The structure of resting bacterial populations in soil and subsoil permafrost

Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica

Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica

Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.

Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost

Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly-cored permafrost from the Siberia Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ∼20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have previously been obtained from non-permafrost environments and have been suggested to show adaptations to long-term energy-starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had higher proportions of clusters of orthologous genes (COGs) from 'Energy production and conversion' and 'Carbohydrate transport and metabolism' than their non-permafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis and cellulose degradation that were less prevalent in non-permafrost genomes. Many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high ionic strength, cold environments of permafrost brine films. Our results suggest that this ancient permafrost contains DNA in high enough quality to assemble MAGs from microorganisms with adaptations to subsist long-term freezing in this extreme environment. Importance Permafrost around the world is thawing rapidly. Many scientists from a variety of disciplines have shown the importance of understanding what will happen to our ecosystem, commerce, and climate when permafrost thaws. The fate of permafrost microorganisms is connected to these predicted rapid environmental changes. Studying ancient permafrost with culture independent techniques can give a glimpse into how these microorganisms function in these extreme low temperature and energy conditions. This will aid understanding of how they will change with the environment. This study presents genomic data from this unique environment aged ∼20,000 to 1,000,000-years-old.

Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization

Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.

Are permafrost microorganisms as old as permafrost?

Permafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about the preservation of paleo-objects in permafrost, knowledge about the geological age of sediments, i.e. when the sediments were formed, and permafrost age, when those sediments became permanently frozen, is essential. There are two types of permafrost-syngenetic and epigenetic. The age of syngenetic permafrost corresponds to the geological age of its sediments, whereas the age of epigenetic permafrost is less than the geological age of its sediments. Both of these formations preserve microorganisms and their metabolic products; however, the interpretations of the microbiological and molecular-biological data are inconsistent. This paper reviews the current knowledge of time-temperature history and age of permafrost in relation to available microbiological and metagenomic data.

Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost

The study of bacterial communities associated with extreme ecosystems is one of the most important tasks in modern microbial ecology. Despite a large number of studies being performed, the ecosystems that have not been sufficiently explored from the microbiological point of view still exist. Such research is needed for improving the understanding of the limits and mechanisms of bacterial survival under extreme conditions, and for revealing previously undescribed species and their role in global biospheric processes and their functional specifics. The results of the complex microbiological characteristics of permafrost and ice—collected on the Severniy Island in the northern part of the Novaya Zemlya archipelago—which have not previously been described from microbiological point of view, are presented in this article. The analysis included both culture-independent and culture-dependent methods, in particular, the spectra of metabolic activity range analysis in vitro under different temperature, pH and salinity conditions. High values for the total number of prokaryotes in situ (1.9 × 108–3.5 × 108 cells/g), a significant part of which was able to return to a metabolically active state after thawing, and moderate numbers of culturable bacteria (3.3 × 106–7.8 × 107 CFU/g) were revealed. Representatives of Proteobacteria, Actinobacteria, and Bacteroidetes were dominant in situ; Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla in vitro. Physiological assays revealed the mesophilic and neutrophilic optima of temperature and pH of culturing conditions, respectively, and wide temperature and pH ranges of culturable communities’ reproduction activity. Isolated strains were characterized by moderate halotolerant properties and antibiotic resistance, including multiple antibiotic resistance. It was found that almost all cultured bacterial diversity revealed (not just a few resistant species) had extremotolerant properties regarding a number of stress factors. This indicates the high adaptive potential of the studied microbial communities and their high sustainability and capability to retain functional activity under changing environmental (including climatic) conditions in wide ranges.

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods

Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.

Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.

IMPORTANCE Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

Alpine soil microbial ecology in a changing world

Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.

Survivability of Soil and Permafrost Microbial Communities after Irradiation with Accelerated Electrons under Simulated Martian and Open Space Conditions

One of the prior current astrobiological tasks is revealing the limits of microbial resistance to extraterrestrial conditions. Much attention is paid to ionizing radiation, since it can prevent the preservation and spread of life outside the Earth. The aim of this research was to study the impact of accelerated electrons (~1 MeV) as component of space radiation on microbial communities in their natural habitat—the arid soil and ancient permafrost, and also on the pure bacterial cultures that were isolated from these ecotopes. The irradiation was carried out at low pressure (~0.01 Torr) and low temperature (−130 °C) to simulate the conditions of Mars or outer space. High doses of 10 kGy and 100 kGy were used to assess the effect of dose accumulation in inactive and hypometabolic cells, depending on environmental conditions under long-term irradiation estimated on a geological time scale. It was shown that irradiation with accelerated electrons in the applied doses did not sterilize native samples from Earth extreme habitats. The data obtained suggests that viable Earth-like microorganisms can be preserved in the anabiotic state for at least 1.3 and 20 million years in the regolith of modern Mars in the shallow subsurface layer and at a 5 m depth, respectively. In addition, the results of the study indicate the possibility of maintaining terrestrial like life in the ice of Europa at a 10 cm depth for at least ~170 years or for at least 400 thousand years in open space within meteorites. It is established that bacteria in natural habitat has a much higher resistance to in situ irradiation with accelerated electrons when compared to their stability in pure isolated cultures. Thanks to the protective properties of the heterophase environment and the interaction between microbial populations even radiosensitive microorganisms as members of the native microbial communities are able to withstand very high doses of ionizing radiation.

Bacterial diversity and production of sulfide in microcosms containing uncompacted bentonites

AIMS

This study examined the diversity and sulfide-producing activity of microorganisms in microcosms containing commercial clay products (e.g., MX-80, Canaprill and National Standard) similar to materials which are currently considered for use in the design specifications for deep geologic repositories (DGR) for spent nuclear fuel.

METHODS AND RESULTS

In anoxic microcosms incubated for minimum of 60 days with 10 g l-1 NaCl, sulfide production varied with temperature, electron donor and bentonite type. Maximum specific sulfide production rates of 0.189 d-1, 0.549 d-1 and 0.157 d-1 occurred in lactate-fed MX-80, Canaprill and National Standard microcosms, respectively. In microcosms with 50 g l-1 NaCl, sulfide production was inhibited. Denaturing gradient gel electrophoresis (DGGE) profiling of microcosms revealed the presence of bacterial classes Clostridia, Bacilli, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, Sphingobacteriia and Erysipelotrichia. Spore-forming and non-spore-forming bacteria were confirmed in microcosms using high-throughput 16S rRNA gene sequencing. Sulfate-reducing bacteria of the genus Desulfosporosinus predominated in MX-80 microcosms; whereas, Desulfotomaculum and Desulfovibrio genera contributed to sulfate-reduction in National Standard and Canaprill microcosms.

CONCLUSIONS

Commercial clays microcosms harbour a sparse bacterial population dominated by spore-forming microorganisms. Detected sulfate- and sulfur-reducing bacteria presumably contributed to sulfide accumulation in the different microcosm systems.

SIGNIFICANCE AND IMPACT OF STUDY

The use of carbon-supplemented, clay-in-water microcosms offered insights into the bacterial diversity present in as-received clays, along with the types of metabolic and sulfidogenic reactions that might occur in regions of a DGR (e.g., interfaces between the bulk clay and host rock, cracks, fissures, etc.) that fail to attain target parameters necessary to inhibit microbial growth and activity.

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia)

Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species.

A New Method and Mass-Spectrometric Instrument for Extraterrestrial Microbial Life Detection Using the Elemental Composition Analyses of Martian Regolith and Permafrost/Ice

We propose a new technique for the detection of microorganisms by elemental composition analyses of a sample extracted from regolith, permafrost, and ice of extraterrestrial bodies. We also describe the design of the ABIMAS instrument, which consists of the onboard time-of-flight laser mass-reflectron (TOF LMR) and the sample preparation unit (SPU) for biomass extraction. This instrument was initially approved to fly on board the ExoMars 2020 lander mission. The instrument can be used to analyze the elemental composition of possible extraterrestrial microbial communities and compare it to that of terrestrial microorganisms. We have conducted numerous laboratory studies to confirm the possibility of biomass identification via the following biomarkers: P/S and Ca/K ratios, and C and N abundances. We underline that only the combination of these factors will allow one to discriminate microbial samples from geological ones. Our technique has been tested experimentally in numerous laboratory trials on cultures of microorganisms and polar permafrost samples as terrestrial analogues for martian polar soils. We discuss various methods of extracting microorganisms and sample preparation. The developed technique can be used to search for and identify microorganisms in different martian samples and in the subsurface of other planets, satellites, comets, and asteroids-in particular, Europa, Ganymede, and Enceladus. Key Words: Mass spectrometry-Life-detection instruments-Biomarkers-Earth Mars-Biomass spectra. Astrobiology 17, 448-458.

Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost

The actinobacterium Rhodococcus sp. JG-3 is an aerobic, eurypsychrophilic, soil bacterium isolated from permafrost in the hyper arid Upper Dry Valleys of Antarctica. It is yellow pigmented, gram positive, moderately halotolerant and capable of growth from 30 °C down to at least −5 °C. The 5.28 Mb high-quality-draft genome is arranged into 6 scaffolds, containing 9 contigs and 4998 protein coding genes, with 64 % GC content. Increasing the availability of genome sequences from cold-adapted species is crucial to gaining a better understanding of the molecular traits of cold adaptation in microbes.

Brine assemblages of ultrasmall microbial cells within the ice cover of Lake Vida, Antarctica

The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions.

Biofilm formation by Psychrobacter arcticus and the role of a large adhesin in attachment to surfaces

Psychrobacter arcticus strain 273-4, an isolate from a Siberian permafrost core, is capable of forming biofilms when grown in minimal medium under laboratory conditions. Biofilms form at 4 to 22°C when acetate is supplied as the lone carbon source and with 1 to 7% sea salt. P. arcticus is also capable of colonizing quartz sand. Transposon mutagenesis identified a gene important for biofilm formation by P. arcticus. Four transposon mutants were mapped to a 20.1-kbp gene, which is predicted to encode a protein of 6,715 amino acids (Psyc_1601). We refer to this open reading frame as cat1, for cold attachment gene 1. The cat1 mutants are unable to form biofilms at levels equivalent to that of the wild type, and there is no impact on the planktonic growth characteristics of the strains, indicating a specific role in biofilm formation. Through time course studies of the static microtiter plate assay, we determined that cat1 mutants are unable to form biofilms equivalent to that of the wild type under all conditions tested. In flow cell experiments, cat1 mutants initially are unable to attach to the surface. Over time, however, they form microcolonies, an architecture very different from that produced by wild-type biofilms. Our results demonstrate that Cat1 is involved in the initial stages of bacterial attachment to surfaces.

Effects of long-term simulated martian conditions on a freeze-dried and homogenized bacterial permafrost community

Indigenous bacteria and biomolecules (DNA and proteins) in a freeze-dried and homogenized Arctic permafrost were exposed to simulated martian conditions that correspond to about 80 days on the surface of Mars with respect to the accumulated UV dose. The simulation conditions included UV radiation, freeze-thaw cycles, the atmospheric gas composition, and pressure. The homogenized permafrost cores were subjected to repeated cycles of UV radiation for 3 h followed by 27 h without irradiation. The effects of the simulation conditions on the concentrations of biomolecules; numbers of viable, dead, and cultured bacteria; as well as the community structure were determined. Simulated martian conditions resulted in a significant reduction of the concentrations of DNA and amino acids in the uppermost 1.5 mm of the soil core. The total number of bacterial cells was reduced in the upper 9 mm of the soil core, while the number of viable cells was reduced in the upper 15 mm. The number of cultured aerobic bacteria was reduced in the upper 6 mm of the soil core, whereas the community structure of cultured anaerobic bacteria was relatively unaffected by the exposure conditions. As explanations for the observed changes, we propose three causes that might have been working on the biological material either individually or synergistically: (i) UV radiation, (ii) UV-generated reactive oxygen species, and (iii) freeze-thaw cycles. Currently, the production and action of reactive gases is only hypothetical and will be a central subject in future investigations. Overall, we conclude that in a stable environment (no wind-/pressure-induced mixing) biological material is efficiently shielded by a 2 cm thick layer of dust, while it is relatively rapidly destroyed in the surface layer, and that biomolecules like proteins and polynucleotides are more resistant to destruction than living biota.

Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic

Culture-dependent and culture-independent methods were used in an investigation of the microbial diversity in a permafrost/massive ground ice core from the Canadian high Arctic. Denaturing gradient gel electrophoresis as well as Bacteria and Archaea 16S rRNA gene clone libraries showed differences in the composition of the microbial communities in the distinct core horizons. Microbial diversity was similar in the active layer (surface) soil, permafrost table and permafrost horizons while the ground ice microbial community showed low diversity. Bacteria and Archaea sequences related to the Actinobacteria (54%) and Crenarchaeota (100%) respectively were predominant in the active layer while the majority of sequences in the permafrost were related to the Proteobacteria (57%) and Euryarchaeota (76%). The most abundant phyla in the ground ice clone libraries were the Firmicutes (59%) and Crenarchaeota (82%). Isolates from the permafrost were both less abundant and diverse than in the active layer soil, while no culturable cells were recovered from the ground ice. Mineralization of [1-(14)C] acetic acid and [2-(14)C] glucose was used to detect microbial activity in the different horizons in the core. Mineralization was detected at near ambient permafrost temperatures (-15 degrees C), indicating that permafrost may harbour an active microbial population, while the low microbial diversity, abundance and activity in ground ice suggests a less hospitable microbial habitat.

Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway

The viable and non-viable fractions of the bacterial community in a 2347-year-old permafrost soil from Spitsbergen were subjected to a comprehensive investigation using culture-independent and culture-dependent methods. LIVE/DEAD BacLight staining revealed that 26% of the total number of bacterial cells were viable. Quantitatively, aerobic microcolonies, aerobic colony-forming units and culturable anaerobic bacteria comprised a minor fraction of the total number of viable bacteria, which underlines the necessity for alternative cultivation approaches in bacterial cryobiology. Sulfate reduction was detected at temperatures between -2 degrees C and 29 degrees C while methanogenesis was not detected. Bacterial diversity was high with 162 operational taxonomic units observed from 800 16S rDNA clone sequences. The 158 pure cultures isolated from the permafrost soil affiliated with 29 different bacterial genera, the majority of which have not previously been isolated from permafrost habitats. Most of the strains isolated were affiliated to the genera Cellulomonas and Arthrobacter and several of the pure cultures were closely related to bacteria reported from other cryohabitats. Characterization of viable bacterial communities in permafrost soils is important as it will enable identification of functionally important groups together with the as yet undescribed adaptations that bacteria have evolved for surviving subzero temperatures for millennia.

Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities

The Siberian permafrost is an extreme, yet stable environment due to its continuously frozen state. Microbes maintain membrane potential and respiratory activity at average temperatures of -10 to -12 degrees C that concentrate solutes to an aw=0.90 (5 osm), The isolation of viable Psychrobacter arcticus sp. 273-4 and Exiguobacterium sibiricum sp. 255-15 from ancient permafrost suggests that these bacteria have maintained some level of metabolic activity for thousands of years. Permafrost water activity was simulated using 1/2 TSB+2.79 m NaCl (5 osm) at and cells were held at 22 and 4 degrees C. Many cells reduced cyano-tetrazolium chloride (CTC) indicating functioning electron transport systems. Increased membrane permeability was not responsible for this lack of electron transport, as more cells were determined to be intact by LIVE/DEAD staining than were reducing CTC. Low rates of aerobic respiration were determined by the slope of the reduced resazurin line for P. arcticus, and E. sibiricum. Tritiated leucine was incorporated into new proteins at rates indicating basal level metabolism. The continued membrane potential, electron transport and aerobic respiration, coupled with incorporation of radio-labeled leucine into cell material when incubated in high osmolarity media, show that some of the population is metabolically active under simulated in situ conditions.

Phylogenetic diversity of bacteria isolates from the Qinghai-Tibet Plateau permafrost region

The Qinghai-Tibet Plateau in east Asia is a unique and important permafrost environment. However, its microbiology remains largely unexplored to date. In this study, sediment samples were collected from the Qinghai-Tibet Plateau permafrost region, bacteria isolation procedures were performed 8 times, and the samples incubated at 4 degrees C for nearly 3 months. The number of colony forming units (cfu) ranged from 0 to 10(7)/(g dry soil). The quantity of culturable bacteria grew exponentially within the first few weeks, and then slowed gradually to a plateau. Phylogenetic analyses indicated that all the isolates fell into 6 categories: high G+C Gram-positive bacteria, low G+C Gram-positive bacteria, alpha-Proteobacteria, beta-Proteobacteria, gamma-Proteobacteria, and Cytophaga-Flavobacterium-Bacteroides group bacteria. The isolates belong to 19 genera, but the genera Arthrobacter and Pseudomonas were predominant. With the increase in incubation time, the isolated populations changed in terms of both species and their respective quantities. Of the 33 analyzed isolates, 9 isolates related to 8 genera might be new taxa. These results suggest that the Qinghai-Tibet Plateau permafrost region is a specific ecologic niche that accommodates an original microbial assemblage.

Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains

Bacteria of the genus Exiguobacterium have been repeatedly isolated from ancient permafrost sediments of the Kolyma lowland of Northeast Eurasia. Here we report that the Siberian permafrost isolates Exiguobacterium sibiricum 255-15, E. sibiricum 7-3, Exiguobacterium undae 190-11 and E. sp. 5138, as well as Exiguobacterium antarcticum DSM 14480, isolated from a microbial mat sample of Lake Fryxell (McMurdo Dry Valleys, Antarctica), were able to grow at temperatures ranging from -6 to 40 degrees C. In comparison to cells grown at 24 degrees C, the cold-grown cells of these strains tended to be longer and wider. We also investigated the effect of growth conditions (broth or surface growth, and temperature) on cryotolerance of the Exiguobacterium strains. Bacteria grown in broth at 4 degrees C showed markedly greater survival following freeze-thawing treatments (20 repeated cycles) than bacteria grown in broth at 24 degrees C. Surprisingly, significant protection to repeated freeze-thawing was also observed when bacteria were grown on agar at either 4 or 24 degrees C.

Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods

A combination of culture-dependent and culture-independent methodologies (Bacteria and Archaea 16S rRNA gene clone library analyses) was used to determine the microbial diversity present within a geographically distinct high Arctic permafrost sample. Culturable Bacteria isolates, identified by 16S rRNA gene sequencing, belonged to the phyla Firmicutes, Actinobacteria and Proteobacteria with spore-forming Firmicutes being the most abundant; the majority of the isolates (19/23) were psychrotolerant, some (11/23) were halotolerant, and three isolates grew at -5 degrees C. A Bacteria 16S rRNA gene library containing 101 clones was composed of 42 phylotypes related to diverse phylogenetic groups including the Actinobacteria, Proteobacteria, Firmicutes, Cytophaga - Flavobacteria - Bacteroides, Planctomyces and Gemmatimonadetes; the bacterial 16S rRNA gene phylotypes were dominated by Actinobacteria- and Proteobacteria-related sequences. An Archaea 16S rRNA gene clone library containing 56 clones was made up of 11 phylotypes and contained sequences related to both of the major Archaea domains (Euryarchaeota and Crenarchaeota); the majority of sequences in the Archaea library were related to halophilic Archaea. Characterization of the microbial diversity existing within permafrost environments is important as it will lead to a better understanding of how microorganisms function and survive in such extreme cryoenvironments.

Diversity and distribution of alkaliphilic psychrotolerant bacteria in the Qinghai-Tibet Plateau permafrost region

The Qinghai-Tibet Plateau represents a unique permafrost environment, being a result of high elevation caused by land uplift. And the urgency was that plateau permafrost was degrading rapidly under the current predicted climatic warming scenarios. Hence, the permafrost there was sampled to recover alkaliphilic bacteria populations. The viable bacteria on modified PYGV agar were varied between 10(2) and 10(5 )CFU/g of dry soil. Forty-eight strains were gained from 18 samples. Through amplified ribosomal DNA restriction analysis (ARDRA) and phylogenetic analyses, these isolates fell into three categories: high G + C gram positive bacteria (82.3%), low G + C gram positive bacteria (7.2%), and gram negative alpha-proteobacteria (10.5%). The strains could grow at pH values ranging from 6.5 to 10.5 with optimum pH in the range of 9-9.5. Their growth temperatures were below 37 degrees C and the optima ranging from 10 to 15 degrees C. All strains grew well when NaCl concentration was below 15%. These results indicate that there are populations of nonhalophilic alkaliphilic psychrotolerant bacteria within the permafrost of the Qinhai-Tibet plateau. The abilities of many of the strains to produce extracellular protease, amylase and cellulase suggest that they might be of potential value for biotechnological exploitation.

Semmelweis' present day follow-up: Updating bacterial sampling and enrichment in clinical hygiene

Potentially dangerous antibiotic resistant contaminants have permanently penetrated at least well-off western populations. The danger is so evident that some hospitals have started to refuse accepting patients who carry such bacteria. Sampling and enrichment measures in hygiene monitoring must be updated as they are corner stones in handling the problems and safeguarding the health care units. Their patients, when exposed to microorganisms are strenuous to treat. Sometimes even this fails, if the infections are spreading in weakened patients. The present review summarizes currently used technologies and the abilities of bacteria to avoid detection. Improved protocols on environmental monitoring in healthcare units are required. They should be comparable with contamination control in industries. Actually these measures in health care should be even stricter because human lives are directly endangered as the resistance of especially elderly patients is low.

Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods

The microbial composition of ancient permafrost sediments from the Kolyma lowland of Northeast Eurasia was examined through culture and culture-independent approaches. These sediments have been continuously frozen for 5,000 to 2-3 million years. A total of 265 Bacteria 16S rRNA gene sequences were amplified from the permafrost total-community genomic DNA and screened by amplified ribosomal 16S rRNA restriction analysis. Members of three major lineages were found: gamma-Proteobacteria (mostly Xanthomonadaceae), Actinobacteria, and Firmicutes. We also determined partial 16S rRNA gene sequences of 49 isolates from a collection of 462 aerobes isolated from these sediments. The bacteria included Actinomycetales (Arthrobacter and Microbacteriaceae); followed by the Firmicutes (Exiguobacterium and Planomicrobium); the Bacteroidetes (Flavobacterium); the gamma-Proteobacteria (Psychrobacter); and the alpha-Proteobacteria (Sphingomonas). Both culture and culture-independent approaches showed the presence of high and low G+C Gram-positive bacteria and gamma-Proteobacteria. Some of the 16S rRNA gene sequences of environmental clones matched those of Arthrobacter isolates. Two-thirds of the isolates grew at -2.5 degrees C, indicating that they are psychroactive, and all are closely related to phylogenetic groups with strains from other cold environments, mostly commonly from Antarctica. The culturable and non-culturable microorganisms found in the terrestrial permafrost provide a prototype for possible life on the cryogenic planets of the Solar System.

Microbial ecology and biodiversity in permafrost

Permafrost represents 26% of terrestrial soil ecosystems; yet its biology, essentially microbiology, remains relatively unexplored. The permafrost environment is considered extreme because indigenous microorganisms must survive prolonged exposure to subzero temperatures and background radiation for geological time scales in a habitat with low water activity and extremely low rates of nutrient and metabolite transfer. Yet considerable numbers and biodiversity of bacteria exist in permafrost, some of which may be among the most ancient viable life on Earth. This review describes the permafrost environment as a microbial habitat and reviews recent studies examining microbial biodiversity found in permafrost as well as microbial growth and activity at ambient in situ subzero temperatures. These investigations suggest that functional microbial ecosystems exist within the permafrost environment and may have important implications on global biogeochemical processes as well as the search for past or extant life in permafrost presumably present on Mars and other bodies in our solar system.