials on the functional dynamics of electromethanogenic communities is crucial for the rational design of cathode materials. Replicate enriched electromethanogenic communities were subjected to different potentials (- 1.0 V and - 0.7 V vs. Ag/AgCl) and the potential-induced changes were analyzed using a metagenomic and metatranscriptomic approach. The most abundant and transcriptionally active organism on the biocathodes was a novel species of Methanobacterium sp. strain 34x. The cathode potential-induced changes limited electron donor availability and negatively affected the overall performance of the reactors in terms of CH4 production. Although high expression of key genes within the methane and carbon metabolism pathways was evident, there was no significant difference in transcriptional response to the different set potentials. The acetyl-CoA decarbonylase/synthase (ACDS) complex were the most highly expressed genes, highlighting the significance of carbon assimilation under limited electron donor conditions and its link to the methanogenesis pathway.

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

BACKGROUND

Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward.

RESULTS

Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level.

CONCLUSIONS

Our results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems. Video Abstract.

Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters

Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82-94 % of chromosomes could be correctly recovered and binned, only 38-44 % of GIs and 1-29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0-45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

Ombrotrophic bogs accumulate large stores of soil carbon that eventually decompose to carbon dioxide and methane. Carbon accumulates because Sphagnum mosses slow microbial carbon decomposition processes, leading to the production of labile intermediate compounds. Acetate is a major product of Sphagnum degradation, yet rates of hydrogenotrophic methanogenesis far exceed rates of aceticlastic methanogenesis, suggesting that alternative acetate mineralization processes exist. Two possible explanations are aerobic respiration and anaerobic respiration via humic acids as electron acceptors. While these processes have been widely observed, microbial community interactions linking Sphagnum degradation and acetate mineralization remain cryptic. In this work, we use ordination and network analysis of functional genes from 110 globally distributed peatland metagenomes to identify conserved metabolic pathways in Sphagnum bogs. We then use metagenome-assembled genomes (MAGs) from McLean Bog, a Sphagnum bog in New York State, as a local case study to reconstruct pathways of Sphagnum degradation and acetate mineralization. We describe metabolically flexible Acidobacteriota MAGs that contain all genes to completely degrade Sphagnum cell wall sugars under both aerobic and anaerobic conditions. Finally, we propose a hypothetical model of acetate oxidation driven by changes in peat redox potential that explain how bogs may circumvent aceticlastic methanogenesis through aerobic and humics-driven respiration.

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding

BACKGROUND

The Boran (Bos indicus), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at sub-optimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle.

RESULTS

We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways.

CONCLUSIONS

This study is the first to identify 1200 high-quality African rumen-specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.

Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses

Nitrogen (N₂ )-fixing moss microbial communities play key roles in nitrogen cycling of boreal forests. Forest type and leaf litter inputs regulate moss abundance, but how they control moss microbiomes and N₂ -fixation remains understudied. We examined the impacts of forest type and broadleaf litter on microbial community composition and N₂ -fixation rates of Hylocomium splendens and Pleurozium schreberi. We conducted a moss transplant and leaf litter manipulation experiment at three sites with paired paper birch (Betula neoalaskana) and black spruce (Picea mariana) stands in Alaska. We characterized bacterial communities using marker gene sequencing, determined N₂ -fixation rates using stable isotopes (¹⁵ N₂ ) and measured environmental covariates. Mosses native to and transplanted into spruce stands supported generally higher N₂ -fixation and distinct microbial communities compared to similar treatments in birch stands. High leaf litter inputs shifted microbial community composition for both moss species and reduced N₂ -fixation rates for H. splendens, which had the highest rates. N₂ -fixation was positively associated with several bacterial taxa, including cyanobacteria. The moss microbiome and environmental conditions controlled N₂ -fixation at the stand and transplant scales. Predicted shifts from spruce- to deciduous-dominated stands will interact with the relative abundances of mosses supporting different microbiomes and N₂ -fixation rates, which could affect stand-level N inputs.

The invisible life inside plants: Deciphering the riddles of endophytic bacterial diversity

Endophytic bacteria often promote plant growth and protect their host plant against pathogens, herbivores, and abiotic stresses including drought, increased salinity or pollution. Current agricultural practices are being challenged in terms of climate change and the ever-increasing demand for food. Therefore, the rational exploitation of bacterial endophytes to increase the productivity and resistance of crops appears to be very promising. However, the efficient and larger-scale use of bacterial endophytes for more effective and sustainable agriculture is hindered by very little knowledge on molecular aspects of plant-endophyte interactions and mechanisms driving bacterial communities in planta. In addition, since most of the information on bacterial endophytes has been obtained through culture-dependent techniques, endophytic bacterial diversity and its full biotechnological potential still remain highly unexplored. In this study, we discuss the diversity and role of endophytic populations as well as complex interactions that the endophytes have with the plant and vice versa, including the interactions leading to plant colonization. A description of biotic and abiotic factors influencing endophytic bacterial communities is provided, along with a summary of different methodologies suitable for determining the diversity of bacterial endophytes, mechanisms governing the assembly and structure of bacterial communities in the endosphere, and potential biotechnological applications of endophytes in the future.

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.IMPORTANCE Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the Deltaproteobacteria, Firmicutes, and Euryarchaeota. Advances in next-generation sequencing technologies have enabled large-scale cultivation-independent surveys of diverse and poorly characterized microorganisms from numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators and their depth-discrete activities in thawing permafrost. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog

Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal-associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, soils and groundwater, raising questions regarding their metabolic capacities and evolutionary relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis with hydrogen and carbon dioxide as the substrates. Genomes from two clades of groundwater-associated Elusimicrobia often encode a new group of nitrogenase paralogs that co-occur with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. We identified similar genomic loci in genomes of bacteria from the Gracilibacteria phylum and the Myxococcales order and predict that the gene clusters reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated Elusimicrobia clades nest phylogenetically within two free-living-associated clades. Thus, we propose an evolutionary trajectory in which some Elusimicrobia adapted to animal-associated lifestyles from free-living species via genome reduction.

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 10⁸ cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

To Dereplicate or Not To Dereplicate?

Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences.

Metagenome-assembled genomes (MAGs) expand our understanding of microbial diversity, evolution, and ecology. Concerns have been raised on how sequencing, assembly, binning, and quality assessment tools may result in MAGs that do not reflect single populations in nature. Here, we reflect on another issue, i.e., how to handle highly similar MAGs assembled from independent data sets. Obtaining multiple genomic representatives for a species is highly valuable, as it allows for population genomic analyses; however, when retaining genomes of closely related populations, it complicates MAG quality assessment and abundance inferences. We show that (i) published data sets contain a large fraction of MAGs sharing >99% average nucleotide identity, (ii) different software packages and parameters used to resolve this redundancy remove very different numbers of MAGs, and (iii) the removal of closely related genomes leads to losses of population-specific auxiliary genes. Finally, we highlight some approaches that can infer strain-specific dynamics across a sample series without dereplication.

Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

Microbial genomics amidst the Arctic crisis

The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.

The role of changing temperature in microbial metabolic processes during permafrost thaw

Approximately one fourth of the Earth's Northern Hemisphere is underlain by permafrost, earth materials (soil, organic matter, or bedrock), that has been continuously frozen for at least two consecutive years. Numerous studies point to evidence of accelerated climate warming in the Arctic and sub-Arctic where permafrost is located. Changes to permafrost biochemical processes may critically impact ecosystem processes at the landscape scale. Here, we sought to understand how the permafrost metabolome responds to thaw and how this response differs based on location (i.e. chronosequence of permafrost formation constituting diverse permafrost types). We analyzed metabolites from microbial cells originating from Alaskan permafrost. Overall, permafrost thaw induced a shift in microbial metabolic processes. Of note were the dissimilarities in biochemical structure between frozen and thawed samples. The thawed permafrost metabolomes from different locations were highly similar. In the intact permafrost, several metabolites with antagonist properties were identified, illustrating the competitive survival strategy required to survive a frozen state. Interestingly, the intensity of these antagonistic metabolites decreased with warmer temperature, indicating a shift in ecological strategies in thawed permafrost. These findings illustrate the impact of change in temperature and spatial variability as permafrost undergoes thaw, knowledge that will become crucial for predicting permafrost biogeochemical dynamics as the Arctic and Antarctic landscapes continue to warm.

Niche differentiation is spatially and temporally regulated in the rhizosphere

The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.

Soil carbon loss with warming: New evidence from carbon-degrading enzymes

Climate warming affects soil carbon (C) dynamics, with possible serious consequences for soil C stocks and atmospheric CO2 concentrations. However, the mechanisms underlying changes in soil C storage are not well understood, hampering long-term predictions of climate C-feedbacks. The activity of the extracellular enzymes ligninase and cellulase can be used to track changes in the predominant C sources of soil microbes and can thus provide mechanistic insights into soil C loss pathways. Here we show, using meta-analysis, that reductions in soil C stocks with warming are associated with increased ratios of ligninase to cellulase activity. Furthermore, whereas long-term (≥5 years) warming reduced the soil recalcitrant C pool by 14%, short-term warming had no significant effect. Together, these results suggest that warming stimulates microbial utilization of recalcitrant C pools, possibly exacerbating long-term climate-C feedbacks.

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining

Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.

Climate change microbiology - problems and perspectives

The signs of climate change are undeniable, and the inevitable impact for Earth and all its inhabitants is a serious concern. Ice is melting, sea levels are rising, biodiversity is declining, precipitation has increased, atmospheric levels of carbon dioxide and greenhouse gases are alarmingly high, and extreme weather conditions are becoming increasingly common. But what role do microorganisms have in this global challenge? In this Viewpoint article, several experts in the field discuss the microbial contributions to climate change and consider the effects of global warming, extreme weather, flooding and other consequences of climate change on microbial communities in the ocean and soil, on host-microbiota interactions and on the global burden of infectious diseases and ecosystem processes, and they explore open questions and research needs.

The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities

This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities.

IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems

The discovery of the complete ammonia oxidizing (comammox) bacteria overturns the traditional two-organism nitrification paradigm which largely underpins the design and operation of nitrogen removal during wastewater treatment. Quantifying the abundance, diversity, and activity of comammox bacteria in wastewater treatment systems is important for ensuring a clear understanding of the nitrogen biotransformations responsible for ammonia removal. To this end, we conducted a yearlong survey of 14 full-scale nitrogen removal systems including mainstream conventional and simultaneous nitrification-denitrification and side-stream partial nitrification-anammox systems with varying process configurations. Metagenomics and genome-resolved metagenomics identified comammox bacteria in mainstream conventional and simultaneous nitrification-denitrification systems, with no evidence for their presence in side-stream partial nitrification-anammox systems. Further, comammox bacterial diversity was restricted to clade A and these clade A comammox bacteria were detected in systems with long solids retention times (>10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination.

IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

Microbiome of vineyard soils is shaped by geography and management

BACKGROUND

Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management.

RESULTS

Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil.

CONCLUSIONS

Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.

Microbial Community Structure and Methane Cycling Potential along a Thermokarst Pond-Peatland Continuum

The thawing of ice-rich permafrost soils in northern peatlands leads to the formation of thermokarst ponds, surrounded by organic-rich soils. These aquatic ecosystems are sites of intense microbial activity, and CO₂ and CH₄ emissions. Many of the pond systems in northern landscapes and their surrounding peatlands are hydrologically contiguous, but little is known about the microbial connectivity of concentric habitats around the thermokarst ponds, or the effects of peat accumulation and infilling on the microbial communities. Here we investigated microbial community structure and abundance in a thermokarst pond-peatland system in subarctic Canada. Several lineages were ubiquitous, supporting a prokaryotic continuum from the thermokarst pond to surrounding peatlands. However, the microbial community structure shifted from typical aerobic freshwater microorganisms (Betaproteobacteria and Alphaproteobacteria) in the pond towards acidophilic and anaerobic lineages (Acidobacteria and Choroflexi) in the connected peatland waters, likely selected by the acidification of the water by Sphagnum mosses. Marked changes in abundance and community composition of methane cycling microorganisms were detected along the thermokarst pond-peatland transects, suggesting fine tuning of C-1 carbon cycling within a highly connected system, and warranting the need for higher spatial resolution across the thermokarst landscape to accurately predict net greenhouse gas emissions from northern peatlands.