Spatial Analysis of Archaeal Community Structure in Grassland Soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

Spatial analysis of archaeal community structure in grassland soil

The complex structure of soil and the heterogeneity of resources available to microorganisms have implications for sampling regimens when the structure and diversity of microbial communities are analyzed. To assess the heterogeneity in community structure, archaeal communities, which typically contain sequences belonging to the nonthermophilic Crenarchaeota, were examined at two contrasting spatial scales by using PCR-denaturing gradient gel electrophoresis (DGGE) analysis followed by unweighted pair group method with arithmetic mean analysis of 16S rRNA- and ribosomal DNA-derived profiles. A macroscale analysis was carried out with soil cores taken at 2-m intervals along triplicate 8-m transects from both managed (improved) and natural (unimproved) grassland rhizosphere soils. A microscale analysis was carried out with a single soil core by assessing the effects of both sample size (10, 1, and 0.1 g) and distance between samples. The much reduced complexity of archaeal profiles compared to the complexity typical of the bacterial community facilitated visual comparison of profiles based on band presence and revealed different levels of heterogeneity between sets of samples. At the macroscale level, heterogeneity over the transect could not be related to grassland type. Substantial heterogeneity was observed across both improved and unimproved transects, except for one improved transect that exhibited substantial homogeneity, so that profiles for a single core were largely representative of the entire transect. At the smaller scale, the heterogeneity of the archaeal community structure varied with sample size within a single 8- by 8-cm core. The archaeal DGGE profiles for replicate 10-g soil samples were similar, while those for 1-g samples and 0.1-g samples showed greater heterogeneity. In addition, there was no relationship between the archaeal profiles and the distance between 1- or 0.1-g samples, although relationships between community structure and distance of separation may occur at a smaller scale. Our findings demonstrate the care required when workers attempt to obtain a representative picture of microbial community structure in the soil environment.     

Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils

Grassland management influences soil archaeal communities, which appear to be dominated by nonthermophilic crenarchaeotes. To determine whether methanogenic Archaea associated with the Euryarchaeota lineage are also present in grassland soils, anaerobic microcosms containing both managed (improved) and natural (unimproved) grassland rhizosphere soils were incubated for 28 days to encourage the growth of anaerobic Archaea. The contribution of potential methanogenic organisms to the archaeal community was assessed by the molecular analysis of RNA extracted from soil, using primers targeting all Archaea and Euryarchaeota. Archaeal RT‐PCR products were obtained from all anaerobic microcosms. However, euryarchaeal RT‐PCR products (of putative methanogen origin) were obtained only from anaerobic microcosms of improved soil, their presence coinciding with detectable methane production. Sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) bands revealed the presence of euryarchaeal organisms that could not be detected before anaerobic enrichment. These data indicate that nonmethanogenic Crenarchaeota dominate archaeal communities in grassland soil and suggest that management practices encourage euryarchaeal methanogenic activity.     

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4‐region gene fragments obtained by PCR amplification of community genomic DNA with bacterial‐ or archaeal‐specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158 686 bacterial and 225 591 archaeal sequences from 20 sediment samples, representing five 2‐cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor‐joining analysis using Chao–Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96–99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus‐related sequence abundance was correlated with high solid‐phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.     

A Window to the Subsurface: Microbial Diversity in Hot Springs of a Sulfidic Cave (Kaklik,Turkey)

Caves are windows to the extreme habitats of deep subsurface, and provide answers of unknowns about the underground life. Furthermore, sulfidic caves are important analogues for the early Earth environments, since some environmental conditions are common, such as high sulfur concentration, high temperature and oxygen-poor conditions. Kaklik Cave (Denizli, Turkey) with its travertine formation, carbonate- and sulfur-rich thermal springs, exhibits a unique ecosystem as a sulfidic cave. This study represents the first molecular survey of the microbial community in the Kaklik Cave, Turkey using high-throughput 16S rRNA gene amplicon sequencing analysis. An average of 859–2,416 operational taxonomic units per sample were observed including 25 bacterial phyla and 3 archaeal phyla. The bacterial diversity profiles were generally dominated by Epsilonproteobacteria and Gammaproteobacteria. At the carbonate-rich hot spring, that formed travertine structure, 9.7% of sequence reads affiliated with Thiofaba spp. In contrast, 38.74% of the total sequence reads at the sulfidic hot spring samples associated with the genus Sulfurimonas and Sulfurovum. In the archaeal community composition, Thermoplasmata was the most abundant group in all sampling areas. The 454-pyrotag results provide leads about ammonia-, nitrite- and sulfur-oxidation as well as sulfur-reduction, carbon dioxide fixation, and nitrogen fixation.     

Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan

We investigated microbial methanogenesis and community structure based on 16S rRNA gene sequences from a coal seam aquifer located 843–907 m below ground level in northern Japan; additionally, we studied the δ¹³C and δ²H (δD) of coal‐bed gases and other physicochemical parameters. Although isotopic analysis suggested a thermocatalytic origin for the gases, the microbial activity and community structure strongly implied the existence of methanogenic microbial communities in situ. Methane was generated in the enrichment cultures of the hydrogenotrophic and methylotrophic microorganisms obtained from coal seam groundwater. Methanogen clones dominated the archaeal 16S rRNA gene libraries and were mostly related to the hydrogenotrophic genus Methanoculleus and the methylotrophic genus Methanolobus. Bacterial 16S rRNA gene libraries were dominated by the clones related to the genera Acetobacterium and Syntrophus which have a symbiotic association with methanogens. LIBSHUFF analysis revealed that N₂ gas injected into the coal seam (for enhanced methane production) does not affect the coverage of archaeal and bacterial populations. However, amova analysis does provide evidence for a change in the genetic diversity of archaeal populations that are dominated by methanogens. Therefore, N₂ injection into the coal seam might affect the cycling of matter by methanogens in situ.     

Aerobic and Anaerobic Ammonia-Oxidizing Microorganisms in Low-Temperature Hydrothermal Fe-Si-rich Precipitates of the Southwestern Pacific Ocean

Fe-Si-rich hydrothermal precipitates are distributed widely in low-temperature diffusing hydrothermal fields. Due to the significant contribution of Fe-oxidizing bacteria (FeOB) to the formation of this type of hydrothermal precipitates, previous studies focus mostly on investigating FeOB-related microbial populations, albeit these precipitates actually accommodate abundant other microbial communities, particularly those involved in marine nitrogen cycle. In this study, we investigated the composition, diversity, and abundance of aerobic and anaerobic ammonia-oxidizing microorganisms dwelling in low-temperature Fe-Si-rich hydrothermal precipitates of the Lau Integrated Study Site based on ammonia monooxygenase (amoA) gene and 16S rRNA gene. Phylogenetic analysis revealed the common presence of ammonia-oxidizing archaea (AOA), Nitrosospira-like ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing anammox (bacteria) in the Fe-Si-rich hydrothermal precipitates. Quantitative PCR analysis showed that AOA dominated the whole microbial community and the abundance of archaeal amoA gene was 2–3 orders of magnitude higher than that of AOB and anammox bacteria. Result of glycerol dialkyl glycerol tetraether analysis confirmed the presence and abundance of AOA. Our results suggest that microbial ammonia oxidations, especially archaeal aerobic ammonia oxidation, are prevalent and pivotal processes in low-temperature diffusing hydrothermal fields.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome

The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.     

Microbial Communities in the World's Largest Acidic Volcanic Lake, Kawah Ijen in Indonesia, and in the Banyupahit River Originating from It

A first study was made on the microbial community composition of the Indonesian crater lake Kawah Ijen (pH < 0.3) and the Banyupahit–Banyuputih river (pH 0.4–3.5) originating from it. Culture-independent, rRNA gene-based denaturing gradient gel electrophoresis was used to profile microbial communities in this natural and ancient, extremely acidic environment. Similarity in community profiles of the different sampling locations was low, indicating heterogeneity in community composition. Archaea were present at all sampling locations; archaeal diversity was low at the most acidic locations and increased at pH >2.6. Bacteria were not detected in the water column of the crater lake, but were found at all locations along the acidic river. Bacterial diversity increased with increasing pH. Eukarya were only present at pH >2.6. Retrieved rRNA gene sequences of Bacteria and Archaea were not closely related to known acidophilic species. It is concluded that tolerance to extreme acidity in this system is developed most extensively among Archaea. The acidity gradient of the Banyupahit–Banyuputih river has a clear effect on microbial community composition and biodiversity.     

Response of Archaeal Community Structure to Environmental Changes in Lakes on the Tibetan Plateau,Northwestern China

To study how archaeal community responds to environmental changes, we investigated archaeal community structures in waters of three Tibetan saline lakes in northwestern China (Gahai, Xiaochaidan, and Charhan Lakes) with 16S rRNA gene phylogenetic analysis. Temperature, pH, and water chemistry (major anions and cations) of the lakes were measured. Three archaeal clone libraries were constructed with a total of 297 sequences. Incorporating our previous data obtained from other lakes on the Tibetan Plateau, we performed statistical analyses to identify dominant environmental parameters that could account for the observed variations in archaeal community structure. We concluded that salinity and water chemistry (Na and bicarbonate concentration in particular) played an important role in shaping archaeal community. In particular, the relative abundance of archaeal 16S rRNA genes affiliated with the Halobacteriales of the Euryarchaeota increased with salinity, whereas that of crenarchaeotal 16S rRNA gene sequences showed the opposite trend. Crenarchaeotal 16S rRNA gene sequences were retrieved from lake waters with salinity up to 28.3%. These results have important implications for our understanding of response of archaeal community to environmental changes in high-altitude lake ecosystems.     

Archaeal community dynamics and detection of ammonia-oxidizing archaea during composting of cattle manure using culture-independent DNA analysis

The composting process is carried out under aerobic conditions involving bacteria, archaea, and fungi. Little is known about the diversity of archaeal community in compost, although they may play an important role in methane production and ammonia oxidation. In the present study, archaeal community dynamics during cattle manure composting were analyzed using a clone library of the archaeal 16S rRNA gene. The results indicated that methane-producing archaea (methanogen) and ammonia-oxidizing archaea (AOA) may be the dominant microbes throughout the composting. The community consisted primarily of Methanocorpusculum-like and Methanosarcina-like sequences until day 2, while the number of Candidatus Nitrososphaera-like sequences increased from day 6 to day 30. Methanosarcina thermophila-like sequences were dominant from day 2, suggesting that M. thermophila-like species can adapt to increasing temperature or nutrient loss. A denaturant gradient gel electrophoresis analysis of the archaeal amoA genes revealed that the dominant amoA gene sequence with 99% homology to that of Candidatus Nitrososphaera gargensis was identical to those obtained from a different composting facility. These data suggested that AOA may play a role in ammonia oxidation in several composting practices. Our results provide fundamental information regarding archaeal community dynamics that will help in understanding the collective microbial community in compost.     

Compositional analysis of archaeal communities in high and low microbial abundance sponges in the Misool coral reef system,Indonesia

The high/low microbial abundance (HMA/LMA) dichotomy in sponges has been the subject of several studies over recent years, but few studies have analysed this dichotomy in terms of the sponge archaeal community and function. Using a 16S rRNA gene barcoded pyrosequencing approach and predictive functional analysis (PICRUSt) we compared the archaeal composition, richness and predicted function of one HMA sponge (Xestospongia testudinaria), one LMA sponge (Stylissa carteri) and one sponge species of unknown microbial abundance (Aaptos lobata). Although most of the archaeal sequences were assigned to the Crenarchaeota phylum, S. carteri had the highest percentage of sequences assigned to the Euryarchaeota phylum. Variation among sponge species explained >85% of the variation in archaeal operational taxonomic unit (OTU) composition with each sponge species forming a distinct cluster. There were significant differences in predicted PICRUSt profiles among sponge species, suggesting that archaeal communities present in the studied sponge species may perform different functions. X. testudinaria and A. lobata were similar both in terms of OTU and KEGG orthologues composition, which may indicate that A. lobata is a HMA sponge. Additionally, some of the most enriched functions seem to be related to traits associated with high and low microbial abundance sponges.     

Prokaryotic Abundance and Community Composition in a Freshwater Iron-Rich Microbial Mat at Circumneutral pH

The abundance, diversity and composition of bacterial and archaeal communities in a freshwater iron-rich microbial mat were investigated using culture-dependent and culture-independent methods. The sampling site is a mixing zone where ferrous-iron-rich fluids encounter oxygen-rich environments. Quantitative PCR analysis shows that Bacteria dominated the mat community (>99% of the total cell numbers). Phylotypes related to iron-oxidizers in Gallionellaceae, methano/methylotrophs in Methylophilaceae and Methylococcaceae, sulfide-oxidizers in Sulfuricurvum and an uncultured clone group, called Terrestrial group I or the 1068 group, in the Epsilonproteobacteria were detected in the clone library from the original sample and/or the enrichment cultures. This result suggests that these members may play a role in Fe, S and C cycling in the mixing zone. Although Archaea were minor constituents numerically, phylogenetic analysis indicates that unique and diverse yet-uncultivated Archaea are present in the iron-rich mat. The phylotypes of these yet-uncultivated Archaea belong to environmental clone groups that have been recovered from other mixing zones in terrestrial and marine environments, and some of our phylotypes have significantly low similarity (80% or lower) with the archaeal clones reported previously. Our results provide further insights into the bacterial and archaeal communities in a microaerobic iron-rich freshwater environment in mixing zones.     

Response of microbial community structure to natural and accelerated hydrarch successions in the boreal wetlands in northern Hokkaido, Japan

We estimated the effect of invading Sasa vegetation and accelerated terrestrialization on the microbial community structure in Sarobetsu-genya wetland (SGW) and Nakanominedaira wetland (NW) (original vegetation, Sphagnum). All examined peat-pore water samples were acidic. Electrical conductivity significantly differed between SGW and NW. Nonmetric multidimensional scaling (NMDS) and analysis of similarity based on denaturing gradient gel electrophoresis (DGGE) band patterns revealed differences in the bacterial community structure between the Sasa and Sphagnum vegetations at a depth of 10 cm in NW. In contrast, the bacterial NMDS profiles at all depths differed between the 2 wetlands rather than between the 2 vegetations. The archaeal community structure significantly differed between the wetlands at depths of 30 and 50 cm. The bacterial diversity index derived from the DGGE profiles significantly differed between the wetlands at all depths. The archaeal diversity index significantly differed between the wetlands at a depth of 50 cm. Sasa invasion affected the microbial community structure in the rhizosphere, up to a depth of 10 cm; this effect differed with the terrestrialization speed. These results suggest that in peat bogs subjected to artificially accelerated terrestrialization, the microbial community changes before the occurrence of the natural hydrarch ecological succession involving ground vegetation.     

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir,Beijing, China

Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH₄ ⁺–N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.

     

Shifts in archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock

Subsurface microbial community structure in relation to geochemical gradients and lithology was investigated using a combination of molecular phylogenetic and geochemical analyses. Discreet groundwater and substratum samples were obtained from depths ranging from 182 to 190 m beneath the surface at approximately 10-cm intervals using a multilevel sampler (MLS) that straddled Cretaceous shale and sandstone formations at a site in the southern San Juan Basin in New Mexico. DNA and RNA were extracted directly from quartzite sand substratum loaded into individual cells of the MLS and colonized in situ. Polymerase chain reaction (PCR)-mediated T-RFLP analysis of archaeal rRNA genes (rDNA) in conjunction with partial sequencing analysis of archaeal rDNA libraries and quantitative RNA hybridization with oligonucleotide probes were used to probe community structure and function. Although total microbial populations remained relatively constant over the entire depth interval sampled, significant shifts in archaeal populations, predominantly methanogens, were observed. These shifts coincided with the geochemical transition from relatively high methane (26 mM), low sulphate (< 3 mg l(-1)) conditions in the region adjacent to the organic matter-rich shale to relatively low-methane (< 0.5 mM), high-sulphate (48 mg l(-1)) conditions in the organic-poor sandstone beneath the shale. These results indicated that active, phylogenetically diverse archaeal communities were present in the subsurface Cretaceous rock environment at this site and that major archaeal clades shifted dramatically over scales of tens of centimetres, corresponding to changes in the lithology and geochemical gradients.     

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.     

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

     

The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

The Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were Proteobacteria (relative abundance 0.39 ± 0.12) and Chloroflexi (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and Euryarchaeota (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla Chloroflexi, Bacteroidetes, Atribacteria, Aminicenantes, Chlorobi, TA06, Caldiserica and Spirochaetae; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.