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1.
Nitrincola iocasae sp. nov., a bacterium isolated from sediment collected at a cold seep field in the South China Sea.
Zhang, H, Wang, H, Chen, H, Sun, Q, Zhong, Z, Wang, M, Cao, L, Lian, C, Zhou, L, Li, C
International journal of systematic and evolutionary microbiology. 2020;(9):4897-4902
Abstract
A novel bacterium, designated strain KXZD1103T, was isolated from sediment collected at a cold seep field of the Formosa Ridge in the South China Sea. Cells were Gram-stain-negative, facultatively anaerobic, motile, oxidase- and catalase-positive, and grew optimally at 28 °C, pH 6.0-pH 7.0 and in the presence of 1-3 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 0. The major respiratory ubiquinone was Q-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Analysis of 16S rRNA gene sequences revealed that strain KXZD1103T grouped with members of the genus Nitrincola, with Nitrincola lacisaponensis 4CAT (98.1 % sequence similarity) and Nitrincola schmidtii R4-8T (97.7 %) as its closest neighbours. Genome sequencing revealed a genome size of 4.17 Mb and a DNA G+C content of 50.1 %. Genomic average nucleotide identity values for strain KXZD1103T with the type strains within the genus Nitrincola ranged from 71.0 to 75.7 %, while the in silico DNA-DNA hybridization values for strain KXZD1103T with these strains ranged from 16.1 to 21.6 %. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, strain KXZD1103T is considered to represent a novel species of the genus Nitrincola, for which the name Nitrincola iocasae sp. nov. is proposed. The type strain is KXZD1103T (=KCTC 72678T=MCCC 1K04283T).
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2.
Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018.
Camacho Pozo, MI, Wieme, AD, Pérez, SR, Llauradó Maury, G, Snauwaert, C, Lescaylle Veranes, Y, Peña Zamora, L, Schumann, P, Vandamme, P
International journal of systematic and evolutionary microbiology. 2020;(12):6172-6179
Abstract
An actinomycete, strain D1T, was isolated from a freshwater sediment sample collected from the San Pablo river in the La Risueña community, Santiago de Cuba province, Cuba. The strain was identified as a member of the genus Nocardiopsis by means of a polyphasic taxonomic study. It produced a light yellow non-fragmented substrate mycelium, a white well-developed aerial mycelium and straight to flexuous hyphae. No specific spore chains were observed. Strain D1T contained meso-diaminopimelic acid, no diagnostic sugars, and MK-10(H2), MK-10(H4), MK-10 and MK-10(H6) as predominant menaquinones, but not phosphatidylcholine as diagnostic polar lipid of the genus Nocardiopsis. The predominant fatty acids were iso-C16 : 0, 10-methyl-C18 : 0 and anteiso-C17 : 0. Strain D1T showed the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis synnematoformans DSM 44143T (99.8 %), Nocardiopsis dassonvillei subsp. albirubida NBRC 13392T (99.8 %) and Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T (99.6 %). A genomic OrthoANIu value between D1T and N. dassonvillei subsp. dassonvillei DSM 43111T of 97.63 % and a dDDH value of 78.9 % indicated that strain D1T should be classified in N. dassonvillei. However, phenotypic characteristics distinguished strain D1T from its nearest neighbour taxon. On basis of these results we propose to classify strain D1T (=LMG 30468T=CECT 30033T) as a representative of a novel subspecies of the genus Nocardiopsis, for which the name Nocardiopsis dassonvillei subsp. crassaminis subsp. nov. is proposed. In addition, the genomic distance between N. dassonvillei subsp. albirubida NBRC 13392T and N. dassonvillei subsp. dassonvillei DSM 43111T as determined through OrthoANIu (93.64 %) and dDDH (53.40 %), along with considerable phenotypic and chemotaxonomic differences reported in earlier studies, indicated that the classification of this taxon as Nocardiopsis alborubida Grund and Kroppenstedt 1990 is to be preferred over its classification as N. dassonvillei subsp. albirubida Evtushenko et al. 2000.
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3.
Sub-seafloor biogeochemical processes and microbial life in the Baltic Sea.
Jørgensen, BB, Andrén, T, Marshall, IPG
Environmental microbiology. 2020;(5):1688-1706
Abstract
The post-glacial Baltic Sea has experienced extreme changes that are archived today in the deep sediments. IODP Expedition 347 retrieved cores down to 100 m depth and studied the climate history and the deep biosphere. We here review the biogeochemical and microbiological highlights and integrate these with other studies from the Baltic seabed. Cell numbers, endospore abundance and organic matter mineralization rates are extremely high. A 100-fold drop in cell numbers with depth results from a small difference between growth and mortality in the ageing sediment. Evidence for growth derives from a D:L amino acid racemization model, while evidence for mortality derives from the abundance and potential activity of lytic viruses. The deep communities assemble at the bottom of the bioturbated zone from the founding surface community by selection of organisms suited for life under deep sediment conditions. The mean catabolic per-cell rate of microorganisms drops steeply with depth to a life in slow-motion, typical for the deep biosphere. The subsurface life under extreme energy limitation is facilitated by exploitation of recalcitrant substrates, by biochemical protection of nucleic acids and proteins and by repair mechanisms for random mismatches in DNA or damaged amino acids in proteins.
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4.
Seonamhaeicola maritimus sp. nov., isolated from coastal sediment.
Cao, WR, Lu, DC, Sun, XK, Sun, YY, Saren, G, Yu, XK, Du, ZJ
International journal of systematic and evolutionary microbiology. 2020;(2):902-908
Abstract
A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped and orange-pigmented bacterium, designated 1505T, was isolated from marine sediment that was obtained off the coast of Weihai, PR China. Strain 1505T was found to grow at 10-35 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.5) and in the presence of 1-4 % (w/v) NaCl (optimum, 2 %). Cells were positive for oxidase and catalase activity. The 16S rRNA gene based phylogenetic analysis revealed that the nearest phylogenetic neighbours of strain 1505T were Seonamhaeicola algicola Gy8T (97.1 %), Seonamhaeicola marinus B011T (96.3 %) and Seonamhaeicola aphaedonensis KCTC 32578T (95.6 %). Based on phylogenomic analysis, the average nucleotide identity values between strain 1505T and S. algicola Gy8T, S. marinus B011T and S. aphaedonensis KCTC 32578T were 75.9, 76.0 and 77.7 %, respectively; the digital DNA-DNA hybridization values based on the draft genomes between strain 1505T and S. algicola Gy8T, S. marinus B011T and S. aphaedonensis KCTC 32578T were 20.0, 20.7 and 21.4 %, respectively. Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C15 : 1 G and C18 : 1ω9c. The DNA G+C content of strain 1505T was 33.3 mol%. The polar lipids included phosphatidylethanolamine, six aminolipids and four unidentified lipids. Based on its phylogenetic and phenotypic characteristics, strain 1505T is considered to represent a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola maritimus sp. nov. is proposed. The type strain is 1505T (=KCTC 72528T=MCCC 1H00389T).
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5.
Physiological limits to life in anoxic subseafloor sediment.
Orsi, WD, Schink, B, Buckel, W, Martin, WF
FEMS microbiology reviews. 2020;(2):219-231
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Abstract
In subseafloor sediment, microbial cell densities exponentially decrease with depth into the fermentation zone. Here, we address the classical question of 'why are cells dying faster than they are growing?' from the standpoint of physiology. The stoichiometries of fermentative ATP production and consumption in the fermentation zone place bounds on the conversion of old cell biomass into new. Most fermentable organic matter in deep subseafloor sediment is amino acids from dead cells because cells are mostly protein by weight. Conversion of carbon from fermented dead cell protein into methanogen protein via hydrogenotrophic and acetoclastic methanogenesis occurs at ratios of ∼200:1 and 100:1, respectively, while fermenters can reach conversion ratios approaching 6:1. Amino acid fermentations become thermodynamically more efficient at lower substrate and product concentrations, but the conversion of carbon from dead cell protein into fermenter protein is low because of the high energetic cost of translation. Low carbon conversion factors within subseafloor anaerobic feeding chains account for exponential declines in cellular biomass in the fermentation zone of anoxic sediments. Our analysis points to the existence of a life-death transition zone in which the last biologically catalyzed life processes are replaced with purely chemical reactions no longer coupled to life.
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6.
Formosa maritima sp. nov., isolated from coastal sediment.
Cao, WR, Lu, DC, Li, YJ, Sun, XK, Sun, YY, Saren, G, Du, ZJ
International journal of systematic and evolutionary microbiology. 2020;(2):982-988
Abstract
A Gram-stain-negative, strictly aerobic, gliding-motile, rod-shaped and orange-pigmented bacterium, designated 1494T, was isolated from marine sediment collected off the coast of Weihai, PR China. Strain 1494T was found to grow at 4-37 °C (optimum, 30 °C), at pH 6.0-9.0 (pH 7.0) and in the presence of 0-8 % (w/v) NaCl (2 %). Cells were positive for oxidase and catalase activity. The results of 16S rRNA gene based phylogenetic analysis revealed that strain 1494T belonged to the genus Formosa and exhibited the highest sequence similarity to Formosa spongicola KCTC 22662 T (98.4 %). Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C15 : 1 G and iso-C15 : 0. The DNA G+C content of strain 1494T was 31.1 mol%. The major polar lipids included phosphatidylethanolamine, one unidentified phospholipid and one unidentified lipid. Based on its phylogenetic and phenotypic characteristics, strain 1494T is considered to represent a novel species from the genus Formosa, for which the name Formosa maritima sp. nov. is proposed. The type strain is 1494T (=KCTC 72531T=MCCC 1H00385T).
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7.
Experimental investigation of the effects of water content on the anisotropy of mode I fracture toughness of bedded mudstones.
Yang, J, Li, L, Lian, H
PloS one. 2020;(8):e0237909
Abstract
The influence of water content on mode I fracture toughness (KIc) of mudstones has been studied using semi-circular bend (SCB) specimens subject to three-point bendings. And the mudstone SCB specimens are divided into three types, including Type-A, Type-B and Type-C, corresponding to the three configurations of the bedding planes, including divider direction, arrester direction, and transverse direction, respectively. The test results show that the values of KIc for the three types of specimens are different due to the bedding structure, the Type-A specimens have the largest value of KIc for the same soak period, while the Type-C specimens possess the smallest value. As the soak period increases, the KIc of the three kinds of mudstone specimens decreases, and the fracture mechanisms of the specimens change gradually from the brittle failure form to the ductile failure form. Moreover, the standard deviation was used to quantify the anisotropy degree of the KIc of the mudstone samples. As the water content increases, the standard deviation increases from 0.057 to 0.139, which indicates a significant increase in anisotropy of the KIc of the mudstone specimens. In addition, the acoustic emission (AE) system was used to detect the AE events associated with the fracture initiation and propagation in the mudstone specimens for the different water content, with the raising water content, the cumulative AE events decrease, and the standard deviation of AE events increases, repesenting that the anisotropy of the AE events of the three types of specimens becomes more prominent. Further, the relationship between the tensile strength (σt) and the KIc of the three types of mudstone specimens for different water contents has been proved to be the linear relation.
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8.
Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments.
Sandfeld, T, Marzocchi, U, Petro, C, Schramm, A, Risgaard-Petersen, N
The ISME journal. 2020;(5):1233-1246
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Abstract
Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.
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9.
Marinobacter fonticola sp. nov., isolated from deep sea cold seep sediment.
Sun, QL, Sun, YL, Sun, YY, Luan, ZD, Lian, C
International journal of systematic and evolutionary microbiology. 2020;(2):1172-1177
Abstract
In this study, we report a novel Gram-negative bacterium, designated as strain CS412T, isolated from deep-sea sediment collected in a cold seep area of the South China Sea. Growth of strain CS412T occurred at 4-40 °C (optimum, 28 °C), pH 5.0-11.0 (optimum, pH 6.0) and with 0-19 % (w/v) NaCl (optimum, 1-2 %). Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain CS412T belonged to the genus Marinobacter. The closest phylogenetic neighbours of strain CS412T were Marinobacter pelagius HS225T (96.9 %), Marinobacter szutsaonensis NTU-104T (96.8%), Marinobacter santoriniensis NKSG1T (96.4%) and Marinobacter koreensisdd-M3T (96.3 %). The genomic DNA G+C content of strain CS412T was 58.0 mol%. The principal respiratory quinone was ubiquinone-9 (Q-9). The polar lipids of CS412T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipidand and four glycolipids. The major fatty acids of CS412T contained cyclo-C19 : 0ω8c, C16 : 0, C18 : 1ω7c and C18 : 1ω7c 11-methyl. The results of phylogenetic, physiological, biochemical and morphological analyses suggested that strain CS412T represents a novel species of the genus Marinobacter, and the name Marinobacter fonticola sp. nov. is proposed with the type species CS412T (=CCTCC AB 2019197T=KCTC 72475T).
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Micromonospora fluminis sp. nov., isolated from mountain river sediment.
Camacho Pozo, MI, Wieme, AD, Rodríguez Pérez, S, Llauradó Maury, G, Peeters, C, Snauwaert, C, Lescaylle Veranes, Y, Peña Zamora, L, Schumann, P, Vandamme, PA
International journal of systematic and evolutionary microbiology. 2020;(12):6428-6436
Abstract
During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38T was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus Micromonospora by means of a polyphasic taxonomy study. Strain A38T was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC15:0, 10 methyl C17:0, anteiso-C17:0 and iso-C17:0. The predominant menaquinones were MK-10(H4) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to Micromonospora tulbaghiae DSM 45142T (99.5 %), Micromonospora citrea DSM 43903T (99.4 %), Micromonospora marina DSM 45555T (99.4 %), Micromonospora maritima DSM 45782T (99.3 %), Micromonospora sediminicola DSM 45794T (99.3 %), Micromonospora aurantiaca DSM 43813T (99.2 %) and Micromonospora chaiyaphumensis DSM 45246T (99.2 %). The results of OrthoANIu analysis showed the highest similarity to Micromonospora chalcea DSM 43026T (96.4 %). However, the 16S rRNA and gyrB gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38T as a novel species. On the basis of the results presented here, we propose to classify strain A38T (=LMG 30467T=CECT 30034T) as the type strain of the novel species Micromonospora fluminis sp. nov.