Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier-inhabiting Cryobacterium strains.

The link between guanine-cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (TMGT ) and genomics of 78 Cryobacterium strains to avoid unreliable conclusions resulting from distantly phylogenetic groups. Phylogenomic analysis revealed this taxon had much higher diversification than we knew. Interestingly, these strains showed thermotolerance divergence with phylogenetic cohesion. A significant difference was found between TMGT ≤ 20°C strains and TMGT > 20°C strains in genomic GC content which mainly caused by variation of GC3. TMGT ≤ 20°C strains tended to use synonymous codons ended with A/U, but TMGT > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of TMGT ≤ 20°C strains could provide lower intrinsic DNA flexibility which strongly associated with optimal molecular dynamics, and then guarantee DNA function at lower growth temperatures. This analysis of codon bias revealed close relationships for thermal adaptation, GC content at synonymous sites (≈GC3), intrinsic DNA flexibility and optimal DNA dynamics. Natural selection was main force driving this codon bias; strains with lower TMGT endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

[Hydrogen production from glucose by Acetanaerobacterium elongatum].

Studying the possible factors affecting hydrogen production from glucose by Acetanaerobacterium elongatum, an acetateethanol fermenting anaerobe isolated from sludge of wastewater of a papermill. The results revealed that the maximum hydrogen production could be achieved in PYG liquid at 37 degrees C and initial pH 8.0. The strain produced more hydrogen from glucose and arabiose, with the hydrogen yields of 1.55 mol H2/mol glucose and 1.50 mol H2/mol arabiose, respectively. pH and hydrogen partial pressure were the most severe inhibitors in hydrogen production from glucose, by controlling the broth at neutral pH during the fermentation period could increase hydrogen yield twice, concomitantly glucose consumption for 2.8 times. Hydrogen was another inhibitor for fermentative H2 production, and removing hydrogen by cultivating Acetanaerobacterium elongatum Z7 with a H2-trophic methanogen resulted in higher deduced H2 production for about 4 times. Yeast extract stimulated H2 production by stains Z7. Coculturing A. elongatum Z7 and P. acetatigenes TB107, a proteineous-trophic bacterium, increased the conversion of the glucose and thereby increased the H2 production on peptone. Moreover, acetate when at higher concentration ( > 60 mmol/L) in the medium inhibited the hydrogen production by strain Z7.

[Characterization of hydrogen peroxide production by a novel oral streptococci, S. oligofermentans isolated from human oral cavity].

High level of hydrogen peroxide was produced by S . oligofermentans, a novel oral streptococcus isolated from human oral cavity previously in our laboratory. To characterize the hydrogen peroxide production by S. oligofermentans, hydrogen peroxide yields at different growth phases and from different substrates were assayed. The results turned out that hydrogen peroxide production started at the beginning of logarithmic phase, and reached the maximal yield at the early stationary phase. Peptone and yeast extract could be the main substrates for hydrogen peroxide production. Moreover, lactate, as a fermentative product of glucose, can be another substrate for hydrogen peroxide production. Furthermore three oxidases activities possibly associated with H2O2 production were assayed, and both activities of lactate oxidase and NADH oxidase were detected under aerobic condition, while pyruvate oxidase activity was not detected in the permeabilized cells of S. oligofermentans, implying that S. oligofermentans could mainly rely on the two enzymes activities for H2O2 production.

[A new hydrogen-producing strain and its characterization of hydrogen production].

An anaerobic, thermophilic, hydrogen-producing strain T42 was obtained from a hot spring of South Mountain District, Tibet. Cells are Gram-positive, mobile rod-shaped. Spores were not observed. Temperature range for growth is 32 degrees C to 69 degrees C (optimum temperature, 60 degrees C - 62 degrees C), and pH range for growth is 5.0 to 8.8 (optimum pH, 7.0 - 7.5). The generation time is around 30 min. Organic nitrogen sourc is required for growth. Strain T42 utilizes a wide range of carbohydrates, including starch, dextrin, sucrose, cellobiose, fructose, maltose, ribose, glycogen and galactose. Acetate, ethanol, H2 and CO2 are the end products of glucose fermentation. The (G + C) content of strain T42 is 31.2 mol%. Phylogenetic analysis based on the 16S rDNA sequence similarity indicates that strain T42 is the closest relative to Thermobrachium celere and Caloramator indicus. Biological characteristics and phylogenetic analysis of the 16S rDNA gene indicate the new strain belongs to the genus Thermobrachium. Strain T42 produces H2 from glucose at maximal level when growing at 62 degrees C and initial pH 7.2, the hydrogen yields and maximal hydrogen production rate are 1.06 mol H2/mol glucose and 24.0 mmol H2/gDW/h, respectively. Strain T42 also produced H2 by fermentating from a variety of carbohydrates. 20 mmol/L Magnesium and 2 mmol/L iron increase the hydrogen production content by 20% and 23.3%, respectively, but nickel has no effect on the hydrogen production. In the co-culture of strain T42 and methane-producing strain M. thermautotrophicus Z245, hydrogen pressure is dramatically decreased, meanwhile deduced H2 production and the consumption of glucose are increased markedly by 2.8 fold and 1 fold, and the ratio of acetate/ethanol is enhanced froml to 1.7.

[Partial sequence homology of FtsZ in phylogenetics analysis of lactic acid bacteria].

FtsZ is a structurally conserved protein, which is universal among the prokaryotes. It plays a key role in prokaryote cell division. A partial fragment of the ftsZ gene about 800bp in length was amplified and sequenced and a partial FtsZ protein phylogenetic tree for the lactic acid bacteria was constructed. By comparing the FtsZ phylogenetic tree with the 16S rDNA tree, it was shown that the two trees were similar in topology. Both trees revealed that Pediococcus spp. were closely related with L. casei group of Lactobacillus spp. , but less related with other lactic acid cocci such as Enterococcus and Streptococcus. The results also showed that the discriminative power of FtsZ was higher than that of 16S rDNA for either inter-species or inter-genus and could be a very useful tool in species identification of lactic acid bacteria.

[Development of an identification method for Streptococcus oligofermentans: a new species of oral streptococci with molecular markers].

OBJECTIVE: To establish a quick and reliable method to identify Streptococcus oligofermentans, a new species of oral streptococci. METHODS: With two-step PCR, a pair of the 16S rDNA-specific primers of Streptococcus oligofermentans and a pair of primers of lactate oxidase gene (lox) were used to amplify the gene fragments from the genomic DNAs of 11 strains consisting of 9 species of the pure culture of oral streptococci. Pooled plaque samples from 9 caries-free volunteers were cultured on a selective medium of MSA with erythromycin and tentative strains of Streptococcus oligofermentans were isolated. The isolates were further identified by the two-step PCR and finally confirmed by 16S rDNA sequence analysis. RESULTS: With the two-step PCR, the two gene fragments were only amplified from the three identified strains of Streptococcus oligofermentans, but not the rest of 8 strains of oral streptococci. Isolates from the dental plaque of caries-free volunteers were identified as Streptococcus oligofermentans by PCR and then further confirmed by 16S rDNA sequence homology analysis. CONCLUSIONS: Streptococcus oligofermentans could be identified by the two-step PCR approach with the specific 16S rDNA primers and lactate oxidase gene primers.

Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier.

A novel psychrotolerant, Gram-positive, yellow-pigmented, aerobic bacterium, strain 0549(T), was isolated from the China No. 1 glacier. The cells of the isolate were catalase-positive, motile, irregular rods. The diamino acid content of the cell-wall peptidoglycan was determined to be 2,4-diaminobutyric acid. Strain 0549(T) was able to grow at 4-27 degrees C, with optimum growth occurring at 20-22 degrees C. The major fatty acids were anteiso-C(15 : 0), anteiso-C(15 : 1), iso-C(16 : 0) and anteiso-C(17 : 0). The genomic DNA G+C content was 67 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 0549(T) belonged to the genus Cryobacterium and exhibited 96.5 % similarity to Cryobacterium psychrophilum JCM 1463(T). On the basis of the phenotypic, chemotaxonomic and phylogenetic properties and the DNA-DNA relatedness data, strain 0549(T) represents a novel species of the genus Cryobacterium, for which the name Cryobacterium psychrotolerans is proposed. The type strain is 0549(T) (=CGMCC 1.5382(T)=JCM 13925(T)).

Flavobacterium glaciei sp. nov., a novel psychrophilic bacterium isolated from the China No.1 glacier.

A novel psychrophilic, yellow-pigmented and obligate aerobic bacterium, strain 0499(T), was isolated from the China No.1 glacier. Strain 0499(T) displayed the common phenotypic and chemotaxonomic features of the genus Flavobacterium, containing menaquinone-6 (MK-6) as the major quinone and C(15 : 0), iso-C(15 : 0), C(17 : 1)omega6c and summed feature 3 (C(16 : 1)omega7c/iso-C(15 : 0) 2-OH) as the major fatty acids. Optimal growth occurred at 21 degrees C. The genomic DNA G+C content was 36.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 0499(T) was related to members of the genus Flavobacterium, sharing the highest sequence similarities with Flavobacterium succinicans (97.9 %), Flavobacterium granuli (97.4 %) and Flavobacterium hydatis (97.2 %). On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, a novel species Flavobacterium glaciei is proposed with strain 0499(T) (=CGMCC 1.5380(T)=JCM 13953(T)) as the type strain.

Glaciecola psychrophila sp. nov., a novel psychrophilic bacterium isolated from the Arctic.

A novel bacterial strain, designated 170(T), was collected from high latitude Arctic locations (77 degrees 30' N to approximately 81 degrees 12' N), including the Canadian Basin and Greenland Sea. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 170(T) was related to members of the genus Glaciecola and had the highest 16S rRNA gene sequence similarity to Glaciecola mesophila. Cells were Gram-negative, psychrophilic, motile rods. The temperature range for growth was 4-15 degrees C, with optimum growth at 12 degrees C and at approximately pH 6.0-9.0. Strain 170(T) contained C(16 : 1)omega7c, C(16 : 0), C(12 : 1) 3-OH and C(18 : 1)omega7c as major fatty acids. The genomic DNA G+C content was 42.9 mol%. On the basis of phenotypic characterization, phylogenetic analysis and DNA-DNA relatedness data, strain 170(T) is considered to represent a novel species of the genus Glaciecola, for which the name Glaciecola psychrophila is proposed. The type strain is 170(T) (=CGMCC 1.6130(T)=JCM 13954(T)).