scholarly journals Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere

2016 ◽  
Vol 82 (10) ◽  
pp. 3000-3008 ◽  
Author(s):  
Heather Fullerton ◽  
Craig L. Moyer
Keyword(s):  
Single Cell ◽  
Okinawa Trough ◽  
Reductive Dehalogenation ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Metabolic Potential ◽  
Deep Subsurface ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
The Okinawa Trough

ABSTRACTChloroflexismall-subunit (SSU) rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of the phylum is poorly understood. The phylumChloroflexiis represented by isolates with diverse metabolic strategies, including anoxic phototrophy, fermentation, and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single-cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurfaceChloroflexi. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected from the Okinawa Trough at Iheya North hydrothermal field as part of Integrated Ocean Drilling Program (IODP) expedition 331 (Deep Hot Biosphere). Previous studies of subsurfaceChloroflexisingle amplified genomes (SAGs) suggested heterotrophic or lithotrophic metabolisms and provided no evidence for growth by reductive dehalogenation. Our nineChloroflexiSAGs (seven of which are from the orderAnaerolineales) indicate that, in addition to genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into cells. At least one subunit for pyruvate ferredoxin oxidoreductase was found in four of theChloroflexiSAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the sevenAnaerolinealesSAGs contains a distinct reductive dehalogenase homologous (rdhA) gene.IMPORTANCEThrough the use of single amplified genomes (SAGs), we have extended the metabolic potential of an understudied group of subsurface microbes, theChloroflexi. These microbes are frequently detected in the subsurface biosphere, though their metabolic capabilities have remained elusive. In contrast to previously examinedChloroflexiSAGs, our genomes (several are from the orderAnaerolineales) were recovered from a hydrothermally driven system and therefore provide a unique window into the metabolic potential of this type of habitat. In addition, a reductive dehalogenase gene (rdhA) has been directly linked to marine subsurfaceChloroflexi, suggesting that reductive dehalogenation is not limited to the classDehalococcoidia. This discovery expands the nutrient-cycling and metabolic potential present within the deep subsurface and provides functional gene information relating to this enigmatic group.

scholarly journals Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3668-3675 ◽  
Author(s):  
Yuichi Nogi ◽  
Mariko Abe ◽  
Shinsuke Kawagucci ◽  
Hisako Hirayama
Keyword(s):  
Type Species ◽  
Okinawa Trough ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
The Novel ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough ◽  
Major Respiratory Quinone

A novel psychrophilic, marine, bacterial strain designated BJ-1T was isolated from the Iheya North hydrothermal field in the Okinawa Trough off Japan. Cells were Gram-negative, rod-shaped, non-spore-forming, aerobic chemo-organotrophs and motile by means of a single polar flagellum. Growth occurred at temperatures below 16 °C, with the optimum between 9 and 12 °C. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the closest relatives of strain BJ-1T were Shewanella denitrificans OS-217T (93.5 % similarity), Shewanella profunda DSM 15900T (92.9 %), Shewanella gaetbuli TF-27T (92.9 %), Paraferrimonas sedimenticola Mok-106T (92.1 %) and Ferrimonas kyonanensis Asr22-7T (91.7 %). The major respiratory quinone was Q-8. The predominant fatty acids were C16 : 1ω7c and C16 : 0. The G+C content of the novel strain was 40.5 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain BJ-1T represents a novel species in a new genus, for which the name Psychrobium conchae gen. nov., sp. nov. is proposed. The type strain of Psychrobium conchae is BJ-1T ( = JCM 30103T = DSM 28701T).

scholarly journals Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake

2014 ◽  
Vol 80 (21) ◽  
pp. 6807-6818 ◽  
Author(s):  
Esther A. Gies ◽  
Kishori M. Konwar ◽  
J. Thomas Beatty ◽  
Steven J. Hallam
Keyword(s):  
Single Cell ◽  
Niche Partitioning ◽  
454 Sequencing ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Metabolic Potential ◽  
Content Type ◽  
Lake Ecosystems ◽  
Pathway Reconstruction

ABSTRACTDespite recent advances in metagenomic and single-cell genomic sequencing to investigate uncultivated microbial diversity and metabolic potential, fundamental questions related to population structure, interactions, and biogeochemical roles of candidate divisions remain. Numerous molecular surveys suggest that stratified ecosystems manifesting anoxic, sulfidic, and/or methane-rich conditions are enriched in these enigmatic microbes. Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution. Operational taxonomic units (OTUs) were affiliated with 64 phyla, including more than 25 candidate divisions. Pronounced trends in community structure were observed for all three domains with eukaryotic sequences vanishing almost completely below the mixolimnion, followed by a rapid and sustained increase in methanogen-affiliated (∼10%) and unassigned (∼60%) archaeal sequences as well as bacterial OTUs affiliated withChloroflexi(∼22%) and candidate divisions (∼28%). Network analysis revealed highly correlated, depth-dependent cooccurrence patterns betweenChloroflexi, candidate divisions WWE1, OP9/JS1, OP8, and OD1, methanogens, and unassigned archaeal OTUs indicating niche partitioning and putative syntrophic growth modes. Indeed, pathway reconstruction using recently published Sakinaw Lake single-cell genomes affiliated with OP9/JS1 and OP8 revealed complete coverage of the Wood-Ljungdahl pathway with potential to drive syntrophic acetate oxidation to hydrogen and carbon dioxide under methanogenic conditions. Taken together, these observations point to previously unrecognized syntrophic networks in meromictic lake ecosystems with the potential to inform design and operation of anaerobic methanogenic bioreactors.

scholarly journals Ancylomarina longa sp. nov., isolated from southern Okinawa Trough sediment and emended description of the family Marinifilaceae

2020 ◽  
Vol 70 (4) ◽  
pp. 2531-2536 ◽  
Author(s):  
Tianyu Fu ◽  
Hongchang Cui ◽  
Chao Jia ◽  
Wen Sun ◽  
Shun Zhou ◽  
...  
Keyword(s):  
Okinawa Trough ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough ◽  
The Family ◽  
Long Rod ◽  
Type Strains

A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-CT, was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-CT was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae . Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-CT was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C15 : 0 (38.9 %) and anteiso-C15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-CT was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-CT is considered to represent a novel species of the genus Ancylomarina , for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-CT (=KCTC 15505T=MCCC 1K01617T).

scholarly journals Muricauda alvinocaridis sp. nov., isolated from shrimp gill from the Okinawa Trough

2020 ◽  
Vol 70 (3) ◽  
pp. 1666-1671 ◽  
Author(s):  
Lijun Liu ◽  
Min Yu ◽  
Shun Zhou ◽  
Tianyu Fu ◽  
Wen Sun ◽  
...  
Keyword(s):  
Type Species ◽  
Okinawa Trough ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough ◽  
Gene Sequence Analysis ◽  
Bacterium Strain

A Gram-stain-negative, strictly aerobic, non-motile, long, straight-rod and non-flagellated marine bacterium strain, designated SCR12T, was isolated from the gill of a shrimp collected in the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16–40 °C and the optimum temperature was 37 °C. Optimal growth occurred at pH 6.5 and in the presence of 3 % (w/v) NaCl. The predominant isoprenoid quinone of strain SCR12T was menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C15 : 0 (44.2 %), iso-C15 : 1 G (19.0 %) and iso-C17 : 0 3-OH (12.1 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminolipids and three unidentified lipids. Based on the results of 16S rRNA gene sequence analysis, strain SCR12T was found to be most closely related to Muricauda olearia CL-SS4T (98.09 %), followed by Muricauda beolgyonensis BB-My12T (97.65 %), Muricauda aquimarina SW-63T (97.58 %) and Muricauda ruestringensis DSM 13258T (97.31 %) and with lower sequence similarities (95.74–97.10 %) to other species of the genus Muricauda . Genome relatedness between strain SCR12T and M. olearia CL-SS4T was computed using both average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) and resulted in values of 85.6 % and 29.3±2.3 %, respectively. The genomic DNA G+C content of strain SCR12T was 42.3 mol%. On the basis of polyphasic analysis, the strain SCR12T was considered to represent a novel species of the genus Muricauda, for which the name Muricauda alvinocaridis sp. nov. is proposed. The type strain is SCR12T (=MCCC 1K03731T=JCM 33425T).

scholarly journals Thalassococcus profundi sp. nov., a marine bacterium isolated from deep seawater of the Okinawa Trough

2019 ◽  
Vol 69 (4) ◽  
pp. 920-925 ◽  
Author(s):  
Min Yu ◽  
Qiaomeng Ren ◽  
Yanhong Wu ◽  
Xiaorong Tian ◽  
Xiao-Hua Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Okinawa Trough ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Deep Seawater ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough

A novel Gram-stain-negative, strictly aerobic, rod-shaped motile bacterium with a single flagellum, designated strain WRAS1T, was isolated from deep seawater of the Okinawa Trough. Growth occurred in the presence of 0.0–9.0 % NaCl (w/v; optimum, 3.0–4.0 %), at 4–45 °C (optimum, 28–37 °C) and pH 7.0–10.0 (optimum, pH 7.0–8.0). The major fatty acid (>10 % of total fatty acids) was summed feature 8, comprising C18:1 ω6c and/or C18:1 ω7c. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-10. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WRAS1T was in the genus Thalassococcus and showed the highest 16S rRNA gene sequence similarity of 97.5 % to Thalassococcus halodurans JCM13833T. Genome relatedness between strain WRAS1T and T. halodurans JCM13833T was computed using both average nucleotide identity and DNA–DNA hybridization with values of 74.11 % and 22.70±2.3 %, respectively. The genomic DNA G+C content calculated from the genome sequence of strain WRAS1T was 65.6 %. On the basis of polyphasic analyses, strain WRAS1T is considered to represent a novel species in the genus Thalassococcus , for which the name Thalassococcus profundi sp. nov. is proposed. The type strain is WRAS1T (=CGMCC 1.16123T=MCCC 1K03253T =KCTC 52696T).

scholarly journals Gramella bathymodioli sp. nov., isolated from a mussel inhabiting a hydrothermal field in the Okinawa Trough

2020 ◽  
Vol 70 (11) ◽  
pp. 5854-5860 ◽  
Author(s):  
Lijun Liu ◽  
Shuang Wang ◽  
Shun Zhou ◽  
Wen Sun ◽  
Tianyu Fu ◽  
...  
Keyword(s):  
Type Species ◽  
Okinawa Trough ◽  
Optimal Growth ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
The Okinawa Trough ◽  
Bacterium Strain

A Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and non-flagellated marine bacterium strain, designated BOM4T, was isolated from a mussel inhabiting the Tangyin hydrothermal field of the Okinawa Trough. The growth temperature was in the range of 16–40 °C, and the optimum temperature was 37 °C. Optimal growth occurred at pH 7.0 and in the presence of 1 % (w/v) NaCl. The predominant isoprenoid quinone of strain BOM4T was identified as menaquinone-6 (MK-6). The predominant fatty acids (>10 %) were iso-C15 : 0(43.8 %) and iso-C17 : 0 3-OH (17.5 %). The major polar lipids comprised one phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Based on 16S rRNA gene sequence analyses, strain BOM4T was found to be most closely related to Gramella aestuarii JCM 17790T (96.7 %), followed by Gramella flava JLT2011T (96.1 %), Gramella sediminilitoris GHTF-27T (95.6 %) and Gramella gaetbulicola RA5-111T (95.5 %) and with lower sequence similarities (93.7- 95.4 %) to other species of the genus Gramella . Genome relatedness between strain BOM4T and G. aestuarii JCM 17790T was computed using both average nucleotide identity and DNA–DNA hybridization with values of 75.6 and 19.3±2.4 %, respectively. The DNA G+C content of strain BOM4T was 41.4 mol%. On the basis of polyphasic analysis, strain BOM4T was considered to represent a novel species of the genus Gramella , for which the name Gramella bathymodioli sp. nov. is proposed. The type strain is BOM4T (=MCCC 1K03735T=JCM 33424T).

scholarly journals Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor

2019 ◽  
Vol 86 (5) ◽  
Author(s):  
Jie Liu ◽  
Lorenz Adrian ◽  
Max M. Häggblom
Keyword(s):  
Gene Expression ◽  
Secondary Metabolites ◽  
Electron Acceptor ◽  
Marine Sponge ◽  
Reductive Dehalogenation ◽  
Important Process ◽  
Organohalide Respiration ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Significant Difference

ABSTRACT Organohalide respiration is an important process in the global halogen cycle and for bioremediation. In this study, we compared the global transcriptomic and proteomic analyses of Desulfoluna spongiiphila strain AA1, an organohalide-respiring member of the Desulfobacterota isolated from a marine sponge, with 2,6-dibromophenol or with sulfate as an electron acceptor. The most significant difference of the transcriptomic analysis was the expression of one reductive dehalogenase gene cluster (rdh16), which was significantly upregulated with the addition of 2,6-dibromophenol. The corresponding protein, reductive dehalogenase RdhA16032, was detected in the proteome under treatment with 2,6-dibromophenol but not with sulfate only. There was no significant difference in corrinoid biosynthesis gene expression levels between the two treatments, indicating that the production of corrinoid in D. spongiiphila is constitutive or not specific for organohalide versus sulfate respiration. Electron-transporting proteins or mediators unique for reductive dehalogenation were not revealed in our analysis, and we hypothesize that reductive dehalogenation may share an electron-transporting system with sulfate reduction. The metabolism of D. spongiiphila, predicted from transcriptomic and proteomic results, demonstrates high metabolic versatility and provides insights into the survival strategies of a marine sponge symbiont in an environment rich in organohalide compounds and other secondary metabolites. IMPORTANCE Respiratory reductive dehalogenation is an important process in the overall cycling of both anthropogenic and natural organohalide compounds. Marine sponges produce a vast array of bioactive compounds as secondary metabolites, including diverse halogenated compounds that may enrich for dehalogenating bacteria. Desulfoluna spongiiphila strain AA1 was originally enriched and isolated from the marine sponge Aplysina aerophoba and can grow with both brominated compounds and sulfate as electron acceptors for respiration. An understanding of the overall gene expression and the protein production profile in response to organohalides is needed to identify the full complement of genes or enzymes involved in organohalide respiration. Elucidating the metabolic capacity of this sponge-associated bacterium lays the foundation for understanding how dehalogenating bacteria may control the fate of organohalide compounds in sponges and their role in a symbiotic organobromine cycle.

scholarly journals Unexpected Specificity of Interspecies Cobamide Transfer from Geobacter spp. to Organohalide-Respiring Dehalococcoides mccartyi Strains

2012 ◽  
Vol 78 (18) ◽  
pp. 6630-6636 ◽  
Author(s):  
Jun Yan ◽  
Kirsti M. Ritalahti ◽  
Darlene D. Wagner ◽  
Frank E. Löffler
Keyword(s):  
Reductive Dechlorination ◽  
De Novo ◽  
Synthetic Medium ◽  
Geobacter Sulfurreducens ◽  
Rrna Gene ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Gene Copies ◽  
Pure Cultures

ABSTRACTDehalococcoides mccartyistrains conserve energy from reductive dechlorination reactions catalyzed by corrinoid-dependent reductive dehalogenase enzyme systems.Dehalococcoideslacks the ability forde novocorrinoid synthesis, and pure cultures require the addition of cyanocobalamin (vitamin B12) for growth. In contrast,Geobacter lovleyi, which dechlorinates tetrachloroethene tocis-1,2-dichloroethene (cis-DCE), and the nondechlorinating speciesGeobacter sulfurreducenshave complete sets of cobamide biosynthesis genes and produced 12.9 ± 2.4 and 24.2 ± 5.8 ng of extracellular cobamide per liter of culture suspension, respectively, during growth with acetate and fumarate in a completely synthetic medium.G. lovleyi-D. mccartyistrain BAV1 or strain FL2 cocultures provided evidence for interspecies corrinoid transfer, andcis-DCE was dechlorinated to vinyl chloride and ethene concomitant withDehalococcoidesgrowth. In contrast, negligible increase inDehalococcoides16S rRNA gene copies and insignificant dechlorination occurred inG. sulfurreducens-D. mccartyistrain BAV1 or strain FL2 cocultures. Apparently,G. lovleyiproduces a cobamide that complementsDehalococcoides' nutritional requirements, whereasG. sulfurreducensdoes not. Interestingly,Dehalococcoidesdechlorination activity and growth could be restored inG. sulfurreducens-Dehalococcoidescocultures by adding 10 μM 5′,6′-dimethylbenzimidazole. Observations made with theG. sulfurreducens-Dehalococcoidescocultures suggest that the exchange of the lower ligand generated a cobalamin, which supportedDehalococcoidesactivity. These findings have implications forin situbioremediation and suggest that the corrinoid metabolism ofDehalococcoidesmust be understood to faithfully predict, and possibly enhance, reductive dechlorination activities.

scholarly journals Community Structure Analysis of Methanogens Associated with Rumen Protozoa Reveals Bias in Universal Archaeal Primers

2012 ◽  
Vol 78 (11) ◽  
pp. 4051-4056 ◽  
Author(s):  
Lisa D. Tymensen ◽  
Tim A. McAllister
Keyword(s):  
Community Structure ◽  
Species Composition ◽  
Structure Analysis ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Content Type ◽  
Ssu Rrna Gene ◽  
Rumen Protozoa ◽  
Primer Sets

ABSTRACTThe diversity of protozoan-associated methanogens in cattle was investigated using five universal archaeal small-subunit (SSU) rRNA gene primer sets.Methanobrevibacterspp. and rumen cluster C (distantly related toThermoplasmaspp.) were predominant. Significant differences in species composition among libraries indicate that some primers used previously to characterize rumen methanogens exhibit biased amplification.

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