Vertical structure of archaeal communities and the distribution of ammonia monooxygenase A gene variants in two meromictic High Arctic lakes

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic

Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.

Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia

DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.

Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake

In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium, and organic nitrogen in the deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water body with high concentrations of methane, ferrous iron, and manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to a phytoplankton bloom. The decomposition of the bulk of the organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and is accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimolimnion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrate occurs. Overall, most of the organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.

Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway)

Meromictic lakes are permanently stratified lakes that display steep gradients in salinity, oxygen and sulphur compounds tightly linked to bacterial community structure and diversity. Lake Sælenvannet is a meromictic lake located south of Bergen, Norway. The 26 m deep lake is connected to the open sea and permanently stratified into two layers separated by a chemocline. The upper water layer is brackish with major input from water runoff from the surroundings. The bottom layer consists of old saline water with low or no oxygen concentrations. Bacteria from phylum Planctomycetes are reported to be ubiquitous in lake environments. They are involved in the degradation of complex carbon sources in aquatic environments and are also linked to anaerobic processes such as fermentation and sulphur reduction. To study Planctomycete distribution along a chemical gradient, we sampled the water column throughout Lake Sælenvannet in 2012 and profiled the microbial community using 16S rRNA amplicon sequencing (metabarcoding) with 454 pyrosequencing. Planctomycetes related 16S rRNA gene sequences were found to be present both in the oxic and anoxic parts of the lake and showed an uneven distribution throughout the water column, with the highest relative abundance of 10% found in the saline anoxic layer at 15 m depth. In a follow-up study in 2014, samples from eight different depths were collected for enrichment and isolation of novel Planctomycetes. This study resulted in successful isolation in pure culture of 10 isolates affiliated to four different genera from the family Planctomycetaceae. One strain closely related to Blastopirellula cremea was isolated from 9 m depth, and two novel strains affiliated to the genera Stieleria and Gimesia were isolated at 7 and 9 m depths, respectively. Furthermore, seven isolates with identical 16S rRNA gene sequences were retrieved from seven different depths which varied greatly in salinity and chemical composition. These isolates likely represent a new species affiliated to Rubinisphaera. The adaptation of this novel Planctomycete to water depths spanning the entire chemical gradient could indicate a high phenotypic plasticity and/or a very efficient survival strategy. Overall, our results show the presence of a diverse group of Planctomycetes in Lake Sælenvannet, with a strong potential for novel adaptations to chemical stress factors.

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic.

IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes

Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (10⁵ to 10⁹ copies g^-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.

Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific

Community composition and abundance of ammonia-oxidizing archaea (AOA) in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands) were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA) gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA) reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.

Environmental selection of planktonic methanogens in permafrost thaw ponds

The warming and thermal erosion of ice-containing permafrost results in thaw ponds that are strong emitters of methane to the atmosphere. Here we examined methanogens and other Archaea, in two types of thaw ponds that are formed by the collapse of either permafrost peat mounds (palsas) or mineral soil mounds (lithalsas) in subarctic Quebec, Canada. Using high-throughput sequencing of a hypervariable region of 16S rRNA, we determined the taxonomic structure and diversity of archaeal communities in near-bottom water samples, and analyzed the mcrA gene transcripts from two sites. The ponds at all sites were well stratified, with hypoxic or anoxic bottom waters. Their archaeal communities were dominated by Euryarchaeota, specifically taxa in the methanogenic orders Methanomicrobiales and Methanosarcinales, indicating a potentially active community of planktonic methanogens. The order Methanomicrobiales accounted for most of the mcrA transcripts in the two ponds. The Archaeal communities differed significantly between the lithalsa and palsa ponds, with higher alpha diversity in the organic-rich palsa ponds, and pronounced differences in community structure. These results indicate the widespread occurrence of planktonic, methane-producing Archaea in thaw ponds, with environmental selection of taxa according to permafrost landscape type.

Unanticipated Geochemical and Microbial Community Structure under Seasonal Ice Cover in a Dilute, Dimictic Arctic Lake

Despite most lakes in the Arctic being perennially or seasonally frozen for at least 40% of the year, little is known about microbial communities and nutrient cycling under ice cover. We assessed the vertical microbial community distribution and geochemical composition in early spring under ice in a seasonally ice-covered lake in southwest Greenland using amplicon-based sequencing that targeted 16S rRNA genes and using a combination of field and laboratory aqueous geochemical methods. Microbial communities changed consistently with changes in geochemistry. Composition of the abundant members responded strongly to redox conditions, shifting downward from a predominantly heterotrophic aerobic community in the suboxic waters to a heterotrophic anaerobic community in the anoxic waters. Operational taxonomic units (OTUs) of Sporichthyaceae, Comamonadaceae, and the SAR11 Clade had higher relative abundances above the oxycline and OTUs within the genus Methylobacter, the phylum Lentisphaerae, and purple sulfur bacteria (PSB) below the oxycline. Notably, a 13-fold increase in sulfide at the oxycline was reflected in an increase and change in community composition of potential sulfur oxidizers. Purple non-sulfur bacteria were present above the oxycline and green sulfur bacteria and PSB coexisted below the oxycline, however, PSB were most abundant. For the first time we show the importance of PSB as potential sulfur oxidizers in an Arctic dimictic lake.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France)

Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene) in conjunction with quantitative PCR (DNA and RNA) and fluorescent in situ hybridization (FISH) analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin). This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. Forty-two percent of the OTUs (Operational Taxonomic Units) are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae) and Fungi (Dikarya and Chytrids) are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae) are also present and active in this zone, which opens up questions regarding their metabolism.

Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau

Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region.

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore

Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification

Reservoir thermal stratification drives the water temperature and dissolved oxygen gradient, however, the characteristic of vertical water microbial community during thermal stratification is so far poorly understood. In this work, water bacterial community diversity was determined using the Illumina Miseq sequencing technique. The results showed that epilimnion, metalimnion and hypolimnion were formed steadily in the JINPEN drinking water reservoir. Water temperature decreased steadily from the surface (23.11 °C) to the bottom (9.17 °C). Total nitrogen ranged from 1.07 to 2.06 mg/L and nitrate nitrogen ranged from 0.8 to 1.84 mg/L. The dissolved oxygen concentration decreased sharply below 50 m, and reached zero at 65 m. The Miseq sequencing revealed a total of 4127 operational taxonomic units (OTUs) with 97% similarity, which were affiliated with 15 phyla including Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Caldiserica, Chlamydiae, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, and Verrucomicrobia. The highest Shannon diversity was 4.41 in 45 m, and the highest Chao 1 diversity was 506 in 5 m. Rhodobacter dominated in 55 m (23.24%) and 65 m (12.58%). Prosthecobacter dominated from 0.5 to 50 m. The heat map profile and redundancy analysis (RDA) indicated significant difference in vertical water bacterial community composition in the reservoir. Meanwhile, water quality properties including dissolved oxygen, conductivity, nitrate nitrogen and total nitrogen have a dramatic influence on vertical distribution of bacterial communities.

Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes

Hypersaline meromictic lakes are extreme environments in which water stratification is associated with powerful physicochemical gradients and high salt concentrations. Furthermore, their physical stability coupled with vertical water column partitioning makes them important research model systems in microbial niche differentiation and biogeochemical cycling. Here, we compare the prokaryotic assemblages from Ursu and Fara Fund hypersaline meromictic lakes (Transylvanian Basin, Romania) in relation to their limnological factors and infer their role in elemental cycling by matching taxa to known taxon-specific biogeochemical functions. To assess the composition and structure of prokaryotic communities and the environmental factors that structure them, deep-coverage small subunit (SSU) ribosomal RNA (rDNA) amplicon sequencing, community domain-specific quantitative PCR and physicochemical analyses were performed on samples collected along depth profiles. The analyses showed that the lakes harbored multiple and diverse prokaryotic communities whose distribution mirrored the water stratification patterns. Ursu Lake was found to be dominated by Bacteria and to have a greater prokaryotic diversity than Fara Fund Lake that harbored an increased cell density and was populated mostly by Archaea within oxic strata. In spite of their contrasting diversity, the microbial populations indigenous to each lake pointed to similar physiological functions within carbon degradation and sulfate reduction. Furthermore, the taxonomy results coupled with methane detection and its stable C isotope composition indicated the presence of a yet-undescribed methanogenic group in the lakes' hypersaline monimolimnion. In addition, ultrasmall uncultivated archaeal lineages were detected in the chemocline of Fara Fund Lake, where the recently proposed Nanohaloarchaeota phylum was found to thrive.

Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes

Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.

Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean

Thaumarchaeota and the gene encoding for a subunit of ammonia monooxygenase (amoA) are ubiquitous in Polar Seas, and some Thaumarchaeota also have a gene coding for ureC, diagnostic for urease. Using quantitative PCR we investigated the occurrence of genes and transcripts of ureC and amoA in Arctic samples from winter, spring and summer. AmoA genes, ureC genes and amoA transcripts were always present, but ureC transcripts were rarely detected. Over a 48 h light manipulation experiment amoA transcripts persisted under light and dark conditions, but not ureC transcripts. In addition, maxima for amoA transcript were nearer the surface compared to amoA genes. Clone libraries using DNA template recovered shallow and deep amoA clades but only the shallow clade was recovered from cDNA (from RNA). These results imply environmental control of amoA expression with direct or indirect light effects, and rare ureC expression despite its widespread occurrence in the Arctic Ocean.

Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria

Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity.

Small thaw ponds: an unaccounted source of methane in the Canadian high Arctic

Thawing permafrost in the Canadian Arctic tundra leads to peat erosion and slumping in narrow and shallow runnel ponds that surround more commonly studied polygonal ponds. Here we compared the methane production between runnel and polygonal ponds using stable isotope ratios, ¹⁴C signatures, and investigated potential methanogenic communities through high-throughput sequencing archaeal 16S rRNA genes. We found that runnel ponds had significantly higher methane and carbon dioxide emissions, produced from a slightly larger fraction of old carbon, compared to polygonal ponds. The methane stable isotopic signature indicated production through acetoclastic methanogenesis, but gene signatures from acetoclastic and hydrogenotrophic methanogenic Archaea were detected in both polygonal and runnel ponds. We conclude that runnel ponds represent a source of methane from potentially older C, and that they contain methanogenic communities able to use diverse sources of carbon, increasing the risk of augmented methane release under a warmer climate.

amoA-encoding archaea and thaumarchaeol in the lakes on the northeastern Qinghai-Tibetan Plateau, China

All known ammonia-oxidizing archaea (AOA) belong to the phylum Thaumarchaeota within the domain Archaea. AOA possess the diagnostic amoA gene (encoding the alpha subunit of ammonia monooxygenase) and produce lipid biomarker thaumarchaeol. Although the abundance and diversity of amoA gene-encoding archaea (AEA) in freshwater lakes have been well-studied, little is known about AEA ecology in saline/hypersaline lakes. In this study, the distribution of the archaeal amoA gene and thaumarchaeol were investigated in nine Qinghai–Tibetan lakes with a salinity range from freshwater to salt-saturation (salinity: 325 g L^-1). The results showed that the archaeal amoA gene was present in hypersaline lakes with salinity up to 160 g L^-1. The archaeal amoA gene diversity in Tibetan lakes was different from those in other lakes worldwide, suggesting Tibetan lakes (high elevation, strong ultraviolet, and dry climate) may host a unique AEA population of different evolutionary origin from those in other lakes. Thaumarchaeol was present in all of the studied hypersaline lakes, even in those where no AEA amoA gene was observed. Future research is needed to determine the ecological function of AEA and possible sources of thaumarchaeol in the Qinghai–Tibetan hypersaline lakes.

Spatio-temporal changes in the structure of archaeal communities in two deep freshwater lakes

In this study, we evaluated the driving forces exerted by a large set of environmental and biological parameters on the spatial and temporal dynamics of archaeal community structure in two neighbouring peri-alpine lakes that differ in terms of trophic status. We analysed monthly data from a 2-year sampling period at two depths corresponding to the epi- and hypolimnetic layers. The archaeal communities seemed to be mainly composed of ammonia-oxidizing archaea belonging to the thaumarchaeotal phylum. The spatio-temporal dynamics of these communities were very similar in the two lakes and were characterized by (1) disparities in archaeal community structure in both time and space and (2) no seasonal reproducibility between years. The archaeal communities were regulated by a complex combination of abiotic factors, including temperature, nutrients, chlorophyll a and dissolved oxygen, and biotic factors such as heterotrophic nanoflagellates and ciliates. However, in most cases, these factors explained < 52% of the variance in archaeal community structure, while we showed in a previous study that these factors explained 70-90% of the temporal variance for bacteria. This suggests that Bacteria and Archaea may be influenced by different factors and could occupy different ecological niches despite similar spatio-temporal dynamics.

Vertical distribution of ammonia-oxidizing archaea and bacteria in sediments of a eutrophic lake

In order to characterize the vertical variation of abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediments of a eutrophic lake, Lake Taihu, molecular techniques including real-time PCR, clone library, and sequencing were carried out in this study. Abundances of archaeal amoA gene (ranged from 2.34 × 10(6) to 4.43 × 10(7) copies [g dry sediment](-1)) were higher than those of bacterial amoA gene (ranged from 5.02 × 10(4) to 6.91 × 10(6) copies [g dry sediment](-1)) for all samples and both of them exhibited negative correlations with the increased depths. Diversities of archaeal and bacterial amoA gene increased with the elevated depths. There were no significant variations of AOB community structures derived from different sediment depths, whereas obvious differences were observed for the AOA community compositions. The information acquired in this study would be useful to elucidate the roles of AOA and AOB in the nitrogen cycling of freshwater ecosystems.

Linking isoprenoidal GDGT membrane lipid distributions with gene abundances of ammonia-oxidizing Thaumarchaeota and uncultured crenarchaeotal groups in the water column of a tropical lake (Lake Challa, East Africa)

Stratified lakes are important reservoirs of microbial diversity and provide habitats for niche differentiation of Archaea. In this study, we used a lipid biomarker/DNA-based approach to reveal the diversity and abundance of Archaea in the water column of Lake Challa (East Africa). Concentrations of intact polar lipid (IPL) crenarchaeol, a specific biomarker of Thaumarchaeota, were enhanced (1 ng l(-1) ) at the oxycline/nitrocline. The predominance of the more labile IPL hexose-phosphohexose crenarchaeol indicated the presence of an actively living community of Thaumarchaeota. Archaeal 16S rRNA clone libraries revealed the presence of thaumarchaeotal groups 1.1a and 1.1b at and above the oxycline. In the anoxic deep water, amoA gene abundance was an order of magnitude lower than at the oxycline and high abundance (∼90 ng l(-1) ) of an IPL with the acyclic glycerol dialkyl glycerol tetraether (GDGT-0) was evident. The predominance of archaeal 16S rRNA sequences affiliated to the uncultured crenarchaeota groups 1.2 and miscellaneous crenarchaeotic group (MCG) points to an origin of GDGT-0 from uncultured crenarchaeota. This study demonstrates the importance of thermal stratification and nutrient availability in the distribution of archaeal groups in lakes, which is relevant to constrain and validate temperature proxies based on archaeal GDGTs (i.e. TEX86 ).

Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems

Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms.

Partaking of Archaea to biogeochemical cycling in oxygen-deficient zones of meromictic saline Lake Faro (Messina, Italy)

We used a combination of molecular and microbiological approaches to determine the activity, abundance and diversity of archaeal populations inhabiting meromictic saline Lake Faro (Messina, Italy). Analysis of archaeal 16S rRNA, amoA, accA and hbd genes and transcripts revealed that sub- and anoxic layers of Lake Faro are primarily inhabited by the organisms related to the clusters of Marine Group I.1a of Thaumarchaeota frequently recovered from oxygen-depleted marine ecosystems. These organisms dominated the metabolically active archaea down to the bottom of the lake, indicating their adaptation to recurrent changes in the levels of water column hypoxia. The upper microaerobic layer of Lake Faro redoxcline has the maximal rates of dark primary production much lower than those of other previously studied pelagic redoxclines, but comparable to the values of meso- and bathypelagic areas of Mediterranean Sea. Application of bacterial inhibitors, especially azide, significantly declined the CO2 fixation rates in the low interface and monimolimnion, whereas archaea-specific inhibitor had effect only in upper part of the redoxcline. Based on these findings, we hypothesize that dark bicarbonate fixation in suboxic zone of Lake Faro results mainly from archaeal activity which is affected by the predicted lack in oxygen in lower layers.

Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters

Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered meromictic lakes are particularly stable, with long term constancy in their density profiles. Here we sampled Lake A, a deep meromictic lake at latitude 83°N in High Arctic Canada. Sampling was before (May) and after (August) an unusual ice-out event during the warm 2008 summer. We determined the bacterial and archaeal community composition by high-throughput 16S rRNA gene tag-pyrosequencing. Both prokaryote communities were stratified by depth and the Bacteria differed between dates, indicating locally driven selection processes. We matched taxa to known taxon-specific biogeochemical functions and found a close correspondence between the depth of functional specialists and chemical gradients. These results indicate a rich microbial diversity despite the extreme location, with pronounced vertical structure in taxonomic and potential functional composition, and with community shifts during ice-out.

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91 × 105 to 8.65 × 106 copies/g dry sediment for the archaeal amoA gene and from 3.74 × 104 to 3.86 × 105 copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P < 0.05). Concentrations of ammonia (NH4+), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P < 0.05 or P < 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

Enhancing nitrification at low temperature with zeolite in a mining operations retention pond

Ammonium nitrate explosives are used in mining operations at Diavik Diamond Mines Inc. in the Northwest Territories, Canada. Residual nitrogen is washed into the mine pit and piped to a nearby retention pond where its removal is accomplished by microbial activity prior to a final water treatment step and release into the sub-Arctic lake, Lac de Gras. Microbial removal of ammonium in the retention pond is rapid during the brief ice-free summer, but often slows under ice cover that persists up to 9 months of the year. The aluminosilicate mineral zeolite was tested as an additive to retention pond water to increase rates of ammonium removal at 4°C. Water samples were collected across the length of the retention pond monthly over a year. The structure of the microbial community (bacteria, archaea, and eukarya), as determined by denaturing gradient gel electrophoresis of PCR-amplified small subunit ribosomal RNA genes, was more stable during cold months than during July–September, when there was a marked phytoplankton bloom. Of the ammonia-oxidizing community, only bacterial amoA genes were consistently detected. Zeolite (10 g) was added to retention pond water (100 mL) amended with 5 mM ammonium and incubated at 12°C to encourage development of a nitrifying biofilm. The biofilm community was composed of different amoA phylotypes from those identified in gene clone libraries of native water samples. Zeolite biofilm was added to fresh water samples collected at different times of the year, resulting in a significant increase in laboratory measurements of potential nitrification activity at 4°C. A significant positive correlation between the amount of zeolite biofilm and potential nitrification activity was observed; rates were unaffected in incubations containing 1–20 mM ammonium. Addition of zeolite to retention ponds in cold environments could effectively increase nitrification rates year-round by concentrating active nitrifying biomass.

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter-spring (that is, the 0 (o)C slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer-autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC-1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC-1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC-1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.

Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific)

The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.

Prokaryotic diversity in sediments beneath two polar glaciers with contrasting organic carbon substrates

Microbial ecosystems beneath glaciers and ice sheets are thought to play an active role in regional and global carbon cycling. Subglacial sediments are assumed to be largely anoxic, and thus various pathways of organic carbon metabolism may occur here. We examine the abundance and diversity of prokaryotes in sediment beneath two glaciers (Lower Wright Glacier in Antarctica and Russell Glacier in Greenland) with different glaciation histories and thus with different organic carbon substrates. The total microbial abundance in the Lower Wright Glacier sediment, originating from young lacustrine sediment, was an order of magnitude higher (~8 × 10(6) cells per gram of wet sediment) than in Russell Glacier sediment (~9 × 10(5) cells g(-1)) that is of Holocene-aged soil origin. 4% of the microbes from the Russell Glacier sediment and 0.04-0.35% from Lower Wright Glacier were culturable at 10°C. The Lower Wright Glacier subglacial community was dominated by Proteobacteria, followed by Firmicutes. The Russell Glacier library was much less diverse and also dominated by Proteobacteria. Low numbers and diversity of both Euryarchaeota and Crenarchaeota were found in both sediments. The identified clones were related to bacteria with both aerobic and anaerobic metabolisms, indicating the presence of both oxic and anoxic conditions in the sediments.

Change in gene abundance in the nitrogen biogeochemical cycle with temperature and nitrogen addition in Antarctic soils

The microbial community (bacterial, archaeal, and fungi) and eight genes involved in the nitrogen biogeochemical cycle (nifH, nitrogen fixation; bacterial and archaeal amoA, ammonia oxidation; narG, nitrate reduction; nirS, nirK, nitrite reduction; norB, nitric oxide reduction; and nosZ, nitrous oxide reduction) were quantitatively assessed in this study, via real-time PCR with DNA extracted from three Antarctic soils. Interestingly, AOB amoA was found to be more abundant than AOA amoA in Antarctic soils. The results of microcosm studies revealed that the fungal and archaeal communities were diminished in response to warming temperatures (10 °C) and that the archaeal community was less sensitive to nitrogen addition, which suggests that those two communities are well-adapted to colder temperatures. AOA amoA and norB genes were reduced with warming temperatures. The abundance of only the nifH and nirK genes increased with both warming and the addition of nitrogen. NirS-type denitrifying bacteria outnumbered NirK-type denitrifiers regardless of the treatment used. Interestingly, dramatic increases in both NirS and NirK-types denitrifiers were observed with nitrogen addition. NirK types increase with warming, but NirS-type denitrifiers tend to be less sensitive to warming. Our findings indicated that the Antarctic microbial nitrogen cycle could be dramatically altered by temperature and nitrogen, and that warming may be detrimental to the ammonia-oxidizing archaeal community. To the best of our knowledge, this is the first report to investigate genes associated with each process of the nitrogen biogeochemical cycle in an Antarctic terrestrial soil environment.

The deep biosphere in terrestrial sediments in the chesapeake bay area, virginia, USA

For the first time quantitative data on the abundance of Bacteria, Archaea, and Eukarya in deep terrestrial sediments are provided using multiple methods (total cell counting, quantitative real-time PCR, Q-PCR and catalyzed reporter deposition–fluorescence in situ hybridization, CARD–FISH). The oligotrophic (organic carbon content of ∼0.2%) deep terrestrial sediments in the Chesapeake Bay area at Eyreville, Virginia, USA, were drilled and sampled up to a depth of 140 m in 2006. The possibility of contamination during drilling was checked using fluorescent microspheres. Total cell counts decreased from 10⁹ to 10⁶ cells/g dry weight within the uppermost 20 m, and did not further decrease with depth below. Within the top 7 m, a significant proportion of the total cell counts could be detected with CARD–FISH. The CARD–FISH numbers for Bacteria were about an order of magnitude higher than those for Archaea. The dominance of Bacteria over Archaea was confirmed by Q-PCR. The down core quantitative distribution of prokaryotic and eukaryotic small subunit ribosomal RNA genes as well as functional genes involved in different biogeochemical processes was revealed by Q-PCR for the uppermost 10 m and for 80–140 m depth. Eukarya and the Fe(III)- and Mn(IV)-reducing bacterial group Geobacteriaceae were almost exclusively found in the uppermost meter (arable soil), where reactive iron was detected in higher amounts. The bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi, highly abundant in marine sediments, were found up to the maximum sampling depth in high copy numbers at this terrestrial site as well. A similar high abundance of the functional gene cbbL encoding for the large subunit of RubisCO suggests that autotrophic microorganisms could be relevant in addition to heterotrophs. The functional gene aprA of sulfate reducing bacteria was found within distinct layers up to ca. 100 m depth in low copy numbers. The gene mcrA of methanogens was not detectable. Cloning and sequencing data of 16S rRNA genes revealed sequences of typical soil Bacteria. The closest relatives of the archaeal sequences were Archaea recovered from terrestrial and marine environments. Phylogenetic analysis of the Crenarchaeota and Euryarchaeota revealed new members of the uncultured South African Gold Mine Group, Deep Sea Hydrothermal Vent Euryarchaeotal Group 6, and Miscellaneous Crenarcheotic Group clusters.

Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota

Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.