The green bacterial biosynthesis of lead sulfide nanocrystallites by l-cysteine-desulfurizing bac... more The green bacterial biosynthesis of lead sulfide nanocrystallites by l-cysteine-desulfurizing bacterium Lysinibacillus sphaericus SH72 was demonstrated in this work. Nanocrystals formed by this bacterial method were characterized using the mineralogical and morphological approaches. The results revealed that the microbially synthesized PbS nanocrystals assume a cubic structure, and are often aggregated as spheroids of about 105 nm in size. These spheroids are composed of numerous nanoparticles with diameter 5–10 nm. Surface characterization of the bacterial nanoparticles with FTIR spectroscopy shows that the l-cysteine coats the surface of PbS nanoparticle as a stabilizing ligand. The optical features of the PbS nanocrystallites were assessed by UV–Vis spectroscopy and PL spectroscopy. The maximum absorption wavelength of the bacterial PbS particles occurs at 240 nm, and the photoluminescence emission band ranges from 375 to 550 nm. The band gap energy is calculated to be 4.36 eV, c...
International Biodeterioration & Biodegradation, 2021
Biotransformation of amorphous calcium carbonate into calcite and other inorganic calcium mineral... more Biotransformation of amorphous calcium carbonate into calcite and other inorganic calcium minerals is a worldwide phenomenon in the bacterial kingdom. In this study, it showed that calcite (CaCO3) could be transformed into an organic mineral earlandite [Ca3(C6H5O7)2·4H2O], through the dissolution of calcite and subsequent crystallization by the fungus Trichoderma asperellum BDH65. Observations by light microscopy showed that the fungal induced crystal particles were deposited as irregularly granular accumulations of micro globular particles. Scanning and transmission electron microscopy revealed that each micro globular particle consists of numerous needle-like crystals with domed end assembling radially with their ends pointing outside from its centers. This is clearly different from the shapes of microsheets formed by the chemical method. The mineral phase of the fungal catalyzed crystals is identified as earlandite, which is chemically identical to calcium citrate tetrahydrate. S...
Inspections of bridge substructures in Texas identified surface deterioration of reinforced concr... more Inspections of bridge substructures in Texas identified surface deterioration of reinforced concrete columns on bridges continuously exposed to water. Initial hypothesis was that the surface deterioration was a result of the acidity of the water in which the columns were exposed. However, evaluation of the water acidity indicated that the surrounding waters were only very slightly acidic and near neutral. Discussions between engineers from the Texas Department of Transportation (TxDOT) and researchers at Texas A&M University and the Texas Transportation Institute (TTI) hypothesized that the damage could be a result of microbial attack. Microbial attack is often identified as an acid attack because some microbes can produce sulfuric acid. This research investigated whether microbes were present at areas on the bridge that were exhibiting attack, determined if there was a correlation between degree of damage and number of microbes present, determined if these microbes were acid produc...
This study reports that candicidin-like secondary metabolites produced by microbial cells in natu... more This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the production of candicidin isomers, suggesting that gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.
In this study, we investigated fungal diversity of six Mid-Oceanic Ridge sediment samples collect... more In this study, we investigated fungal diversity of six Mid-Oceanic Ridge sediment samples collected in the East Pacific and the South Indian Oceans by culture-dependent as well as culture-independent approaches. A total of 97 fungal isolates were cultured, belonging to 7 genera and 10 species, including Penicillium (2 species), Rhodotorula, Meyerozyma, Ophiocordyceps, Vishniacozyma, Aspergillus (3 species) and Phoma. Forty-six operational taxonomic units (OTUs) were identified from 933 clones selected from 12 clone libraries based on the internal transcribed spacers including 5.8S (ITS) and 18S rDNA. Two cultured fungi and 9 OTUs from the clone libraries showed similarities less than 97% with the existing sequences in GenBank, suggesting possible new fungal taxa. Most of the fungi belonged to the Ascomycota, to a lesser extent the Basidiomycota. Five fungal genera including Aspergillus, Rhodotorula, Ophiocordyceps, Phoma and Penicillium were recovered by both culture-dependent and c...
A Gram-positive, rod-shaped, endospore-forming bacterium with multiple flagella, designated XXST-... more A Gram-positive, rod-shaped, endospore-forming bacterium with multiple flagella, designated XXST-01T, was isolated from deep-sea sediment of Yap Trench with a depth of 6300 m. Activity of oxidase and catalase were found to be positive. Growth was observed at 10–45 °C (optimum 37 °C), pH 6–9 (optimum 7.0), 0–6% NaCl (optimum 0–0.5%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XXST-01T belonged to the genus Bacillus. Strain XXST-01T was closely related to Bacillus kyonggiensis NB22T (98.4%), Bacillus siralis 171544T (97.53%), Bacillus massiliosenegalensis JC6T (97.30%), Bacillus oceanisediminis H2T (97.27%), Bacillus mesophilum IITR-54T (97.12%) and Bacillus depressus BZ1T (97.09%). The ANI and the DNA–DNA hybridization estimate values between strain XXST-01T and closely related type strains were 70.91–90.15% and 19.80–40.50%, respectively. The principal fatty acids were iso-C15:0, anteiso-C15:0, iso-C16:0, and iso-C14:0. The G+C content of the chromosomal DNA was 38.2 mol%. The respiratory quinone was determined to be MK-7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and four unidentified aminophospholipids. The combined genotypic and phenotypic data show that strain XXST-01T represents a novel species within the genus Bacillus, for which the name Bacillus yapensis sp. nov. is proposed, with the type strain XXST-01T (=MCCC 1A14143T = JCM 33181T).
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, n... more 16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4–V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3–V4 regions) and A751f/AU1204r (V5–V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
International Journal of Systematic and Evolutionary Microbiology
Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Y... more Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Yap Trench located in the Pacific Ocean. Cells of the strains were Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YLB-02T belonged to the genus Oceanobacillus and strain YLB-04T belonged to the genus Bacillus. Strain YLB-02T showed similarities of 96.9 % with Ornithinibacillus contaminans CCUG 53201T, 96.3 % with Oceanobacillus profundus CL-MP28T, 96.1 % with Oceanobacillus halophilus J8BT and 95.7 % with Oceanobacillus bengalensis Ma-21T. Strain YLB-04T showed the highest sequence similarity of 97.4 % with Bacillus notoginsengisoli SYP-B691T. The average nucleotide identity (ANI) and the DNA-DNA hybridisation (DDH) estimate values for strain YLB-02T and YLB-04T with their related type strains were below the respective threshold for species differentiation. The G+C contents of strains YLB-02T and YLB-04T were 37.3 and 45.4 mol%. The predominant (>10 %) cellular fatty acids of strain YLB-02T were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 1ω7c alcohol, and those of strain YLB-04T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 0. Their predominant ubiquinone was MK-7. The cell-wall peptidoglycan of strain YLB-02T contained glutamic acid, alanine, aspartic acid, lysine and ornithine, but no meso-diaminopimelic acid, while strain YLB-04T contained meso-diaminopimelic acid, glutamic acid, alanine, aspartic acid, lysine and ornithine. In addition to diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), the polar lipids of strain YLB-02T also consisted of an unidentified glycolipid (GL), two unidentified polar lipids (L1 and L2) and two unidentified phospholipids (PL1 and PL2), and those of strain YLB-04T also consisted of phosphatidylethanolamine (PE) and an unidentified phospholipid (PL). Based on phenotypic, genotypic and chemotaxonomic characteristics, two novel species are proposed, Oceanobacillus piezotolerans sp. nov. with YLB-02T (=MCCC 1A12699T=JCM 32870T) and Bacillus piezotolerans sp. nov. with YLB-04T (=MCCC 1A12711T=JCM 32872T) as the type strains.
A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrich... more A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15–50°C (optimum 37°C), pH 5–10.5 (optimum 7), 0–5% NaCl (optimum 1%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03T was a member of the genus Lysinibacillus. Strain YLB-03T was closely related to Lysinibacillus sinduriensis BLB-1T and Lysinibacillus chungkukjangi 2RL3-2T (98.4%), Lysinibacillus halotolerans LAM-612T (98.0%), Lysinibacillus telephonicus KT735049T (97.5%), Lysinibacillus endophyticus C9T (97.5%), Lysinibacillus composti NCCP-36T and Lysinibacillus massiliensis 4400831T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03T and closely related type strains were 73.7–76.3% and 34.7–38.7%, respectively. The principal fatty acids were anteiso-C15:0 and iso-C15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03T (= MCCC 1A12698T = JCM 32871T).
International Journal of Systematic and Evolutionary Microbiology
A Gram-stain-negative, aerobic and rod-shaped strain, YLB-05T, was isolated from a sample of deep... more A Gram-stain-negative, aerobic and rod-shaped strain, YLB-05T, was isolated from a sample of deep-sea sediment (depth, 6796 m) from the Yap Trench. It was motile, oxidase-positive and catalase-positive. Growth was observed at salinities of 1-12 % (NaCl, w/v), with the optimum at 5 %. The strain was able to thrive at low (4 °C) temperatures, with the optimum at 37 °C, but did not grow at 50 °C. The optimum pressure for growth was 0.1 MPa with tolerance up to 50 MPa. The 16S rRNA gene sequencing analysis showed that YLB-05T was most closely related to Marinomonas communis LMG 2864T (97.8 %). Phylogenetic analysis placed strain YLB-05T within the genus Marinomonas. The average nucleotide identity and the DNA-DNA hybridization values between strain YLB-05T and closely related type strains were below the respective thresholds for species differentiation. The principal fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1ω7c/C16 : 1 ω6c). The DNA G+C content was 45.7 mol%. The respiratory quinone was determined to be Q-8. The polar lipids were an unidentified phospholipid and an unidentified aminophospholipid. The combined genotypic and phenotypic data showed that strain YLB-05T represents a novel species within the genus Marinomonas, for which the name Marinomonaspiezotolerans sp. nov. is proposed, with the type strain YLB-05T (=MCCC 1A12712T=KCTC 62812T).
Wetlands are an important methane (CH) emission source. CHis mainly produced during the biogeoche... more Wetlands are an important methane (CH) emission source. CHis mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are ...
Extremophiles : life under extreme conditions, Jan 10, 2018
Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost c... more Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition,...
Accompanying the thawing permafrost expected to result from the climate change, microbial decompo... more Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU...
The green bacterial biosynthesis of lead sulfide nanocrystallites by l-cysteine-desulfurizing bac... more The green bacterial biosynthesis of lead sulfide nanocrystallites by l-cysteine-desulfurizing bacterium Lysinibacillus sphaericus SH72 was demonstrated in this work. Nanocrystals formed by this bacterial method were characterized using the mineralogical and morphological approaches. The results revealed that the microbially synthesized PbS nanocrystals assume a cubic structure, and are often aggregated as spheroids of about 105 nm in size. These spheroids are composed of numerous nanoparticles with diameter 5–10 nm. Surface characterization of the bacterial nanoparticles with FTIR spectroscopy shows that the l-cysteine coats the surface of PbS nanoparticle as a stabilizing ligand. The optical features of the PbS nanocrystallites were assessed by UV–Vis spectroscopy and PL spectroscopy. The maximum absorption wavelength of the bacterial PbS particles occurs at 240 nm, and the photoluminescence emission band ranges from 375 to 550 nm. The band gap energy is calculated to be 4.36 eV, c...
International Biodeterioration & Biodegradation, 2021
Biotransformation of amorphous calcium carbonate into calcite and other inorganic calcium mineral... more Biotransformation of amorphous calcium carbonate into calcite and other inorganic calcium minerals is a worldwide phenomenon in the bacterial kingdom. In this study, it showed that calcite (CaCO3) could be transformed into an organic mineral earlandite [Ca3(C6H5O7)2·4H2O], through the dissolution of calcite and subsequent crystallization by the fungus Trichoderma asperellum BDH65. Observations by light microscopy showed that the fungal induced crystal particles were deposited as irregularly granular accumulations of micro globular particles. Scanning and transmission electron microscopy revealed that each micro globular particle consists of numerous needle-like crystals with domed end assembling radially with their ends pointing outside from its centers. This is clearly different from the shapes of microsheets formed by the chemical method. The mineral phase of the fungal catalyzed crystals is identified as earlandite, which is chemically identical to calcium citrate tetrahydrate. S...
Inspections of bridge substructures in Texas identified surface deterioration of reinforced concr... more Inspections of bridge substructures in Texas identified surface deterioration of reinforced concrete columns on bridges continuously exposed to water. Initial hypothesis was that the surface deterioration was a result of the acidity of the water in which the columns were exposed. However, evaluation of the water acidity indicated that the surrounding waters were only very slightly acidic and near neutral. Discussions between engineers from the Texas Department of Transportation (TxDOT) and researchers at Texas A&M University and the Texas Transportation Institute (TTI) hypothesized that the damage could be a result of microbial attack. Microbial attack is often identified as an acid attack because some microbes can produce sulfuric acid. This research investigated whether microbes were present at areas on the bridge that were exhibiting attack, determined if there was a correlation between degree of damage and number of microbes present, determined if these microbes were acid produc...
This study reports that candicidin-like secondary metabolites produced by microbial cells in natu... more This study reports that candicidin-like secondary metabolites produced by microbial cells in natural soil environments can effectively control soilborne fungal diseases, revealing a novel mechanism of microbial biocontrol agents. We demonstrated that the main antifungal activity and biocontrol activity of Streptomyces albidoflavus strain W68 are attributable to the production of candicidin isomers, suggesting that gene clusters for candicidin-like compound biosynthesis might be used as molecular markers to screen and breed microbial strains for biocontrol agent development.
In this study, we investigated fungal diversity of six Mid-Oceanic Ridge sediment samples collect... more In this study, we investigated fungal diversity of six Mid-Oceanic Ridge sediment samples collected in the East Pacific and the South Indian Oceans by culture-dependent as well as culture-independent approaches. A total of 97 fungal isolates were cultured, belonging to 7 genera and 10 species, including Penicillium (2 species), Rhodotorula, Meyerozyma, Ophiocordyceps, Vishniacozyma, Aspergillus (3 species) and Phoma. Forty-six operational taxonomic units (OTUs) were identified from 933 clones selected from 12 clone libraries based on the internal transcribed spacers including 5.8S (ITS) and 18S rDNA. Two cultured fungi and 9 OTUs from the clone libraries showed similarities less than 97% with the existing sequences in GenBank, suggesting possible new fungal taxa. Most of the fungi belonged to the Ascomycota, to a lesser extent the Basidiomycota. Five fungal genera including Aspergillus, Rhodotorula, Ophiocordyceps, Phoma and Penicillium were recovered by both culture-dependent and c...
A Gram-positive, rod-shaped, endospore-forming bacterium with multiple flagella, designated XXST-... more A Gram-positive, rod-shaped, endospore-forming bacterium with multiple flagella, designated XXST-01T, was isolated from deep-sea sediment of Yap Trench with a depth of 6300 m. Activity of oxidase and catalase were found to be positive. Growth was observed at 10–45 °C (optimum 37 °C), pH 6–9 (optimum 7.0), 0–6% NaCl (optimum 0–0.5%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XXST-01T belonged to the genus Bacillus. Strain XXST-01T was closely related to Bacillus kyonggiensis NB22T (98.4%), Bacillus siralis 171544T (97.53%), Bacillus massiliosenegalensis JC6T (97.30%), Bacillus oceanisediminis H2T (97.27%), Bacillus mesophilum IITR-54T (97.12%) and Bacillus depressus BZ1T (97.09%). The ANI and the DNA–DNA hybridization estimate values between strain XXST-01T and closely related type strains were 70.91–90.15% and 19.80–40.50%, respectively. The principal fatty acids were iso-C15:0, anteiso-C15:0, iso-C16:0, and iso-C14:0. The G+C content of the chromosomal DNA was 38.2 mol%. The respiratory quinone was determined to be MK-7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and four unidentified aminophospholipids. The combined genotypic and phenotypic data show that strain XXST-01T represents a novel species within the genus Bacillus, for which the name Bacillus yapensis sp. nov. is proposed, with the type strain XXST-01T (=MCCC 1A14143T = JCM 33181T).
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, n... more 16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4–V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3–V4 regions) and A751f/AU1204r (V5–V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
International Journal of Systematic and Evolutionary Microbiology
Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Y... more Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Yap Trench located in the Pacific Ocean. Cells of the strains were Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YLB-02T belonged to the genus Oceanobacillus and strain YLB-04T belonged to the genus Bacillus. Strain YLB-02T showed similarities of 96.9 % with Ornithinibacillus contaminans CCUG 53201T, 96.3 % with Oceanobacillus profundus CL-MP28T, 96.1 % with Oceanobacillus halophilus J8BT and 95.7 % with Oceanobacillus bengalensis Ma-21T. Strain YLB-04T showed the highest sequence similarity of 97.4 % with Bacillus notoginsengisoli SYP-B691T. The average nucleotide identity (ANI) and the DNA-DNA hybridisation (DDH) estimate values for strain YLB-02T and YLB-04T with their related type strains were below the respective threshold for species differentiation. The G+C contents of strains YLB-02T and YLB-04T were 37.3 and 45.4 mol%. The predominant (>10 %) cellular fatty acids of strain YLB-02T were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 1ω7c alcohol, and those of strain YLB-04T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 0. Their predominant ubiquinone was MK-7. The cell-wall peptidoglycan of strain YLB-02T contained glutamic acid, alanine, aspartic acid, lysine and ornithine, but no meso-diaminopimelic acid, while strain YLB-04T contained meso-diaminopimelic acid, glutamic acid, alanine, aspartic acid, lysine and ornithine. In addition to diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), the polar lipids of strain YLB-02T also consisted of an unidentified glycolipid (GL), two unidentified polar lipids (L1 and L2) and two unidentified phospholipids (PL1 and PL2), and those of strain YLB-04T also consisted of phosphatidylethanolamine (PE) and an unidentified phospholipid (PL). Based on phenotypic, genotypic and chemotaxonomic characteristics, two novel species are proposed, Oceanobacillus piezotolerans sp. nov. with YLB-02T (=MCCC 1A12699T=JCM 32870T) and Bacillus piezotolerans sp. nov. with YLB-04T (=MCCC 1A12711T=JCM 32872T) as the type strains.
A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrich... more A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated YLB-03T, with peritrichous flagella was isolated from deep-sea sediment of the Yap Trench at a depth of 4435 m. The bacterium was found to be catalase-positive but oxidase-negative. Growth of this bacterium was observed at 15–50°C (optimum 37°C), pH 5–10.5 (optimum 7), 0–5% NaCl (optimum 1%, w/v) and 0.1–50 MPa (optimum 0.1 MPa). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YLB-03T was a member of the genus Lysinibacillus. Strain YLB-03T was closely related to Lysinibacillus sinduriensis BLB-1T and Lysinibacillus chungkukjangi 2RL3-2T (98.4%), Lysinibacillus halotolerans LAM-612T (98.0%), Lysinibacillus telephonicus KT735049T (97.5%), Lysinibacillus endophyticus C9T (97.5%), Lysinibacillus composti NCCP-36T and Lysinibacillus massiliensis 4400831T (97.3%). The ANI and the GGDC DNA-DNA hybridization estimate values between strain YLB-03T and closely related type strains were 73.7–76.3% and 34.7–38.7%, respectively. The principal fatty acids were anteiso-C15:0 and iso-C15:0. The G+C content of the chromosomal DNA was 39.6 mol%. The respiratory quinone was determined to be MK-7. The diagnostic amino acids in the cell wall peptidoglycan contained Lys-Asp (type A4α) and the cell-wall sugars were glucose and xylose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The combined genotypic and phenotypic data showed that strain YLB-03T represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus yapensis sp. nov. is proposed, with the type strain YLB-03T (= MCCC 1A12698T = JCM 32871T).
International Journal of Systematic and Evolutionary Microbiology
A Gram-stain-negative, aerobic and rod-shaped strain, YLB-05T, was isolated from a sample of deep... more A Gram-stain-negative, aerobic and rod-shaped strain, YLB-05T, was isolated from a sample of deep-sea sediment (depth, 6796 m) from the Yap Trench. It was motile, oxidase-positive and catalase-positive. Growth was observed at salinities of 1-12 % (NaCl, w/v), with the optimum at 5 %. The strain was able to thrive at low (4 °C) temperatures, with the optimum at 37 °C, but did not grow at 50 °C. The optimum pressure for growth was 0.1 MPa with tolerance up to 50 MPa. The 16S rRNA gene sequencing analysis showed that YLB-05T was most closely related to Marinomonas communis LMG 2864T (97.8 %). Phylogenetic analysis placed strain YLB-05T within the genus Marinomonas. The average nucleotide identity and the DNA-DNA hybridization values between strain YLB-05T and closely related type strains were below the respective thresholds for species differentiation. The principal fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1ω7c/C16 : 1 ω6c). The DNA G+C content was 45.7 mol%. The respiratory quinone was determined to be Q-8. The polar lipids were an unidentified phospholipid and an unidentified aminophospholipid. The combined genotypic and phenotypic data showed that strain YLB-05T represents a novel species within the genus Marinomonas, for which the name Marinomonaspiezotolerans sp. nov. is proposed, with the type strain YLB-05T (=MCCC 1A12712T=KCTC 62812T).
Wetlands are an important methane (CH) emission source. CHis mainly produced during the biogeoche... more Wetlands are an important methane (CH) emission source. CHis mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are ...
Extremophiles : life under extreme conditions, Jan 10, 2018
Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost c... more Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition,...
Accompanying the thawing permafrost expected to result from the climate change, microbial decompo... more Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by Crenarchaeota and Euryarchaeota. The active layer contained a proportion of Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis. OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively, were widely distributed in all sediment layers. However, OTU...
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Papers by Shiping Wei