Discovery of Eremiobacterota with nifH homologues in tundra soil.

We describe the genome of an Eremiobacterota population from tundra soil that contains the minimal set of nif genes needed to fix atmospheric N2. This putative diazotroph population, which we name Candidatus Lamibacter sapmiensis, links for the first time Eremiobacterota and N2 fixation. The integrity of the genome and its nif genes are well supported by both environmental and taxonomic signals. Ca. Lamibacter sapmiensis contains three nifH homologues and the complementary set of nifDKENB genes that are needed to assemble a functional nitrogenase. The putative diazotrophic role of Ca. Lamibacter sapmiensis is supported by the presence of genes that regulate N2 fixation and other genes involved in downstream processes such as ammonia assimilation. Similar to other Eremiobacterota, Ca. Lamibacter sapmiensis encodes the potential for atmospheric chemosynthesis via CO2 fixation coupled with H2 and CO oxidation. Interestingly, the presence of a N2O reductase indicates that this population could play a role as a N2O sink in tundra soils. Due to the lack of activity data, it remains uncertain if Ca. Lamibacter sapmiensis is able to assemble a functional nitrogenase and participate in N2 fixation. Confirmation of this ability would be a testament to the great metabolic versatility of Eremiobacterota, which appears to underlie their ecological success in cold and oligotrophic environments.

Metagenome-assembled genomes from mineral tundra soils in Rásttigáisá, northern Norway.

Microbial communities in tundra soils remain largely unknown despite their important roles in the cycling of greenhouse gases. Here, we report 59 non-redundant metagenome-assembled genomes (MAGs) recovered from mineral tundra soils in Rásttigáisá, northern Norway. The MAGs were obtained by clustering contigs according to tetranucleotide frequency and differential coverage and were manually curated to remove contigs with outlying GC content and/or mean coverage. Most MAGs were assigned to the bacterial phyla Candidatus Dormibacterota (n=12), Verrucomicrobiota (n=10), and Acidobacteriota (n=9). All archaeal MAGs (n=4) belong to the genus Candidatus Nitrosopolaris (phylum Thermoproteota). The 59 Rásttigáisá MAGs expand our knowledge of the diversity and ecological roles of tundra microbiomes.

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics.

Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.

The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types.

Due to climate change, increased microbial activity in high-latitude soils may lead to higher greenhouse gas (GHG) emissions. However, microbial GHG production and consumption mechanisms in tundra soils are not thoroughly understood. To investigate how the diversity and functional potential of bacterial and archaeal communities vary across vegetation types and soil layers, we analyzed 116 soil metatranscriptomes from 73 sites in the Finnish sub-Arctic. Meadow soils were characterized by higher pH and lower soil organic matter (SOM) and carbon/nitrogen ratio. By contrast, dwarf shrub-dominated ecosystems had higher SOM and lower pH. Although Actinobacteria, Acidobacteria, Alphaproteobacteria and Planctomycetes were dominant in all communities, there were significant differences at the genus level between vegetation types; plant polymer-degrading groups were more active in shrub-dominated soils than in meadows. Given that climate-change scenarios predict the expansion of shrubs at high latitudes, our results indicate that tundra soil microbial communities harbor potential decomposers of increased plant litter, which may affect the rate of carbon turnover in tundra soils. Additionally, transcripts of methanotrophs were detected in the mineral layer of all soils, which may moderate methane fluxes. This study provides new insights into possible shifts in tundra microbial diversity and activity due to climate change.

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.

BACKGROUND: In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. RESULTS: We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. CONCLUSIONS: By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.

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.

Marked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic.

Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10-20 years since deglaciation), mid (30-50 years), and late (80-100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa.

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits.

Moonmilk are cave carbonate deposits that host a rich microbiome, including antibiotic-producing Actinobacteria, making these speleothems appealing for bioprospecting. Here, we investigated the taxonomic profile of the actinobacterial community of three moonmilk deposits of the cave "Grotte des Collemboles" via high-throughput sequencing of 16S rRNA amplicons. Actinobacteria was the most common phylum after Proteobacteria, ranging from 9% to 23% of the total bacterial population. Next to actinobacterial operational taxonomic units (OTUs) attributed to uncultured organisms at the genus level (~44%), we identified 47 actinobacterial genera with Rhodoccocus (4 OTUs, 17%) and Pseudonocardia (9 OTUs, ~16%) as the most abundant in terms of the absolute number of sequences. Streptomycetes presented the highest diversity (19 OTUs, 3%), with most of the OTUs unlinked to the culturable Streptomyces strains that were previously isolated from the same deposits. Furthermore, 43% of the OTUs were shared between the three studied collection points, while 34% were exclusive to one deposit, indicating that distinct speleothems host their own population, despite their nearby localization. This important spatial diversity suggests that prospecting within different moonmilk deposits should result in the isolation of unique and novel Actinobacteria. These speleothems also host a wide range of non-streptomycetes antibiotic-producing genera, and should therefore be subjected to methodologies for isolating rare Actinobacteria.

Community structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats.

The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their prominent role in the primary production and nutrient cycling in Antarctic lakes, cyanobacteria were only poorly represented in the biological dataset used to delineate these ACBRs. Here, we provide a first high-throughput sequencing insight into the spatial distribution of benthic cyanobacterial communities in Antarctic lakes located in four distinct, geographically distant ACBRs and covering a range of limnological conditions. Cyanobacterial community structure differed between saline and freshwater lakes. No clear bioregionalization was observed, as clusters of community similarity encompassed lakes from distinct ACBRs. Most phylotypes (77.0%) were related to cyanobacterial lineages (defined at ≥99.0% 16S rRNA gene sequence similarity) restricted to the cold biosphere, including lineages potentially endemic to Antarctica (55.4%). The latter were generally rare and restricted to a small number of lakes, while more ubiquitous phylotypes were generally abundant and present in different ACBRs. These results point to a widespread distribution of some cosmopolitan cyanobacterial phylotypes across the different Antarctic ice-free regions, but also suggest the existence of dispersal barriers both within and between Antarctica and the other continents.

Cyanobacteria inhabiting biological soil crusts of a polar desert: Sør Rondane Mountains, Antarctica.

Molecular and morphological methods were applied to study cyanobacterial community composition in biological soil crusts (BSCs) from four areas (two nunataks and two ridges) in the Sør Rondane Mountains, Antarctica. The sampling sites serve as control areas for open top chambers (OTCs) that were put in place in 2010 at the time of sample collection and will be compared with BSC samples taken from the OTCs in the future. Cyanobacterial cell biovolume was estimated using epifluorescence microscopy, which revealed the dominance of filamentous cyanobacteria in all studied sites except the Utsteinen ridge, where unicellular cyanobacteria were the most abundant. Cyanobacterial diversity was studied by a combination of molecular fingerprinting methods based on the 16S rRNA gene (denaturing gradient gel electrophoresis (DGGE) and 454 pyrosequencing) using cyanobacteria-specific primers. The number of DGGE sequences obtained per site was variable and, therefore, a high-throughput method was subsequently employed to improve the diversity coverage. Consistent with previous surveys in Antarctica, both methods showed that filamentous cyanobacteria, such as Leptolyngbya sp., Phormidium sp. and Microcoleus sp., were dominant in the studied sites. In addition, the studied localities differed in substrate type, climatic conditions and soil parameters, which probably resulted in differences in cyanobacterial community composition. Furthermore, the BSC growing on gneiss pebbles had lower cyanobacterial abundances than BSCs associated with granitic substrates.

Cyanobacterial Contribution to Travertine Deposition in the Hoyoux River System, Belgium.

Travertine deposition is a landscape-forming process, usually building a series of calcareous barriers differentiating the river flow into a series of cascades and ponds. The process of carbonate precipitation is a complex relationship between biogenic and abiotic causative agents, involving adapted microbial assemblages but also requiring high levels of carbonate saturation, spontaneous degassing of carbon dioxide and slightly alkaline pH. We have analysed calcareous crusts and water chemistry from four sampling sites along the Hoyoux River and its Triffoy tributary (Belgium) in winter, spring, summer and autumn 2014. Different surface textures of travertine deposits correlated with particular microenvironments and were influenced by the local water flow. In all microenvironments, we have identified the cyanobacterium Phormidium incrustatum (Nägeli) Gomont as the organism primarily responsible for carbonate precipitation and travertine fabric by combining morphological analysis with molecular sequencing (16S rRNA gene and ITS, the Internal Transcribed Spacer fragments), targeting both field populations and cultures to exclude opportunistic microorganisms responding favourably to culture conditions. Several closely related cyanobacterial strains were cultured; however, only one proved identical with the sequences obtained from the field population by direct PCR. This strain was the dominant primary producer in the calcareous deposits under study and in similar streams in Europe. The dominance of one organism that had a demonstrated association with carbonate precipitation presented a valuable opportunity to study its function in construction, preservation and fossilisation potential of ambient temperature travertine deposits. These relationships were examined using scanning electron microscopy and Raman microspectroscopy.

Draft Genome Sequence of the Axenic Strain Phormidesmispriestleyi ULC007, a Cyanobacterium Isolated from Lake Bruehwiler (Larsemann Hills, Antarctica).

Phormidesmis priestleyi ULC007 is an Antarctic freshwater cyanobacterium. Its draft genome is 5,684,389 bp long. It contains a total of 5,604 protein-encoding genes, of which 22.2% have no clear homologues in known genomes. To date, this draft genome is the first one ever determined for an axenic cyanobacterium from Antarctica.

Cyanobacterial community composition in Arctic soil crusts at different stages of development.

Cyanobacterial diversity in soil crusts has been extensively studied in arid lands of temperate regions, particularly semi-arid steppes and warm deserts. Nevertheless, Arctic soil crusts have received far less attention than their temperate counterparts. Here, we describe the cyanobacterial communities from various types of soil crusts from Svalbard, High Arctic. Four soil crusts at different development stages (ranging from poorly-developed to well-developed soil crusts) were analysed using 454 pyrosequencing of the V3-V4 variable region of the cyanobacterial 16S rRNA gene. Analyses of 95 660 cyanobacterial sequences revealed a dominance of OTUs belonging to the orders Synechococcales, Oscillatoriales and Nostocales. The most dominant OTUs in the four studied sites were related to the filamentous cyanobacteria Leptolyngbya sp. Phylotype richness estimates increased from poorly- to mid-developed soil crusts and decreased in the well-developed lichenized soil crust. Moreover, pH, ammonium and organic carbon concentrations appeared significantly correlated with the cyanobacterial community structure.

Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula.

Several studies have shown that microbial communities in Antarctic environments are highly diverse. However, considering that the Antarctic Peninsula is among the regions with the fastest warming rates, and that regional climate change has been linked to an increase in the mean rate of glacier retreat, the microbial diversity in Antarctic soil is still poorly understood. In this study, we analysed more than 40 000 sequences of the V5-V6 hypervariable region of the 16S rRNA gene obtained by 454 pyrosequencing from four soil samples from the Wanda Glacier forefield, King George Island, Antarctic Peninsula. Phylotype diversity and richness were surprisingly high, and taxonomic assignment of sequences revealed that communities are dominated by Proteobacteria, Bacteroidetes and Euryarchaeota, with a high frequency of archaeal and bacterial phylotypes unclassified at the genus level and without cultured representative strains, representing a distinct microbial community signature. Several phylotypes were related to marine microorganisms, indicating the importance of the marine environment as a source of colonizers for this recently deglaciated environment. Finally, dominant phylotypes were related to different microorganisms possessing a large array of metabolic strategies, indicating that early successional communities in Antarctic glacier forefield can be also functionally diverse.