Microbial Communities and Processes in Arctic Permafrost Environments. In: Dion P, Nautiyal CS, editors. Microbiology of Extreme Soils. Berlin: Springer Berlin Heidelberg; 2008. pp. 133-54. [DOI: 10.1007/978-3-540-74231-9_7]

Calcium carbonate precipitating extremophilic bacteria in an Alpine ice cave

Extensive research has provided a wealth of data on prokaryotes in caves and their role in biogeochemical cycles. Ice caves in carbonate rocks, however, remain enigmatic environments with limited knowledge of their microbial taxonomic composition. In this study, bacterial and archaeal communities of the Obstans Ice Cave (Carnic Alps, Southern Austria) were analyzed by next-generation amplicon sequencing and by cultivation of bacterial strains at 10 °C and studying their metabolism. The most abundant bacterial taxa were uncultured Burkholderiaceae and Brevundimonas spp. in the drip water, Flavobacterium, Alkanindiges and Polaromonas spp. in the ice, Pseudonocardia, Blastocatella spp., uncultured Pyrinomonadaceae and Sphingomonadaceae in carbonate precipitates, and uncultured Gemmatimonadaceae and Longimicrobiaceae in clastic cave sediments. These taxa are psychrotolerant/psychrophilic and chemoorganotrophic bacteria. On a medium with Mg2+/Ca2+ = 1 at 21 °C and 10 °C, 65% and 35% of the cultivated strains precipitated carbonates, respectively. The first ~ 200 µm-size crystals appeared 2 and 6 weeks after the start of the cultivation experiments at 21 °C and 10 °C, respectively. The crystal structure of these microbially induced carbonate precipitates and their Mg-content are strongly influenced by the Mg2+/Ca2+ ratio of the culture medium. These results suggest that the high diversity of prokaryotic communities detected in cryogenic subsurface environments actively contributes to carbonate precipitation, despite living at the physical limit of the presence of liquid water.

Soil microbes: a natural solution for mitigating the impact of climate change

Soil microbes are microscopic organisms that inhabit the soil and play a significant role in various ecological processes. They are essential for nutrient cycling, carbon sequestration, and maintaining soil health. Importantly, soil microbes have the potential to sequester carbon dioxide (CO2) from the atmosphere through processes like carbon fixation and storage in organic matter. Unlocking the potential of microbial-driven carbon storage holds the key to revolutionizing climate-smart agricultural practices, paving the way for sustainable productivity and environmental conservation. A fascinating tale of nature's unsung heroes is revealed by delving into the realm of soil microbes. The guardians of the Earth are these tiny creatures that live beneath our feet and discreetly work their magic to fend off the effects of climate change. These microbes are also essential for plant growth enhancement through their roles in nutrient uptake, nitrogen fixation, and synthesis of growth-promoting chemicals. By understanding and managing soil microbial communities, it is possible to improve soil health, soil water-holding capacity, and promote plant growth in agricultural and natural ecosystems. Added to it, these microbes play an important role in biodegradation, bioremediation of heavy metals, and phytoremediation, which in turn helps in treating the contaminated soils. Unfortunately, climate change events affect the diversity, composition, and metabolism of these microbes. Unlocking the microbial potential demands an interdisciplinary endeavor spanning microbiology, ecology, agronomy, and climate science. It is a call to arms for the scientific community to recognize soil microbes as invaluable partners in the fight against climate change. By implementing data-driven land management strategies and pioneering interventions, we possess the means to harness their capabilities, paving the way for climate mitigation, sustainable agriculture, and promote ecosystem resilience in the imminent future.

Species interactions and distinct microbial communities in high Arctic permafrost affected cryosols are associated with the CH4 and CO2 gas fluxes

Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO₂ and CH₄ fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH₄ and CO₂ flux at a high Arctic ice-wedge polygon terrain site, with higher CO₂ emissions and lower CH₄ uptake at troughs compared to polygon interior soils. The pmoA sequencing suggested that USCα cluster of uncultured methanotrophs is likely responsible for observed methane sink. Community profiling revealed distinct assemblages across the terrain at different depths. Deeper soils contained higher abundances of Verrucomicrobia and Gemmatimonadetes, whereas the polygon interior had higher Acidobacteria and lower Betaproteobacteria and Deltaproteobacteria abundances. Genome sequencing of isolates from the terrain revealed presence of carbon cycling genes including ones involved in serine and ribulose monophosphate pathways. A novel hybrid network analysis identified key members that had positive and negative impacts on other species. Operational Taxonomic Units (OTUs) with numerous positive interactions corresponded to Proteobacteria, Candidatus Rokubacteria and Actinobacteria phyla, while Verrucomicrobia and Acidobacteria members had negative impacts on other species. Results indicate that topography and microbial interactions impact community composition.

Response of Methanogenic Archaea from Siberian Permafrost and Non-permafrost Environments to Simulated Mars-like Desiccation and the Presence of Perchlorate

Numerous preflight investigations were necessary prior to the exposure experiment BIOMEX on the International Space Station to test the basic potential of selected microorganisms to resist or even to be active under Mars-like conditions. In this study, methanogenic archaea, which are anaerobic chemolithotrophic microorganisms whose lifestyle would allow metabolism under the conditions on early and recent Mars, were analyzed. Some strains from Siberian permafrost environments have shown a particular resistance. In this investigation, we analyzed the response of three permafrost strains (Methanosarcina soligelidi SMA-21, Candidatus Methanosarcina SMA-17, Candidatus Methanobacterium SMA-27) and two related strains from non-permafrost environments (Methanosarcina mazei, Methanosarcina barkeri) to desiccation conditions (-80°C for 315 days, martian regolith analog simulants S-MRS and P-MRS, a 128-day period of simulated Mars-like atmosphere). Exposure of the different methanogenic strains to increasing concentrations of magnesium perchlorate allowed for the study of their metabolic shutdown in a Mars-relevant perchlorate environment. Survival and metabolic recovery were analyzed by quantitative PCR, gas chromatography, and a new DNA-extraction method from viable cells embedded in S-MRS and P-MRS. All strains survived the two Mars-like desiccating scenarios and recovered to different extents. The permafrost strain SMA-27 showed an increased methanogenic activity by at least 10-fold after deep-freezing conditions. The methanogenic rates of all strains did not decrease significantly after 128 days S-MRS exposure, except for SMA-27, which decreased 10-fold. The activity of strains SMA-17 and SMA-27 decreased after 16 and 60 days P-MRS exposure. Non-permafrost strains showed constant survival and methane production when exposed to both desiccating scenarios. All strains showed unaltered methane production when exposed to the perchlorate concentration reported at the Phoenix landing site (2.4 mM) or even higher concentrations. We conclude that methanogens from (non-)permafrost environments are suitable candidates for potential life in the martian subsurface and therefore are worthy of study after space exposure experiments that approach Mars-like surface conditions.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica)

Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 10⁴-10⁵) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health

The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. From the samples, 110,000 quality-checked bacterial 16S rRNA gene sequences were obtained and analyzed, resulting in an observation of 4500 bacterial operational taxonomic units (OTUs). The most abundant bacteria were Mycobacterium and Arthrobacter of the Actinobacteria (33.2%), Exiguobacterium and Paenisporosarcina of the Firmicutes (23.4%), Planktothrix and Synechococcus of the Cyanobacteria (20.8%), and Methylocystis and Polynucleobacter of the Proteobacteria (16.3%). Considerable spatial and temporal variations were observed in the bacterial community of Actinobacteria, Cyanobacteria, and Firmicutes, where the bacterial community structure was greatly influenced by hydrological and weather conditions. The most influential factors were (1) water inflow for Bacteroidia and Clostridia, (2) turbidity for Gammaproteobacteria, (3) precipitation for Bacilli, and (4) temperature and pH for Cyanobacteria. One noticeable microbial interaction in the bacterial community was a significant negative relationship between Cyanobacteria and Bacilli (P < 0.05). Concerning beach water quality, the level of the genetic markers for cyanobacterial toxin (mcyA) was linked to the abundance of Cyanobacteria. In addition, unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.

Bacterial diversity and composition of an alkaline uranium mine tailings-water interface

The microbial diversity and biogeochemical potential associated with a northern Saskatchewan uranium mine water-tailings interface was examined using culture-dependent and -independent techniques. Morphologically-distinct colonies from uranium mine water-tailings and a reference lake (MC) obtained using selective and non-selective media were selected for 16S rRNA gene sequencing and identification, revealing that culturable organisms from the uranium tailings interface were dominated by Firmicutes and Betaproteobacteria; whereas, MC organisms mainly consisted of Bacteroidetes and Gammaproteobacteria. Ion Torrent (IT) 16S rRNA metagenomic analysis carried out on extracted DNA from tailings and MC interfaces demonstrated the dominance of Firmicutes in both of the systems. Overall, the tailings-water interface environment harbored a distinct bacterial community relative to the MC, reflective of the ambient conditions (i.e., total dissolved solids, pH, salinity, conductivity, heavy metals) dominating the uranium tailings system. Significant correlations among the physicochemical data and the major bacterial groups present in the tailings and MC were also observed. Presence of sulfate reducing bacteria demonstrated by culture-dependent analyses and the dominance of Desulfosporosinus spp. indicated by Ion Torrent analyses within the tailings-water interface suggests the existence of anaerobic microenvironments along with the potential for reductive metabolic processes.

Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica

Antarctic glacier forefields are extreme environments and pioneer sites for ecological succession. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats, and new terrain is becoming exposed to soil formation and microbial colonization. However, only little is known about the impact of environmental changes on microbial communities and how they develop in connection to shifting habitat characteristics. In this study, using a combination of molecular and geochemical analysis, we determine the structure and development of bacterial communities depending on soil parameters in two different glacier forefields on Larsemann Hills, East Antarctica. Our results demonstrate that deglaciation-dependent habitat formation, resulting in a gradient in soil moisture, pH and conductivity, leads to an orderly bacterial succession for some groups, for example Cyanobacteria, Bacteroidetes and Deltaproteobacteria in a transect representing 'classical' glacier forefields. A variable bacterial distribution and different composed communities were revealed according to soil heterogeneity in a slightly 'matured' glacier forefield transect, where Gemmatimonadetes, Flavobacteria, Gamma- and Deltaproteobacteria occur depending on water availability and soil depth. Actinobacteria are dominant in both sites with dominance connected to certain trace elements in the glacier forefields.

Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica)

In this study we examined the microbial community composition and operating metabolisms on the surface and in the permafrost of Deception Island, (Antarctica) with an on site antibody microarray biosensor. Samples (down to a depth of 4.2 m) were analysed with LDChip300 (Life Detector Chip), an immunosensor containing more than 300 antibodies targeted to bacterial and archaeal antigens. The immunograms showed positive antigen-antibody reactions in all surface samples (lichens, pyroclasts) and the top layer of the permafrost. The results indicated the presence of exopolysaccharides, bacteria belonging to the Alpha-, Delta- and Gammaproteobacteria, Bacteroidetes, Gram-positive Actinobacteria and Firmicutes, as well as archaeal species, most probably Methanobacterium spp. Positive reactions with antibodies to proteins and peptides revealed the presence of nitrogen fixation (NifHD, GlnB, HscA), methanogenic (McrB), iron homeostasis and iron scavenging (ferritins and DPS proteins) proteins, as well as ABC transporters, which indicated that these processes were operating at the time of sampling. These results were validated with other molecular ecology techniques such as oligonucleotide microarrays, 16S bacterial rRNA gene sequence analysis, aerobic viable counts and microscopy. Molecular ecology results showed a differentiated pattern along the depth of the drill, being the top active layer the most diverse, with Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes and the phototrophs Cyanobacteria and Chloroflexi as dominant groups. Actinobacteria and Firmicutes were dominant in depths from 0.5 to 2 m, and Betaproteobacteria from 3 to 4.2 m. The geochemical analysis revealed the presence of low molecular weight organic acids (acetate, formate) which could be used by microorganisms as energy sources for sulfate, nitrate and metal reduction under anaerobic conditions.

Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia

With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.