Permafrost Active Layer Microbes From Ny Ålesund, Svalbard (79°N) Show Autotrophic and Heterotrophic Metabolisms With Diverse Carbon-Degrading Enzymes

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.

Temperature-mediated microbial carbon utilization in China's lakes

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems

Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Structure, stability, and potential function of groundwater microbial community responses to permafrost degradation on varying permafrost of the Qinghai-Tibet Plateau

The ongoing permafrost degradation under climate warming has modified aboveground biogeochemical processes mediated by microbes, yet groundwater microbial structure and function as well as their response to permafrost degradation remain poorly understood. We separately collect 20 and 22 sub-permafrost groundwater samples from Qilian Mountain (alpine and seasonal permafrost) and Southern Tibet Valley (plateau isolated permafrost) on the Qinghai-Tibet Plateau (QTP) to investigate the effects of permafrost groundwater characteristics on the diversity, structure, stability, and potential function of bacterial and fungal communities. Regional discrepancy of groundwater microbes between two permafrost regions reveals that permafrost degradation might reshape microbial community structure, increase community stability and potential functions relevant to carbon metabolism. Bacterial community assembly in permafrost groundwater is governed by deterministic processes, whereas fungal communities are mainly controlled by stochastic processes, suggesting that bacterial biomarkers might provide the better 'early warning signals' to permafrost degradation in deeper layers. Our study highlights the importance of groundwater microbes in ecological stability and carbon emission on the QTP.

Ruegeria alba sp. nov., Isolated from a Tidal Flat Sediment

A novel Gram-staining-negative, aerobic, rod-shaped, and white-colored bacterium designated as 1NDH52C^T was isolated from a tidal flat sediment and its taxonomic position was determined using a polyphasic taxonomic approach. The microorganism was found to grow at 10-37 °C, pH 6.0-9.0, and in the presence of 0-2% (w/v) NaCl, and to hydrolyze gelatin and aesculin. The major cellular fatty acid of strain 1NDH52C^T was summed feature 8 (C_19:1 ω7c and/or C_18:1 ω6c); the polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid, and a lipid; the respiratory quinone was ubiquinone-10. The 16S rRNA gene-based phylogenetic analysis showed that strain 1NDH52C^T was closely related to members of the genus Ruegeria with the identity of 98.2% to the type strain Ruegeria pomeroyi DSM 15711^T. The genome DNA G + C content of strain 1NDH52C^T was 63.6%. The phylogenomic analysis indicated that strain 1NDH52C^T formed an independent branch distinct from reference type strains of species within this genus. Digital DNA-DNA hybridization and average nucleotide identity values between strain 1NDH52C^T and reference strains were, respectively, 19.1-41.5% and 78.3-91.3%, which are far below the thresholds of 70% and 95-96% for species definition, respectively, indicating that strain 1NDH52C^T represents a novel genospecies of the genus Ruegeria. Based on phenotypic and genotypic data, strain 1NDH52C^T is concluded to represent a novel species of the genus Ruegeria, for which the name Ruegeria alba sp. nov., is proposed. The type strain of the species is 1NDH52C^T (= GDMCC 1.2382^T = KCTC 82664^T).

Draft Genome Sequences of 10 Pseudomonas sp. Isolates from the Active Layer of Permafrost in Ny Ålesund, Svalbard, Norway

Ten distinct isolates from the genus Pseudomonas were isolated in culture. The genomes of these isolates were sequenced using the Illumina MiSeq platform and assembled in order to provide insight into the metabolic and carbon-degrading potential of bacteria residing in soils at high latitudes.