Brian E. Jones

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60–65 °C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72 °C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, ‘Deinococcus-Thermus’, Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.

We used cultivation-independent methods to investigate the prokaryotic biogeography of the water column in six salt lakes in Inner Mongolia, China, and a salt lake in Argentina. These lakes had different salt compositions and pH values and were at variable geographic distances, on both local and intercontinental scales, which allowed us to explore the microbial community composition within the context of both contemporary environmental conditions and geographic distance. Fourteen 16S rRNA gene clone libraries were constructed, and over 200 16S rRNA gene sequences were obtained. These sequences were used to construct biotic similarity matrices, which were used in combination with environmental similarity matrices and a distance matrix in the Mantel test to discover which factors significantly influenced biotic similarity. We showed that archaeal biogeography was influenced by contemporary environmental factors alone (Na ⁺ , CO ₃ ²⁻ , and HCO ₃ ⁻ ion concentrations; pH; and temperature). Bacterial biogeography was influenced both by contemporary environmental factors (Na ⁺ , Mg ²⁺ , and HCO ₃ ⁻ ion concentrations and pH) and by geographic distance.

A rapid and effective method for direct detection, selection and testing of microorganisms able to produce both cell-bound and extracellular true lipases is described. The method is based on...

A Gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain BG-1T, was isolated from a salt lake, Lake Bagaejinnor, in Inner Mongolia, China. Strain BG-1T was able to grow at 25–55 °C, required at least 2.5 M NaCl for growth (with an optimum at 3.4 M NaCl) and grew at pH 6.0–9.0 (with an optimum at pH 7.5). Hypotonic treatment with less than 2.0 M NaCl caused cell lysis. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence positioned the isolate within the genus Halorubrum in the family Halobacteriaceae. Strain BG-1T was most closely related to Halorubrum aidingense 31-hongT (98.8 % sequence similarity), Halorubrum saccharovorum NCIMB 2081T (98.6 %), Halorubrum lacusprofundi ACAM 34T (98.6 %) and Halorubrum lipolyticum 9-3T (98.4 %). However, values for DNA–DNA hybridization between strain BG-1T and the most closely related members of the genus Halorubrum were below 40 %. Analysis of the polar lipids of strain BG-1T revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid found in neutrophilic species of the genus Halorubrum. The G+C content of the genomic DNA was 69.4 mol% (T m). Comparison of the phenotypic characteristics of the strain with those of Halorubrum species supported the conclusion that BG-1T represents a novel species within this genus, for which the name Halorubrum kocurii sp. nov. is proposed. The type strain is BG-1T (=CECT 7322T =CGMCC 1.7018T =JCM 14978T).

A Gram-positive, moderately halophilic bacterium, designated strain EN8dT, was isolated from sediment from Lake Erliannor in the Inner Mongolia Autonomous Region, China. Cells were facultatively anaerobic, rod-shaped and motile and did not display endospore formation. Isolate EN8dT grew in a complex medium supplemented with 0–20 % (w/v) marine salts (optimally at 5–7.5 %, w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain EN8dT was a member of the family Bacillaceae, belonging to a cluster with Thalassobacillus (96.3 % gene sequence similarity) and Halobacillus (95.0–96.0 %), albeit emerging as an independent lineage from members of these two genera. Strain EN8dT contained cell-wall peptidoglycan based on meso-diaminopimelic acid and possessed MK-7 as the major respiratory isoprenoid quinone. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The DNA G+C content was 47.5 mol%. Strain EN8dT could be clearly differentiated from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore strain EN8dT is considered to represent a novel genus and species, for which the name Sediminibacillus halophilus gen. nov., sp. nov. is proposed. The type strain of Sediminibacillus halophilus is EN8dT (=CCM 7364T =CECT 7148T =CGMCC 1.6199T =DSM 18088T).

A novel moderately halophilic, non-motile, rod-shaped bacterium was isolated from a saline lake, Lake Shangmatala, in the Inner Mongolia Autonomous Region, China. This bacterium, designated SH4sT, was strictly aerobic, catalase-positive and oxidase-negative. It grew at salinities of 3–20 % (w/v) NaCl, with an optimum at 10 % (w/v) NaCl. The cell-wall peptidoglycan was of the A4β type, based on l-Orn–d-Asp, and the major quinone was a menaquinone with seven isoprene units (MK-7). The major fatty acids were iso-C16 : 0 and iso-C15 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a glycolipid and four different unidentified phospholipids. The DNA G+C content was 45.9 mol%. In a maximum-parsimony phylogenetic tree based on 16S rRNA gene sequences, strain SH4sT was found to belong to the family Bacillaceae and to be most closely related to members of the genera Filobacillus (95.9 % sequence similarity), Piscibacillus (95.7 %) and Tenuibacillus (95.4 %). DNA–DNA hybridization experiments revealed 10 % relatedness (12 %, reciprocally) between strain SH4sT and Filobacillus milosensis DSM 13259T, the sole species of the genus. All of these data show that strain SH4sT represents a novel genus and species in the family Bacillaceae, for which the name Aquisalibacillus elongatus gen. nov., sp. nov. is proposed. The type strain of Aquisalibacillus elongatus is SH4sT (=CCM 7366T =CECT 7149T =DSM 18090T).

A novel halophilic archaeon, strain CGSA15T, was isolated from water of Lake Chagannor in China. The strain grew optimally at 33–37 °C, pH 9.5–10.0 and 4.0–4.3 M NaCl. The major polar lipids were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. The genomic DNA G+C content of strain CGSA15T was 60.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CGSA15T was a member of the genus Halorubrum and was related most closely to Halorubrum alkaliphilum AS 1.3528T (96.1 % similarity) and Halorubrum tibetense AS 1.3239T (96.9 %). Levels of DNA–DNA relatedness between strain CGSA15T and Hrr. alkaliphilum AS 1.3528T and Hrr. tibetense AS 1.3239T were 36.7 and 28.9 %, respectively. According to the phenotypic and genotypic data presented, strain CGSA15T is considered to represent a novel species of the genus Halorubrum, for which the name Halorubrum luteum sp. nov. is proposed. The type strain is CGSA15T (=CGMCC 1.6783T =CECT 7303T).

The Nanoarchaeota, proposed as the fourth sub-division of the Archaea in 2002, are known from a single isolate, Nanoarchaeum equitans, which exists in a symbiotic association with the hyperthermophilic Crenarchaeote, Ignicoccus. N. equitans fails to amplify with standard archaeal 16S PCR primers and can only be amplified using specifically designed primers. We have designed a new set of universal archaeal primers that amplify the 16S rRNA gene of all four archaeal sub-divisions, and present two new sets of Nanoarchaeota-specific primers based on all known nanoarchaeal 16S rRNA gene sequences. These primers can be used to detect N. equitans and have generated nanoarchaeal amplicons from community DNA extracted from Chinese, New Zealand, Chilean and Tibetan hydrothermal sites. Sequence analysis indicates that these environments harbour novel nanoarchaeal phylotypes, which, however, do not cluster into clear phylogeographical clades. Mesophilic hypersaline environments from Inner Mongolia and South Africa were analysed using the nanoarchaeal-specific primers and found to contain a number of nanoarchaeal phylotypes. These results suggest that nanoarchaeotes are not strictly hyperthermophilic organisms, are not restricted to hyperthermophilic hosts and may be found in a large range of environmental conditions.

Background: We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus. Results: Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content of ~65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained. Conclusion: The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system.