Archaeal 16S rRNA Gene Research Articles

Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir

Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.

Intact Ether Lipids in Trench Sediments Related to Archaeal Community and Environmental Conditions in the Deepest Ocean

AbstractArchaea play an important role in marine biogeochemical cycle; however, their phylogenetic distribution and lipid composition in the hadal zone (6–11 km water depth) are poorly known. Here, we analyzed archaeal membrane lipids and 16S rRNA gene sequences in sediments from Mariana Trench (MT), Massau Trench (MS), and New Britain Trench (NBT), varying from 1,560 to 10,840 m depth. Forty‐two intact polar lipids (IPLs) were identified, including glycerol dialkyl glycerol tetraethers (GDGTs), OH‐GDGTs, glycerol dialkyl diethers (GDDs), and archaeol (AR) with polar headgroups of monohexose (1G), dihexose (2G), trihexose (3G), and hexose‐phosphohexose (HPH). Compositional and spatial distribution patterns of archaeal lipids suggest benthic Thaumarchaeota as a major source for IPLs, consistent with the predominance of Thaumarchaeota genes (>80%). The redundancy analysis (RDA) based on lipid and 16S rRNA data separates samples into three groups: extremely deep water (MT), significant terrestrial influence (NBT 1, 4, and 6), and predominant marine influence (MS, NBT 2, 3, 7, and 10). 1G‐GDDs and 1G‐AR positively correlate with water depth, likely reflecting the adaptation of benthic archaea to elevated hydrostatic pressure or variation of archaeal community in trench sediments. Bathyarchaeota are more abundant in sediments receiving terrestrial input; this pattern was attributed to their capability of utilizing terrestrial organic matter as an energy source. Our study highlights important environmental influences (e.g., pressure and organic matter quality and quantity) on benthic archaeal community and archaeal IPL compositions, which should be considered when IPLs and core lipids are applied as chemotaxonomic markers and paleo‐proxies.

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89′N–9°59.70′S, 87°58.90′E–88°00.03′E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman’s correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).

Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir

Nitrite (NO2−)- and nitrate (NO3−)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO2−- and NO3−-dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 107 to 2.8 × 108 copies g−1 dry sediment) than upstream sediments (2.4 × 107 to 3.5 × 107 copies g−1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 105 to 4.8 × 105 copies g−1 dry sediment). The 13CH4 tracer experiments suggested the occurrence of NO2−- and NO3−-dependent AOM activities, and their rates were 4.7–14.1 and 0.8–2.6 nmol CO2 g−1 (dry sediment) d−1, respectively. Further, the rates of NO2−-dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO3− concentration was the key factor affecting the spatial variations of abundance and activity of NO2−-dependent anaerobic methanotrophs. Overall, our results showed different responses of NO2−- and NO3−-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.

The effects of crude oil on microbial nitrogen cycling in coastal sediments

Crude oil could affect certain critical microbial processes of nitrogen cycling (N-cycling) in coastal sediments, and disturb the nitrogen balance. However, the understanding of the effects of crude oil on coastal sediments N-cycling under human disturbance was still limited. In this study, two sediments (named SY and HB with heavy and slight pollution, respectively) were sampled from Hangzhou Bay, China. After an incubation with exposure to different amounts of crude oil in above two sediments for 30 days, we found that crude oil affected microbial N-cycling in multiple levels. Potential rate measurements revealed that crude oil stimulated potential denitrification and N2O emissions in both sediments, which showed a higher influence on denitrification rates in higher concentration of oil. Quantitative PCR revealed that crude oil greatly increased abundances of bacterial and archaeal 16S rRNA genes and N-cycling genes (nirS, nosZ, nrfA, part of AOA and AOB amoA). On the other hand, only a few genes (16S rRNA and nrfA) showed higher transcriptional activities in oil-addition treatments. Results about relative changes of N-cycling genes revealed that the variations of N-cycling genes in oil-addition treatments were related to sediment types but not crude oil concentrations, and the genes in HB were more sensitive to crude oil than SY. Network analysis of N-cycling genes found that crude oil decreased the complexity of N-cycling gene networks in SY, while increased complexity in HB, and led to more competition among N-cycling microbes. Our findings help to look into the effects of crude oil on key N-cycling processes, and improve the understanding of the interactions among N-cycling under crude oil contamination.

Calcium propionate supplementation alters the ruminal bacterial and archaeal communities in pre- and postweaning calves

The aim of this study was to determine the effect of calcium propionate (CaP) on rumen microbiota, fermentation indicators, and weight gain in calves both pre- and postweaning. Twenty-four newborn calves were randomly divided into 4 groups (2 × 2 factorial treatment arrangement): either pre- (90 d) or postweaning (160 d), and either without or with dietary CaP supplementation (5% dry matter). The CaP supplementation increased the body weight and rumen weight of the calves and lowered NH3-N concentration in the rumen. Microbiota composition was characterized by sequencing the amplicons of the bacterial and archaeal 16S rRNA genes. The CaP supplementation decreased the relative abundance of the phylum Bacteroidetes but tended to increase that of Proteobacteria. In addition, CaP supplementation decreased the diversity of bacteria and archaea in the rumen compared with the calves fed the control diet. Linear discriminant analysis of the rumen microbiota revealed that Succinivibrionaceae and Methanobrevibacter were enriched in the CaP group postweaning. A correlation was also present between the acetate to propionate ratio and the species that acted as co-occurrence network hubs, including Succiniclasticum, Treponema, and Megasphaera. In conclusion, CaP supplementation can improve body weight gain and rumen growth and alter the ruminal microbiota in calves both pre- and postweaning.

Spatial variations in bacterial and archaeal abundance and community composition in boreal forest pine mycorrhizospheres

Mycorrhizal fungi have a strong impact on soil biota. In this study, bacterial and archaeal populations in different parts of Suillus bovinus - Pinus sylvestris mycorrhizospheres in boreal forest were quantified and identified by DNA analysis. The numbers of bacterial and archaeal 16S rRNA gene copies were highest in uncolonized humus and lowest in fruiting bodies. The numbers of bacterial 16S rRNA gene copies varied from 1.3 × 107 to 3.1 × 109 copies g−1 fw and archaeal copies from 4.1 × 107 to 9.6 × 108 copies g−1 fw. The relatively high number of archaeal 16S rRNA gene copies was likely due to the cold and highly organic habitat. The presence of hyphae appeared to further promote archaeal numbers and the archaea:bacteria ratio was over one in samples containing only fungal material. Most detected archaea belonged to terrestrial Thaumarchaeota. Proteobacteria, Actinobacteria and Acidobacteria were predictably the dominating bacterial taxa in the samples with clear trend of Betaproteobacteria preferring the pine root habitats.

Methane emission suppression in flooded soil from Amazonia

The coupling between ferrous iron and methane production has important global implications, with iron ions acting as electron acceptors for anaerobic oxidation of methane (AOM) and inhibitors of methanogenesis in different environments, including floodplain soils. In this sense, we analyzed the relationship between Fe(II) concentration and methane production in soil layers collected at 0–15 cm and 15–30 cm from flooded-forest and -agroforestry in Amazonian clear water floodplain incubated in anaerobic batch reactors using acetate, formate and glucose as organic sources. High throughput sequencing of archaeal and bacterial 16S rRNA genes was employed to assess the abundance and composition of the active methanogenic and methanotrophic microbial groups potentially involved in Fe(III)-dependent AOM in the soil used as inoculum. Positive correlation was revealed between Fe(II) concentration and methane production, with higher accumulation of Fe(II) in incubated soil layer collected at 0–15 cm in both forest and agroforestry sites for all the three organic sources. The accumulation of Fe(II) in the incubated soil evidenced the oxidation of Fe(III) potentially by Methanobacterium, Desulfobulbus and ‘Candidatus methanoperedens nitroreducens’ living in anaerobic condition at this soil layer. The results point out to the microbial ferric iron reduction as an important potential pathway for anaerobic organic matter decomposition in Amazonian floodplain, evidencing methanogenesis suppression by Fe(III) reduction in flooded-forest and -agroforestry in Amazonian clear water river floodplain.

Methanogenic response to long-term permafrost thaw is determined by paleoenvironment.

ABSTRACTMethane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO2) and enumerated methanogenic (mcrA) gene copies in long-term (2–7 years) anoxic incubations at 4 °C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin. Changes in archaeal community composition were determined by sequencing of the archaeal 16S rRNA gene. Long-term thaw stimulated methanogenesis where methanogens initially dominated the archaeal community. Deposits of interstadial and interglacial (Eemian) origin, formed under higher temperatures and precipitation, displayed the greatest response to thaw. At the end of the incubations, a substantial shift in methanogenic community composition and a relative increase in hydrogenotrophic methanogens had occurred except for Eemian deposits in which a high abundance of potential acetoclastic methanogens were present. This study shows that only anaerobic CO2 production but not methane production correlates significantly with carbon and nitrogen content and that the methanogenic response to permafrost thaw is mainly constrained by the paleoenvironmental conditions during soil formation.

Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters.

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary

Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO3−, dissolved Mn and Fe, SO42+, NH4+; dissolved inorganic carbon (DIC), δ13CDIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ13CTOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO42− and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH4+, δ13CTOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.

Impact of euxinic holomictic conditions on prokaryotic assemblages in a marine meromictic lake

The water column of marine Rogoznica Lake (Croatia) is stratified throughout the year. However, on rare occasions, the lake exhibits complete mixing, primarily driven by meteorological conditions. On such occasions, anoxic, sulfide-rich bottom water mixes with the oxic surface layer, triggering both the oxidation of sulfide predominantly to colloidal sulfur and the establishment of euxinic conditions throughout the water column. We investigated prokaryotic communities during euxinic holomictic conditions. High-throughput sequencing of the 16S rRNA gene showed that these sulfur-driven communities were dominated by Planctomycetales, chemolithotrophic Epsilonbactereota (mainly Arcobacteraceae) and Gammaproteobacteria (Thioglobaceae), followed by Alpha- (Rhodobacteraceae) and Deltaproteobacteria (Desulfobulbaceae and Desulfobacteraceae). The majority of archaeal sequences belonged to Nanoarchaeota, all of which were designated as Woesearchaeia. This class has not been recorded in other meromictic lakes. Both bacterial and archaeal 16S rRNA gene abundance did not vary significantly across the vertical profile of the lake, as shown by quantitative PCR. However, hierarchical clustering showed a significant difference between the microbial assemblage structure in stratified periods and during a holomictic event. Besides the structure, this stressful event had a manifold effect on bacterial and archaeal assemblages by decreasing their diversity and abundance when compared to the usual stratified conditions.

Analysis of the microbial communities in soils of different ages following volcanic eruptions

Volcanism is a primary process of land formation. It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments. The objective of this study was to identify the microbial communities involved in soil formation. DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries (1640, 1751, and 1957). Bacterial and archaeal 16S rRNA genes were analyzed using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Results showed that microbial diversity increased with soil age, particularly between the 1751 and 1640 soils. For archaeal communities, Thaumarchaeota was detected in similar abundances in all soils, but Euryarchaeota was rare in the older soils. The analysis of bacterial 16S rRNA genes showed high abundances of Chloroflexi (37%), Planctomycetes (18%), and Verrucomicrobia (10%) in the youngest soil. Proteobacteria and Acidobacteria were highly abundant in the older soils (16% in 1640 and 15% in 1751 for Acidobacteria; 38% in 1640 and 27% in 1751 for Proteobacteria). The microbial profiles in the youngest soils were unusual, with a high abundance of bacteria belonging to the order Ktedonobacterales (Chloroflexi) in the 1957 soil (37%) compared with the 1751 (18%) and 1640 (7%) soils. In this study, we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery.

Long-term submergence of non-methanogenic oxic upland field soils helps to develop the methanogenic archaeal community as revealed by pot and field experiments

The community structure of methanogenic archaea is relatively stable, i.e., it is sustained at a high abundance with minimal changes in composition, in paddy field soils irrespective of submergence and drainage. In contrast, the abundance in non-methanogenic oxic soils is much lower than that in paddy field soils. This study aimed to describe methanogenic archaeal community development following the long-term submergence of non-methanogenic oxic upland field soils in pot and field experiments. In the pot experiment, a soil sample obtained from an upland field was incubated under submerged conditions for 275 d. Soil samples periodically collected were subjected to culture-dependent most probable number (MPN) enumeration, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of archaeal 16S rRNA gene, and quantitative PCR analysis of the methyl-coenzyme M reductase alpha subunit gene (mcrA) of methanogenic archaea. The abundance of methanogenic archaea increased from 102 to 103 cells g−1 dry soil and 104 to 107 copies of mcrA gene g−1 dry soil after submergence. Although no methanogenic archaeon was detected prior to incubation by the DGGE analysis, members from Methanocellales, Methanosarcinaceae, and Methanosaetaceae proliferated in the soils, and the community structure was relatively stable once established. In the field experiment, the number of viable methanogenic archaea in a rice paddy field converted from meadow (reclaimed paddy field) was monitored by MPN enumeration over five annual cycles of field operations. Viability was also determined simultaneously in a paddy field where the plow layer soil from a farmer's paddy field was dressed onto the meadow (dressed paddy field) and an upland crop field converted from the meadow (reclaimed upland field). The number of viable methanogenic archaea in the reclaimed paddy field was below the detection limit before the first cultivation of rice and in the reclaimed upland field. Then, the number gradually increased over five years and finally reached 103–104 cells g−1 dry soil, which was comparable to that in the dressed paddy field. These findings showed that the low abundance of autochthonous methanogenic archaea in the non-methanogenic oxic upland field soils steadily proliferated, and the community structure was developed following repeated and long-term submergence. These results suggest that habitats suitable for methanogenic archaea were established in soil following repeated and long-term submergence.

Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites.

Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.

Presence of Archaea in dental caries biofilms

ObjectiveAlthough the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet. DesignTo detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated. ResultsThe high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota. ConclusionsArchaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.

Bacterial and Archaeal Communities in Sediments from the Adjacent Waters of Rushan Bay (China) Revealed by Illumina Sequencing

In this study, bacterial and archaeal communities in sediments from the adjacent waters of Rushan Bay were studied based on 16S ribosomal RNA (rRNA) gene. Illumina sequencing and quantitative PCR (qPCR) analyses were used to analyze the bacterial and archaeal community characteristics. The ecological analyses of sequences revealed that the diversity of bacterial communities was higher than that of archaeal communities. The abundance of bacterial 16S rRNA genes was observed to be greater than that of archaeal 16S rRNA genes. Proteobacteria and Piscirickettsiaceae were the most abundant bacterial phylum and family; Thaumarchaeota dominated the archaeal communities, and MGI in Thaumarchaeota and Halobacteria in Euryarchaeota were prevalent and the predominant archaeal class in this study. Temperature and ammonium concentration were related to the bacterial communities, whereas the nitrite concentration and ammonium concentration had a correlation with the archaeal communities; meanwhile, a complex combination of environmental factors might shape the bacterial and archaeal communities in this dynamic environment. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis showed that most bacterial sequences were involved in chemoheterotrophy, sulfate respiration, respiration of sulfur compounds, aerobic nitrite oxidation and nitrification; for the archaeal communities, the essential ecological functions were chemoheterotrophy, other ecological functions such as aerobic ammonia oxidation and methanogenesis, were also predicted to be present in this study. The comparison of bacterial and archaeal communities in different environments suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal community structure.

Archaeal Communities in Deep Terrestrial Subsurface Underneath the Deccan Traps, India

Archaeal community structure and potential functions within the deep, aphotic, oligotrophic, hot, igneous provinces of ∼65 Myr old basalt and its Archean granitic basement was explored through archaeal 16S rRNA gene amplicon sequencing from extracted environmental DNA of rocks. Rock core samples from three distinct horizons, basaltic (BS), transition (weathered granites) (TZ) and granitic (GR) showed limited organic carbon (4–48 mg/kg) and varied concentrations (<1.0–5000 mg/kg) of sulfate, nitrate, nitrite, iron and metal oxides. Quantitative PCR estimated the presence of nearly 103–104 archaeal cells per gram of rock. Archaeal communities within BS and GR horizons were distinct. The absence of any common OTU across the samples indicated restricted dispersal of archaeal cells. Younger, relatively organic carbon- and Fe2O3-rich BS rocks harbor Euryarchaeota, along with varied proportions of Thaumarchaeota and Crenarchaeota. Extreme acid loving, thermotolerant sulfur respiring Thermoplasmataceae, heterotrophic, ferrous-/H-sulfide oxidizing Ferroplasmaceae and Halobacteriaceae were more abundant and closely interrelated within BS rocks. Samples from the GR horizon represent a unique composition with higher proportions of Thaumarchaeota and uneven distribution of Euryarchaeota and Bathyarchaeota affiliated to Methanomicrobia, SAGMCG-1, FHMa11 terrestrial group, AK59 and unclassified taxa. Acetoclastic methanogenic Methanomicrobia, autotrophic SAGMCG-1 and MCG of Thaumarcheaota could be identified as the signature groups within the organic carbon lean GR horizon. Sulfur-oxidizing Sulfolobaceae was relatively more abundant in sulfate-rich amygdaloidal basalt and migmatitic gneiss samples. Methane-oxidizing ANME-3 populations were found to be ubiquitous, but their abundance varied greatly between the analyzed samples. Changes in diversity pattern among the BS and GR horizons highlighted the significance of local rock geochemistry, particularly the availability of organic carbon, Fe2O3 and other nutrients as well as physical constraints (temperature and pressure) in a niche-specific colonization of extremophilic archaeal communities. The study provided the first deep sequencing-based illustration of an intricate association between diverse extremophilic groups (acidophile-halophile-methanogenic), capable of sulfur/iron/methane metabolism and thus shed new light on their potential role in biogeochemical cycles and energy flow in deep biosphere hosted by hot, oligotrophic igneous crust.

Highly Diverse Aquatic Microbial Communities Separated by Permafrost in Greenland Show Distinct Features According to Environmental Niches.

The Greenland Analog Project (GAP) study area in the vicinity of Kangarlussuaq, Western Greenland, was sampled for surface water and deep groundwater in order to determine the composition and estimate the metabolic features of the microbial communities in water bodies separated by permafrost. The sampling sites comprised a freshwater pond, talik lake, deep anoxic groundwater, glacier ice and supraglacial river, meltwater river and melting permafrost active layer. The microbial communities were characterized by amplicon sequencing of the bacterial and archaeal 16S rRNA genes and fungal ITS1 spacer. In addition, bacterial, archaeal and fungal numbers were determined by qPCR and plate counts, and the utilization pattern of carbon and nitrogen substrates was determined with Biolog AN plates and metabolic functions were predicted with FAPROTAX. Different sample types were clearly distinguishable from each other based on community composition, microbial numbers, and substrate utilization patterns, forming four groups, (1) pond/lake, (2) deep groundwater, (3) glacial ice, and (4) meltwater. Bacteria were the most abundant microbial domain, ranging from 0.2–1.4 × 107 16S rRNA gene copies mL-1 in pond/lake and meltwater, 0.1-7.8 × 106 copies mL-1 in groundwater and less than 104 copies mL-1 in ice. The number of archaeal 16S and fungal 5.8S rRNA genes was generally less than 6.0 × 103 and 1.5 × 103, respectively. N2-fixing and methane-oxidizing Actinomycetes, Bacteroidetes and Verrucomicrobia were the dominant microorganisms in the pond/lake samples, whereas iron reducing Desulfosporosinus sp. dominated the deep anaerobic groundwater. The glacial ice was inhabited by Cyanobacteria, which were mostly Chloroplast-like. The meltwater contained methano- and methylotrophic Proteobacteria, but had also high relative abundances of the nano-sized Parcubacteria. The archaea composed approximately 1% of the 16S rRNA gene pool in the pond/lake samples with nano-sized Woesearchaeota as the dominating taxon, while in the other sample types archaea were almost negligent. Fungi were also most common in the pond/lake communities, were zoospore-forming Chytridiomycetes dominated. Our results show highly diverse microbial communities inhabiting the different cold Greenlandic aqueous environments and show clear segregation of the microbial communities according to habitat, with distinctive dominating metabolic features specifically inhabiting defined environmental niches and a high relative abundance of putatively parasitic or symbiotic nano-sized taxa.

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area.

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.