Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core

Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.

Higher Microbial Biomass Accumulation on El Médano 464 Meteorite Compared with Adjacent Soils in the Atacama Desert

Chondritic meteorites can be appropriate substrates for the colonization of terrestrial microorganisms. However, determining whether organic compounds are intrinsic to the meteorite or come from external (terrestrial) contamination is still controversial. This research explores the molecular distribution and carbon isotopic composition of three lipid families (hydrocarbons, alkanoic acids, and alcohols) as well as DNA extracted from the interior of a CO carbonaceous chondrite named El Médano 464 (EM 464), discovered in the Atacama Desert in 2019. Three soil samples from the discovery area of EM 464 were collected and used as a background control for the composition and distribution of organic compounds. Our results revealed a higher abundance of the three lipid families in EM 464 compared with the surrounding soil samples. The organic compounds in EM 464 showed a mean δ13C value of -27.8 ± 0.5 for hydrocarbons (N = 20), -27.6 ± 1.1 for alkanoic acids (N = 17), and -27.5 ± 2.2‰ for alcohols (N = 18). These δ13C-depleted values are compatible with terrestrial biosignatures and are within isotopic values produced as a result of carbon fixation due to the Calvin cycle (δ13C of ca. from -19 to -34‰) widely used by photosynthetic terrestrial microorganisms. The DNA analysis (based on the bacterial 16S rRNA gene) showed a dominance of Proteobacteria (now Pseudomonadota) and Actinobacteriota in both meteorite and soils but exhibited different bacterial composition at the family level. This suggests that the microbial material inside the meteorite may have partially come from the adjacent soils, but we cannot rule out other sources, such as windborne microbes from distant locations. In addition, the meteorite showed higher bacterial diversity (H' = 2.4-2.8) compared with the three soil samples (H' = 0.3-1.8). Based on the distribution and δ13C value of organic compounds as well as DNA analysis, we suggest that most, if not all, of the organic compounds detected in the studied CO chondrite are of terrestrial origin (i.e., contamination). The terrestrial contamination of EM 464 by a diverse microbial community indicates that Atacama chondrites can offer distinctive ecological conditions for microorganisms to thrive in the harsh desert environment, which can result in an accumulation of microbial biomass and preservation of molecular fossils over time.

Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments

Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.

Diverse non-canonical electron bifurcating [FeFe]-hydrogenases of separate evolutionary origins in Hydrogenedentota

Hydrogenedentota, a globally distributed bacterial phylum-level lineage, is poorly understood. Here, we established a comprehensive genomic catalog of Hydrogenedentota, including a total of seven clades (or families) with 179 genomes, and explored the metabolic potential and evolutionary history of these organisms. We show that a single genome, especially those belonging to Clade 6, often encodes multiple hydrogenases with genomes in Clade 2, which rarely encode hydrogenases being the exception. Notably, most members of Hydrogenedentota contain a group A3 [FeFe]-hydrogenase (BfuABC) with a non-canonical electron bifurcation mechanism, in addition to substrate-level phosphorylation and electron transport-linked phosphorylation pathways, in energy conservation. Furthermore, we show that BfuABC from Hydrogenedentota fall into five sub-types. Phylogenetic analysis reveals five independent routes for the evolution of BfuABC homologs in Hydrogenedentota. We speculate that the five sub-types of BfuABC might be acquired from Bacillota (synonym Firmicutes) through separate horizontal gene transfer events. These data shed light on the diversity and evolution of bifurcating [FeFe]-hydrogenases and provide insight into the strategy of Hydrogenedentota to adapt to survival in various habitats.

IMPORTANCE

The phylum Hydrogenedentota is widely distributed in various environments. However, their physiology, ecology, and evolutionary history remain unknown, primarily due to the limited availability of the genomes and the lack of cultured representatives of the phylum. Our results have increased the knowledge of the genetic and metabolic diversity of these organisms and shed light on their diverse energy conservation strategies, especially those involving electron bifurcation with a non-canonical mechanism, which are likely responsible for their wide distribution. Besides, the organization and phylogenetic relationships of gene clusters coding for BfuABC in Hydrogenedentota provide valuable clues to the evolutionary history of group A3 electron bifurcating [FeFe]-hydrogenases.

Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments

BACKGROUND

The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS

The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO42--S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS

The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

IMPORTANCE

As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Comparative genomics reveals the adaptation of ammonia-oxidising Thaumarchaeota to arid soils

Thaumarchaeota are predominant in oligotrophic habitats such as deserts and arid soils, but their adaptations to these arid conditions are not well understood. In this study, we assembled 23 Thaumarchaeota genomes from arid and semi-arid soils collected from the Inner Mongolia Steppe and the Qinghai-Tibet Plateau. Using a comparative genomics approach, integrated with 614 Thaumarchaeota genomes from public databases, we identified the traits and evolutionary forces that contribute to their adaptations to aridity. Our results showed that the newly assembled genomes represent an early diverging group within the lineage of ammonia-oxidising Thaumarchaeota. While the genomic functions previously identified in arid soil lineages were conserved across terrestrial, shallow-ocean and deep-ocean lineages, several traits likely contribute to Thaumarchaeota's adaptation to aridity. These include chlorite dismutase, arsenate reductase, V-type ATPase and genes dealing with oxidative stresses. The acquisition and loss of traits at the last common ancestor of arid soil lineages may have facilitated the specialisation of Thaumarchaeota in arid soils. Additionally, the acquisition of unique adaptive traits, such as a urea transporter, Ca2+ :H+ antiporter, mannosyl-3-phosphoglycerate synthase and phosphatase, DNA end-binding protein Ku and phage shock protein A, further distinguishes arid soil Thaumarchaeota. This study provides evidence for the adaptations of Thaumarchaeota to arid soil, enhancing our understanding of the nitrogen and carbon cycling driven by Thaumarchaeota in drylands.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Niche breadth specialization impacts ecological and evolutionary adaptation following environmental change

Ecological theory predicts that organismal distribution and abundance depend on the ability to adapt to environmental change. It also predicts that eukaryotic specialists and generalists will dominate in extreme environments or following environmental change, respectively. This theory has attracted little attention in prokaryotes, especially in archaea, which drive major global biogeochemical cycles. We tested this concept in Thaumarchaeota using pH niche breadth as a specialization factor. Responses of archaeal growth and activity to pH disturbance were determined empirically in manipulated, long-term, pH-maintained soil plots. The distribution of specialists and generalists was uneven over the pH range, with specialists being more limited to the extreme range. Nonetheless, adaptation of generalists to environmental change was greater than that of specialists, except for environmental changes leading to more extreme conditions. The balance of generalism and specialism over longer timescales was further investigated across evolutionary history. Specialists and generalists diversified at similar rates, reflecting balanced benefits of each strategy, but a higher transition rate from generalists to specialists than the reverse was demonstrated, suggesting that metabolic specialism is more easily gained than metabolic versatility. This study provides evidence for a crucial ecological concept in prokaryotes, significantly extending our understanding of archaeal adaptation to environmental change.

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis

SUMMARY

Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.

Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction

BACKGROUND

While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs.

RESULTS

We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies.

CONCLUSION

Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.

Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa

IMPORTANCE

The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.

Microbes within the building envelope-a case study on the patterns of colonization and potential sampling bias

Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces.

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Geographically Disperse, Culturable Seed-Associated Microbiota in Forage Plants of Alfalfa (Medicago sativa L.) and Pitch Clover (Bituminaria bituminosa L.): Characterization of Beneficial Inherited Strains as Plant Stress-Tolerance Enhancers

Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20-80%). This situation is even more noticeable in plants used as fodder for animals, such as alfalfa and pitch trefoil, since their productivity is linked not only to the number of seeds produced, but also to the vegetative growth of the plant itself. Thus, we decided to study the microbiota associated with their seeds in different locations on the Iberian Peninsula, with the aim of identifying culturable bacteria strains that have adapted to harsh environments and that can be used as biotreatments to improve plant growth and resistance to stress. As potentially inherited microbiota, they may also represent a treatment with medium- and long-term adaptative effects. Hence, isolated strains showed no clear relationship with their geographical sampling location, but had about 50% internal similarity with their model plants. Moreover, out of the 51 strains isolated, about 80% were capable of producing biofilms; around 50% produced mid/high concentrations of auxins and grew notably in ACC medium; only 15% were characterized as xerotolerant, while more than 75% were able to sporulate; and finally, 65% produced siderophores and more than 40% produced compounds to solubilize phosphates. Thus, Paenibacillus amylolyticus BB B2-A, Paenibacillus xylanexedens MS M1-C, Paenibacillus pabuli BB Oeiras A, Stenotrophomonas maltophilia MS M1-B and Enterobacter hormaechei BB B2-C strains were tested as plant bioinoculants in lentil plants (Lens culinaris Medik.), showing promising results as future treatments to improve plant growth under stressful conditions.

Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.