Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis

Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau

Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.

Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau

Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15W^T and AIY15W^T) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15W^T and AIY15W^T share 16S rRNA gene sequence similarities 98.4 % with Aquiflexum aquatile Z0201^T, but only about 95.0 % with Aquiflexum balticum DSM 16537^T. The 16S rRNA gene sequence similarity between strains LQ15W^T and AIY15W^T was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15W^T and AIY15W^T take A. aquatile Z0201^T as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus Aquiflexum was splited into two clusters by Mariniradius saccharolyticus. Strains LQ15W^T, AIY15W^T and A. aquatile Z0201^T still formed a close cluster, and A. balticum DSM 16537^T and Aquiflexum lacus CUG 91378^T formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA-DNA hybridization values among strains LQ15W^T, AIY15W^T, A. aquatile Z0201^T, A. balticum DSM 16537^T and A. lacus CUG 91378^T were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15W^T and AIY15W^T were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C_15 : 0, C_18 : 1  ω9c, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15W^T also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains A. aquatile Z0201^T and A. balticum DSM 16537^T, it is proposed to reclassify A. aquatile into a novel genus Cognataquiflexum gen. nov. as Cognataquiflexum aquatile comb. nov., and strains LQ15W^T and AIY15W^T should represent two independent novel species of the genus Cognataquiflexum, for which the names Cognataquiflexum nitidum sp. nov. (type strain: LQ15W^T=CICC 24711^T=JCM 34222^T) and Cognataquiflexum rubidum sp. nov. (type strain: AIY15W^T=CICC 24708^T=JCM 34612^T) are proposed.

Validation of the names Cyanobacterium and Cyanobacterium stanieri, and proposal of Cyanobacteriota phyl. nov

The decision by the International Committee on Systematics of Prokaryotes (ICSP) to place the rank of phylum under the rules of the International Code of Nomenclature of Prokaryotes (ICNP), with phylum names ending in –ota based on the name of a type genus, enables the valid publication of the phylum name Cyanobacteriota with Cyanobacterium as the type genus. The names Cyanobacterium and its type species Cyanobacterium stanieri were effectively published in 1983 by Rippka and Cohen-Bazire, but the names were not validly published under the rules of the ICNP (then named the International Code of Nomenclature of Bacteria) or the rules of the ICN (International Code of Nomenclature for algae, fungi, and plants, then named the International Code of Botanical Nomenclature). We here propose the names Cyanobacterium gen. nov and Cyanobacterium stanieri sp. nov. for valid publication under the provisions of the ICN. Upon validation these names are also validly published under the ICNP according to General Consideration 5 and Rule 30. We also propose the phylum name Cyanobacteriota phyl. nov. under the rules of the ICNP.

Aquirufa lenticrescens sp. nov. and Aquirufa aurantiipilula sp. nov.: two new species of a lineage of widespread freshwater bacteria

Two bacterial strains, 9H-EGSE^T and 15D-MOB^T, were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa (Bacteroidota). Genome-based phylogenetic reconstructions with 119 amino acid sequences assigned the new taxa to the two distinct branches of the genus Aquirufa. Whole-genome average nucleotide identities were calculated with all possible pairs belonging to the genus. Values between 75.4% and 88.6% revealed that the two new strains represent each a new species. Like all, so far described members of the genus, they grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented, and motile by gliding, and showed genome sizes of about 3 Mbp and G + C values of about 40%. They could be distinguished by some phenotypic and chemotaxonomic features from their nearest related species. Until now, strain 9H-EGSE^T is the only one among the Aquirufa strains which contained traces of MK8 as respiratory quinone, and strain 15D-MOB^T is the only one that formed tiny orange globules in liquid medium. The genome of strain 9H-EGSE^T comprised genes for the complete light-harvesting rhodopsin / retinal system, in the case of 15D-MOB^T genes predicted for a nitrous oxide reductase were present. For the two new species of the genus Aquirufa, we propose to establish the names Aquirufa lenticrescens for strain 9H-EGSE^T (= JCM 34077 ^T = CIP 111926 ^T) and Aquirufa aurantiipilula for strain 15D-MOB^T (= JCM 34078 ^T = CIP 111925 ^T).

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria)

Among the thousands of species that comprise marine bacterioplankton communities, most remain functionally obscure. One key cosmopolitan group in this understudied majority is the OM252 clade of Gammaproteobacteria. Although frequently found in sequence data and even previously cultured, the diversity, metabolic potential, physiology, and distribution of this clade has not been thoroughly investigated. Here, we examined these features of OM252 bacterioplankton using a newly isolated strain and genomes from publicly available databases. We demonstrated that this group constitutes a globally distributed novel genus ("Candidatus Halomarinus"), sister to Litoricola, comprising two subclades and multiple distinct species. OM252 organisms have small genomes (median, 2.21 Mbp) and are predicted obligate aerobes capable of alternating between chemoorganoheterotrophic and chemolithotrophic growth using reduced sulfur compounds as electron donors. Subclade I genomes encode genes for the Calvin-Benson-Bassham cycle for carbon fixation. One representative strain of subclade I, LSUCC0096, had extensive halotolerance and a mesophilic temperature range for growth, with a maximum rate of 0.36 doublings/h at 35°C. Cells were curved rod/spirillum-shaped, ∼1.5 by 0.2 μm. Growth yield on thiosulfate as the sole electron donor under autotrophic conditions was roughly one-third that of heterotrophic growth, even though calculations indicated similar Gibbs energies for both catabolisms. These phenotypic data show that some "Ca. Halomarinus" organisms can switch between serving as carbon sources or sinks and indicate the likely anabolic cost of lithoautotrophic growth. Our results thus provide new hypotheses about the roles of these organisms in global biogeochemical cycling of carbon and sulfur. IMPORTANCE Marine microbial communities are teeming with understudied taxa due to the sheer numbers of species in any given sample of seawater. One group, the OM252 clade of Gammaproteobacteria, has been identified in gene surveys from myriad locations, and one isolated organism has even been genome sequenced (HIMB30). However, further study of these organisms has not occurred. Using another isolated representative (strain LSUCC0096) and publicly available genome sequences from metagenomic and single-cell genomic data sets, we examined the diversity within the OM252 clade and the distribution of these taxa in the world's oceans, reconstructed the predicted metabolism of the group, and quantified growth dynamics in LSUCC0096. Our results generate new knowledge about the previously enigmatic OM252 clade and point toward the importance of facultative chemolithoautotrophy for supporting some clades of ostensibly "heterotrophic" taxa.

Aquiluna borgnonia gen. nov., sp. nov., a member of a Microbacteriaceae lineage of freshwater bacteria with small genome sizes

The actinobacterial strain 15G-AUS-rot^T was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rot^T to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rot^T were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C_16 : 0, antiso-C_15 : 0 and iso-C_14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rot^T (=DSM 107803^T=JCM 32974^T).

Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

Metagenomics Uncovers a Core SAR11 Population in Brackish Surface Waters of the Baltic Sea

The Baltic Sea represents one of the largest brackish ecosystems where various environmental factors control dynamic seasonal shifts in the structure, diversity, and function of the planktonic microbial communities. In this study, despite seasonal fluctuations, several bacterial populations (<2% of the total OTUs) that are highly dominant (25% of relative abundance) and highly frequently occurring (>85% of occurrence) over four seasons were identified. Mathematical models using occurrence frequency and relative abundance data were able to describe community assembly persisting over time. Further, this work uncovered one of the core bacterial populations phylogenetically affiliated to SAR11 subclade IIIa. The analysis of the hypervariable region of 16S rRNA gene and single copy housekeeping genes recovered from metagenomic datasets suggested that the population was unexpectedly evolutionarily closely related to those inhabiting a mesosaline lacustrine ecosystem rather than other marine/coastal members. Our metagenomic results further revealed that the newly-identified population was the major driver facilitating the seasonal shifts in the overall community structure over the brackish waters of the Baltic Sea. The core community uncovered in this study supports the presence of a brackish water microbiome distinguishable from other marine and freshwater counterparts and will be a useful sentinel for monitoring local/global environmental changes posed on brackish surface waters.

The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds (Litopenaeus vannamei) in Soc Trang Province

Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10–20.29%), Methylophilus (13.26–24.28%), and Flavobacterium (2.6–19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH₄Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment.

A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups

During the last five decades, the Aral Sea has gradually changed from a saline water body to a hypersaline lake. Microbial community inhabiting the Aral Sea has been through a succession and continuous adaptation during the last 50 years of increasing salinization, but so far, the microbial diversity has not been explored. Prokaryotic diversity of the Large Aral Sea using cultivation‐independent methods based on determination of environmental 16S rRNA gene sequences revealed a microbial community related to typical marine or (hyper) saline‐adapted Bacteria and Archaea. The archaeal sequences were phylogenetically affiliated with the order Halobacteriales, with a large number of operational taxonomic units constituting a novel cluster in the Haloferacaceae family. Bacterial community analysis indicated a higher diversity with representatives belonging to Proteobacteria, Actinobacteria and Bacteroidetes. Many members of Alphaproteobacteria and Gammaproteobacteria were affiliated with genera like Roseovarius, Idiomarina and Spiribacter which have previously been found in marine or hypersaline waters. The majority of the phylotypes was most closely related to uncultivated organisms and shared less than 97% identity with their closest match in GenBank, indicating a unique community structure in the Large Aral Sea with mostly novel species or genera.

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China

Spatial distribution (horizonal and vertical) of groundwater microbial communities and the hydrogeochemistry in confined aquifers were studied approximately along the groundwater flow path from coteau to plain in the Nomhon area, Qinghai-Tibet plateau, China. The confined groundwater samples at different depths and locations were collected in three boreholes through a hydrogeological section in this arid and semi-arid area. The phylogenetic analysis of 16S rRNA genes and multivariate statistical analysis were used to elucidate similarities and differences between groundwater microbial communities and hydrogeochemical properties. The integrated isotopic geochemical measurements were applied to estimate the source and recharge characteristics of groundwater. The results showed that groundwater varied from fresh to saline water, and modern water to ancient water following the flowpath. The recharge characteristics of the saline water was distinct with that of fresh water. Cell abundance did not vary greatly along the hydrogeochemical zonality; however, dissimilarities in habitat-based microbial community structures were evident, changing from Betaproteobacteria in the apex of alluvial fan to Gammaproteobacteria and then to Epsilonproteobacteria in the core of the basin (alluvial-lacustrine plain). Rhodoferax, Hydrogenophaga, Pseudomonas, and bacterium isolated from similar habitats unevenly thrived in the spatially distinct fresh water environments, while Sulfurimonas dominanted in the saline water environment. The microbial communities presented likely reflected to the hydrogeochemical similarities and zonalities along groundwater flowpath.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae

There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109^T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109^T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109^T (=JCM 31876^T=DSM 102886^T). In addition, examination of the phylogenetics of strain HL-109^T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).

Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting

The factors that shape microbial community assembly in aquatic ecosystems have been widely studied; yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus, they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea, we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst. Environmental and spatial variation within ponds explain <9% of the community structure, while identity of the pond that samples were taken from explains 50% of community variation. That is, ponds each host distinct assemblages despite similarities in size, environment and position in the landscape, indicating a dominant role for local species sorting. The ponds contain a substantial amount of previously unknown microbial taxa, reflecting the unusual nature of this inland system. Rare marine taxa, possibly dispersed from seawater assemblages via the underground karst connection, are abundant within the inland system, suggesting an important role for regional dispersal within the metacommunities.

Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H₂S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

Bacterial abundance and diversity in pond water supplied with different feeds

The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

Evolution and adaptation of SAR11 and Cyanobium in a saline Tibetan lake

Lake Qinghai is a unique lacustrine ecosystem located on the Tibetan Plateau and exhibits oligotrophic, alkaline, and saline conditions. Previous studies have focused on the community phylogenetic diversity of bacterioplankton in the ecosystem. This study aimed to address the ecotype diversity of bacterioplankton populations in the unique microbial habitat, using metagenomic sequencing and analysis. Phylogenetic analysis revealed two major bacterial populations: SAR11 IIIa (14% of the total) and Cyanobium (14%). Although the two populations shared high 16S rRNA gene sequence identity (> 98% identity) with their closest marine counterparts, they displayed substantial genomic divergence (≤ 80% average amino acid sequence identity). Comparative genomic analysis identified conservation of carbon and energy storage metabolism (biosynthesis of polyphosphate and polyhydroxyalkanoate) gene operons in the SAR11 IIIa and a cyanate (potential nitrogen source in alkaline conditions) transporter gene operon in the Cyanobium. We further identified genetic signature of positive selection acting on an exodeoxyribonuclease gene of the SAR11 IIIa population, which is potentially associated with DNA repair responsive to strong UV radiation on the high altitude mountain. Taken together, our results revealed the ecosystem-specific gene content of the bacterioplankton populations and provided new insights into their adaptations unique to the Tibetan lake.

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

As a better understanding of Beijing surface water ecosystems can provide clues for environmental management and public health, here, we report a study of the bacterial communities of five Beijing surface waters conducted using 454 pyrosequencing of 16S ribosomal RNA (rRNA) genes. We expected to observe a core bacterial community among the surface waters and differences in bacterial community abundance over the different locations of sampling. In this study, we obtained a total of 60,810 trimmed reads from the five samples after the removal of unqualified reads. Bacterial sequences from the five samples were classified into taxonomic classes using the default settings of the mothur platform. Our results provided insight into the bacterial community composition of surface waters and revealed that there was a core microbial community in the microbial populations of surface samples at different geographic locations, with 13 phyla and 40 genera in common. Our findings also revealed the differences in bacterial communities among five surface water samples obtained at different locations.

Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems

Oligosaline lakes in arid regions provide indispensable water resources for humans; however, information on the bacterial community composition (BCC) of this ecosystem is limited. In the present study, we explored seasonal and vertical variations in BCC in Lake Bosten, a unique oligosaline lake (1.2‰ salinity) in arid, northwestern China, using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing. We obtained 544 clones and 98 operational taxonomic units (OTUs) from six clone libraries. The top 10 OTUs represented 59.4% of the entire bacterial community. Betaproteobacteria (22.1%), Gammaproteobacteria (19.9%), Bacteroidetes (18.8%), and Firmicutes (11.4%) dominated in Lake Bosten. Although seasonal variations were recorded in BCC, the vertical changes observed were not significant. Water temperature and salinity were the most important factors shaping the dynamics of BCC. A low degree of overlap was observed in BCC between Lake Bosten and freshwater ecosystems, especially for Betaproteobacteria and Bacteroidetes. An RDP seqmatch analysis showed that 169 sequences (31%) were novel bacterial sequences (<97% similarity to the closest sequences in GenBank), which suggested that specific indigenous bacteria inhabit this oligosaline environment. Our results support bacterial endemicity being more common than previously considered, particularly in oligosaline lakes. An analysis of these communities may reveal how bacteria respond to increases in salinity and nutrients in the early stage of salinization and eutrophication.

Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake

SAR11 clade bacteria are abundant and play a key role in the nutrient cycles of marine and, presumably, inland aquatic environments. We report here the draft genome sequence of a novel species in the SAR11 cluster, reconstructed from a metagenomic data set obtained from a Tibetan lake.

Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22T fell within the class Bacteroidia . Its closest phylogenetic neighbour was the recently described species Draconibacterium orientale , the sole member of the family Draconibacteriaceae , with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family Draconibacteriaceae . The type strain is G22T ( = CICC 10587T = DSM 27063T).

Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics

A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium 'Spiribacter salinus' were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the 'salt-in' strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.