scholarly journals Macroscopic Biofilms in Fracture-Dominated Sediment That Anaerobically Oxidize Methane

2011 ◽  
Vol 77 (19) ◽  
pp. 6780-6787 ◽  
Author(s):  
B. R. Briggs ◽  
J. W. Pohlman ◽  
M. Torres ◽  
M. Riedel ◽  
E. L. Brodie ◽  
...  
Keyword(s):  
Isotope Composition ◽  
Stable Carbon Isotope ◽  
Cold Seep ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anaerobic Oxidation Of Methane ◽  
Isolated Cells ◽  
Content Type ◽  
Bacterial Phyla ◽  
Oxidation Of Methane

ABSTRACTMethane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 107to 108cells cm−3. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated byDeltaproteobacteria, candidate division WS3, andChloroflexi, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade,Thermoplasmatales, andDesulfurococcales, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla ofMethanosarcinalesandDesulfurococcales. The stable carbon isotope composition of the biofilm from the SMT (−35 to −43‰) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments.

scholarly journals Detection of Putatively Thermophilic Anaerobic Methanotrophs in Diffuse Hydrothermal Vent Fluids

2012 ◽  
Vol 79 (3) ◽  
pp. 915-923 ◽  
Author(s):  
Alexander Y. Merkel ◽  
Julie A. Huber ◽  
Nikolay A. Chernyh ◽  
Elizaveta A. Bonch-Osmolovskaya ◽  
Alexander V. Lebedinsky
Keyword(s):  
16S Rrna ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Phylogenetic Groups ◽  
Content Type

ABSTRACTThe anaerobic oxidation of methane (AOM) is carried out by a globally distributed group of uncultivatedEuryarchaeota, the anaerobic methanotrophic arachaea (ANME). In this work, we used G+C analysis of 16S rRNA genes to identify a putatively thermophilic ANME group and applied newly designed primers to study its distribution in low-temperature diffuse vent fluids from deep-sea hydrothermal vents. We found that the G+C content of the 16S rRNA genes (PGC) is significantly higher in the ANME-1GBa group than in other ANME groups. Based on the positive correlation between thePGCand optimal growth temperatures (Topt) of archaea, we hypothesize that the ANME-1GBa group is adapted to thrive at high temperatures. We designed specific 16S rRNA gene-targeted primers for the ANME-1 cluster to detect all phylogenetic groups within this cluster, including the deeply branching ANME-1GBa group. The primers were successfully tested bothin silicoand in experiments with sediment samples where ANME-1 phylotypes had previously been detected. The primers were further used to screen for the ANME-1 microorganisms in diffuse vent fluid samples from deep-sea hydrothermal vents in the Pacific Ocean, and sequences belonging to the ANME-1 cluster were detected in four individual vents. Phylotypes belonging to the ANME-1GBa group dominated in clone libraries from three of these vents. Our findings provide evidence of existence of a putatively extremely thermophilic group of methanotrophic archaea that occur in geographically and geologically distinct marine hydrothermal habitats.

scholarly journals Paleo-environmental imprint on microbiology and biogeochemistry of coastal quaternary sediments

2010 ◽  
Vol 7 (4) ◽  
pp. 5463-5496
Author(s):  
M. Beck ◽  
T. Riedel ◽  
J. Graue ◽  
J. Köster ◽  
N. Kowalski ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Tidal Flat ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anaerobic Oxidation Of Methane ◽  
Deep Biosphere ◽  
Shallow Subsurface ◽  
Oxidation Of Methane ◽  
Key Genes ◽  
Close Distance

Abstract. To date, North Sea tidal flat sediments have been intensively studied down to a depth of 5 m below sea floor (mbsf). However, little is known about the biogeochemistry, microbial abundance, and activity of sulfate reducers as well of methanogens in deeper layers. For this study, we hypothesized that the imprint of the paleo-environment is reflected in current microbiogeochemical processes. Therefore, 20 m-long cores were retrieved from the tidal-flat area of Spiekeroog Island, NW Germany. Two drill sites were selected with a close distance of only 900 meters, but where sedimentation occurred under different environmental conditions: first, a paleo-channel filled with Holocene sediments and second, a mainly Pleistocene sedimentary succession. In general, the numbers of bacterial 16S rRNA genes are one to two orders of magnitude higher than those of Archaea. The abundances of key genes for sulfate reduction and methanogenesis (dsrA and mcrA) correspond to the sulfate and methane profiles. A co-variance of these key genes at sulfate-methane interfaces and enhanced potential AOM rates suggest that anaerobic oxidation of methane may occur in these layers. Microbial and biogeochemical profiles are vertically stretched relative to 5 m-deep cores from shallower sediments in the same study area. Compared to the deep marine environment, the profiles are transitional between the shallow subsurface and the marine deep biosphere. Our interdisciplinary analysis shows that the microbial abundances and metabolic rates are elevated in the Holocene compared to Pleistocene sediments. However, this is mainly due to present environmental conditions such as pore water flow and organic matter availability. The paleo-environmental imprint is still visible but superimposed by these processes.

scholarly journals Imprint of past and present environmental conditions on microbiology and biogeochemistry of coastal Quaternary sediments

2011 ◽  
Vol 8 (1) ◽  
pp. 55-68 ◽  
Author(s):  
M. Beck ◽  
T. Riedel ◽  
J. Graue ◽  
J. Köster ◽  
N. Kowalski ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Tidal Flat ◽  
Ex Situ ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Anaerobic Oxidation Of Methane ◽  
Oxidation Of Methane ◽  
Depositional Settings ◽  
Key Genes ◽  
Close Distance

Abstract. To date, North Sea tidal-flat sediments have been intensively studied down to a depth of 5 m below seafloor (mbsf). However, little is known about the biogeochemistry, microbial abundance, and activity of sulfate reducers as well as methanogens in deeper layers. In this study, two 20 m-long cores were retrieved from the tidal-flat area of Spiekeroog Island, NW Germany. The drill sites were selected with a close distance of 900 m allowing to compare two depositional settings: first, a paleo-channel filled with Holocene sediments and second, a mainly Pleistocene sedimentary succession. Analyzing these cores, we wanted to test to which degree the paleo-environmental imprint is superimposed by present processes. In general, the numbers of bacterial 16S rRNA genes are one to two orders of magnitude higher than those of Archaea. The abundances of key genes for sulfate reduction and methanogenesis (dsrA and mcrA) correspond to the sulfate and methane profiles. A co-variance of these key genes at sulfate-methane interfaces and enhanced ex situ AOM rates suggest that anaerobic oxidation of methane may occur in these layers. Microbial and biogeochemical profiles are vertically stretched relative to 5 m-deep cores from shallower sediments in the same study area, but still appear compressed compared to deep sea sediments. Our interdisciplinary analysis shows that the microbial abundances and metabolic rates are elevated in the Holocene compared to Pleistocene sediments. However, this is mainly due to present environmental conditions such as pore water flow and organic matter availability. The paleo-environmental imprint is still visible but superimposed by these processes.

scholarly journals Diversity of NC10 Bacteria and ANME-2d Archaea in Sediments of Fault Zones at Lake Baikal

Diversity ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 10
Author(s):  
Anna Lomakina ◽  
Tatyana Pogodaeva ◽  
Gennady Kalmychkov ◽  
Svetlana Chernitsyna ◽  
Tamara Zemskaya
Keyword(s):  
Lake Baikal ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Anaerobic Oxidation Of Methane ◽  
Oxidation Of Methane ◽  
Different Types ◽  
Freshwater Reservoir ◽  
Deep Sediments

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems, but we know little about AOM in freshwater reservoirs. Lake Baikal is the world’s only freshwater reservoir where gas hydrates (GH) are found. Despite that AOM has been demonstrated in deep sediments of Lake Baikal did not reveal methane-oxidizing archaea ANME1, 2, or 3, which are responsible for AOM in marine sediments. A search for representatives Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria (NC10) and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea (ANME-2d) has been carried out in the different types of Lake Baikal methane enriched sediments. We used different molecular biology methods including high-throughput sequencing and PCR analysis, using 16S rRNA genes as well as different functional genes of AOM (mcrA and pmoA). We found diverse M. oxyfera-like bacteria and M. nitroreducens-like archaea in various geological structures in Lake Baikal (methane seep and mud volcano), which were different from the composition of the discharged fluid. We also considered possible electron acceptors for this process in the sediments of Lake Baikal.

scholarly journals Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep

2007 ◽  
Vol 57 (6) ◽  
pp. 1243-1249 ◽  
Author(s):  
Ngoc-Phuc Hua ◽  
Atsuko Kanekiyo ◽  
Katsunori Fujikura ◽  
Hisato Yasuda ◽  
Takeshi Naganuma
Keyword(s):  
Deep Sea ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Cold Seep ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
High Sequence Similarity ◽  
Moderately Halophilic ◽  
Type Strains ◽  
Moderately Halophilic Bacteria

Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1 ω7c alcohol and C18 : 1 ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

scholarly journals Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR

2016 ◽  
Vol 82 (10) ◽  
pp. 3022-3031 ◽  
Author(s):  
Ayako Fujiwara ◽  
Katsuhiro Kawato ◽  
Saori Kato ◽  
Kiyoshi Yasukawa ◽  
Ryota Hidese ◽  
...  
Keyword(s):  
Noise Reduction ◽  
Dna Polymerase ◽  
Biological Activities ◽  
Genetic Diagnosis ◽  
Gc Content ◽  
Dna Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Thermococcus Kodakarensis

ABSTRACTDNA/RNA helicases, which are enzymes for eliminating hydrogen bonds between bases of DNA/DNA, DNA/RNA, and RNA/RNA using the energy of ATP hydrolysis, contribute to various biological activities. In the present study, theEuryarchaeota-specific helicase EshA (TK0566) from the hyperthermophilic archaeonThermococcus kodakarensis(Tk-EshA) was obtained as a recombinant form, and its enzymatic properties were examined.Tk-EshA exhibited maximal ATPase activity in the presence of RNA at 80°C. Unwinding activity was evaluated with various double-stranded DNAs (forked, 5′ overhung, 3′ overhung, and blunt end) at 50°C.Tk-EshA unwound forked and 3′ overhung DNAs. These activities were expected to unwind the structured template and to peel off misannealed primers whenTk-EshA was added to a PCR mixture. To examine the effect ofTk-EshA on PCR, various target DNAs were selected, and DNA synthesis was investigated. When 16S rRNA genes were used as a template, several misamplified products (noise DNAs) were detected in the absence ofTk-EshA. In contrast, noise DNAs were eliminated in the presence ofTk-EshA. Noise reduction byTk-EshA was also confirmed whenTaqDNA polymerase (a family A DNA polymerase, PolI type) and KOD DNA polymerase (a family B DNA polymerase, α type) were used for PCR. Misamplified bands were also eliminated duringtoxAgene amplification fromPseudomonas aeruginosaDNA, which possesses a high GC content (69%).Tk-EshA addition was more effective than increasing the annealing temperature to reduce misamplified DNAs duringtoxAamplification.Tk-EshA is a useful tool to reduce noise DNAs for accurate PCR.IMPORTANCEPCR is a technique that is useful for genetic diagnosis, genetic engineering, and detection of pathogenic microorganisms. However, troubles with nonspecific DNA amplification often occur from primer misannealing. In order to achieve a specific DNA amplification by eliminating noise DNAs derived from primer misannealing, a thermostableEuryarchaeota-specific helicase (Tk-EshA) was included in the PCR mixture. The addition ofTk-EshA has reduced noise DNAs in PCR.

Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1471-1478 ◽  
Author(s):  
Morio Ishikawa ◽  
Kazuhide Yamasato ◽  
Kayo Kodama ◽  
Hinako Yasuda ◽  
Mioko Matsuyama ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molar Ratio ◽  
Phylogenetic Position ◽  
Growth Responses ◽  
Cultivation Conditions ◽  
Content Type ◽  
Link Type

Nine novel strains of halophilic and alkaliphilic lactic acid bacteria isolated from European soft and semi-hard cheeses by using a saline, alkaline medium (7 % NaCl, pH 9.5) were taxonomically characterized. The isolates were Gram-stain-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from d-glucose with the production of formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from d-glucose. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth ranged between 2.0 % and 5.0 % (w/v), with a growth range of 0–1 % to 15–17.5 %. The optimum pH for growth ranged between 8.5 and 9.5, with a growth range of 7.0–7.5 to 9.5–10.0. Comparative sequence analysis of the 16S rRNA genes revealed that the isolates occupied a phylogenetic position within the genus Alkalibacterium , showing the highest sequence similarity (98.2 %) to Alkalibacterium kapii T22-1-2T. The isolates constituted a single genomic species with DNA–DNA hybridization values of 79–100 % among the isolates and <29 % between the isolates and other members of the genus Alkalibacterium , from which the isolates were different in motility and flagellation, growth responses to NaCl concentrations and pH, and profiles of sugar fermentation. The DNA G+C contents were between 36.0 and 37.6 mol%. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major components of cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9c. Based on the phenotypic characteristics and genetic distinctness, the isolates are classified as a novel species within the genus Alkalibacterium , for which the name Alkalibacterium gilvum sp. nov. is proposed. The type strain is 3AD-1T ( = DSM 25751T = JCM 18271T).

scholarly journals Phosphorus Species in Deep-Sea Carbonate Deposits: Implications for Phosphorus Cycling in Cold Seep Environments

Minerals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 645
Author(s):  
Junlie Zhou ◽  
Mengran Du ◽  
Jiwei Li ◽  
Hengchao Xu ◽  
Kaiwen Ta ◽  
...  
Keyword(s):  
Deep Sea ◽  
Cold Seep ◽  
Anaerobic Oxidation Of Methane ◽  
Cold Seeps ◽  
Organic P ◽  
Anaerobic Oxidation ◽  
Phosphorus Species ◽  
China Sea ◽  
Oxidation Of Methane ◽  
Deep Sediments

Phosphorus (P) is an important nutrient for biological communities in cold seeps. However, our knowledge on the source, species, and cycling of P in cold seep environments is limited. In this study, the concentration, species, and micro to nanometer scale distribution of P in seep carbonates were examined at three deep-sea cold seeps in the South China Sea and East China Sea. The Ca-P accounts for the largest proportion of P—followed by detrital-P, Fe-P, organic-P, and exchangeable-P. The distribution patterns of Ca-P, detrital-P, and organic-P in the seep carbonates differ from one another, as shown by elemental mapping with NanoSIMS and scanning electron microscopy. The covariation of P with Ca and C reveals that Ca-P co-precipitates with Ca-carbonate, which is linked to the process of sulfate-driven anaerobic oxidation of methane. Organic-P is also observed within biofilm-like organic carbon aggregates, revealing the microbial enrichment of P by fluids in the process of anaerobic oxidation of methane. P with a granulated morphology was identified as detrital-P derived from deep sediments. Most importantly, it is evident that Ca-P is positively correlated to the Fe content in all the seep carbonates. This indicates the likelihood that the dissolved P in cold-seep fluids is released primarily from Fe oxides through Fe-driven anaerobic oxidation of methane in deep sediments. These processes associated with different species of P may have significant implications for P geochemical cycling and anaerobic oxidation of methane impelled by Fe and sulfate reduction in cold seep environments.

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