scholarly journals Vertical distribution of methane oxidation and methanotrophic response to elevated methane concentrations in stratified waters of the Arctic fjord Storfjorden (Svalbard, Norway)

2013 ◽  
Vol 10 (10) ◽  
pp. 6267-6278 ◽  
Author(s):  
S. Mau ◽  
J. Blees ◽  
E. Helmke ◽  
H. Niemann ◽  
E. Damm
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Column ◽  
Methane Oxidation ◽  
Deep Water ◽  
Water Masses ◽  
The Arctic ◽  
Rrna Gene ◽  
Type I ◽  
Arctic Fjord

Abstract. The bacterially mediated aerobic methane oxidation (MOx) is a key mechanism in controlling methane (CH4) emissions from the world's oceans to the atmosphere. In this study, we investigated MOx in the Arctic fjord Storfjorden (Svalbard) by applying a combination of radio-tracer-based incubation assays (3H-CH4 and 14C-CH4), stable C-CH4 isotope measurements, and molecular tools (16S rRNA gene Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting, pmoA- and mxaF gene analyses). Storfjorden is stratified in the summertime with melt water (MW) in the upper 60 m of the water column, Arctic water (ArW) between 60 and 100 m, and brine-enriched shelf water (BSW) down to 140 m. CH4 concentrations were supersaturated with respect to the atmospheric equilibrium (about 3–4 nM) throughout the water column, increasing from ∼20 nM at the surface to a maximum of 72 nM at 60 m and decreasing below. MOx rate measurements at near in situ CH4 concentrations (here measured with 3H-CH4 raising the ambient CH4 pool by <2 nM) showed a similar trend: low rates at the sea surface, increasing to a maximum of ∼2.3 nM day−1 at 60 m, followed by a decrease in the deeper ArW/BSW. In contrast, rate measurements with 14C-CH4 (incubations were spiked with ∼450 nM of 14C-CH4, providing an estimate of the CH4 oxidation at elevated concentration) showed comparably low turnover rates (<1 nM day−1) at 60 m, and peak rates were found in ArW/BSW at ∼100 m water depth, concomitant with increasing 13C values in the residual CH4 pool. Our results indicate that the MOx community in the surface MW is adapted to relatively low CH4 concentrations. In contrast, the activity of the deep-water MOx community is relatively low at the ambient, summertime CH4 concentrations but has the potential to increase rapidly in response to CH4 availability. A similar distinction between surface and deep-water MOx is also suggested by our molecular analyses. The DGGE banding patterns of 16S rRNA gene fragments of the surface MW and deep water were clearly different. A DGGE band related to the known type I MOx bacterium Methylosphaera was observed in deep BWS, but absent in surface MW. Furthermore, the Polymerase Chain Reaction (PCR) amplicons of the deep water with the two functional primers sets pmoA and mxaF showed, in contrast to those of the surface MW, additional products besides the expected one of 530 base pairs (bp). Apparently, different MOx communities have developed in the stratified water masses in Storfjorden, which is possibly related to the spatiotemporal variability in CH4 supply to the distinct water masses.

scholarly journals Different methanotrophic potentials in stratified polar fjord waters (Storfjorden, Spitsbergen) identified by using a combination of methane oxidation techniques

2013 ◽  
Vol 10 (4) ◽  
pp. 6461-6491 ◽  
Author(s):  
S. Mau ◽  
J. Blees ◽  
E. Helmke ◽  
H. Niemann ◽  
E. Damm
Keyword(s):  
Water Column ◽  
Methane Oxidation ◽  
Deep Water ◽  
Oxidation Potential ◽  
Water Masses ◽  
Spatiotemporal Variability ◽  
The Arctic ◽  
Type I ◽  
Turnover Rates ◽  
Arctic Water

Abstract. The bacterially mediated aerobic methane oxidation (MOx) is a key mechanism in controlling methane (CH4) emissions from the world's oceans to the atmosphere. In this study, we investigated MOx in the Arctic fjord Storfjorden (Spitsbergen) by applying a combination of radio-tracer based incubation assays (3H-CH4 and 14H-CH4), stable C-CH4 isotope measurements, and molecular tools (16S rRNA DGGE-fingerprinting, pmoA- and mxaF gene analyses). Strofjorden is stratified in the summertime with melt water (MW) in the upper 60 m of the water column, Arctic water (ArW) between 60–100 m and brine-enriched shelf water (BSW) down to 140 m. CH4 concentrations were supersaturated with respect to the atmospheric equilibrium (∼3 nM) throughout the water column, increasing from ∼20 nM at the surface to a maximum of 72 nM at 60 m and decreasing below. MOx rate measurements at near in situ CH4 concentrations (here measured with 3H-CH4 raising the ambient CH4 pool by <2 nM) showed a similar trend: low rates at the sea surface increasing to a maximum of ∼2.3 nM d−1 at 60 m followed by a decrease in the deeper ArW/BSW. In contrast, rate measurements with 14H-CH4 at elevated CH4 concentrations (incubations were spiked with ∼450 nM of 14H-CH4, providing an estimate of the CH4 oxidation potential) showed comparably low turnover rates (<1 nMd−1) at 60 m, but peaked in ArW/BSW at ∼100 m water depth, concomitant with increasing 14C-values in the residual CH4 pool. Our results indicate that the MOx community in the surface MW is adapted to relatively low CH4 concentrations. In contrast, the activity of the deep water MOx community is relatively low at the ambient, summertime CH4 concentrations but has the potential to increase rapidly in response to CH4 availability. A similar distinction between surface and deep water MOx is also suggested by our molecular analyses. Although, we found pmoA and maxF gene sequences throughout the water column attesting the ubiquitous presence of MOx communities in Storfjorden, deep water amplicons of pmoA and maxF were unusually long. Also a DGGE band related to the known Type I MOx Mehtylosphera was observed in deep BWS, but absent in surface MW. Apparently, different MOx communities have developed in the stratified water masses in Storfjorden, which is possibly related to the spatiotemporal variability in CH4 supply to the distinct water masses.

scholarly journals Different seasonality of pelagic and benthic <i>Thaumarchaeota</i> in the North Sea

2013 ◽  
Vol 10 (8) ◽  
pp. 12593-12624
Author(s):  
N. J. Bale ◽  
L. Villanueva ◽  
E. C. Hopmans ◽  
S. Schouten ◽  
J. S. Sinninghe Damsté
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Column ◽  
North Sea ◽  
Winter Season ◽  
Water Masses ◽  
Rrna Gene ◽  
Southern North Sea ◽  
The North ◽  
Key Factor

Abstract. We have examined the spatial and seasonal distribution of Thaumarchaeota in the water column and sediment of the southern North Sea using the specific intact polar lipid (IPL) hexose, phosphohexose (HPH) crenarchaeol, as well as thaumarchaeotal 16S rRNA gene abundances and expression. In the water column, a higher abundance of Thaumarchaeota was observed in the winter season than in the summer, which is in agreement with previous studies, but this was not the case in the sediment where Thaumarchaeota were most abundant in spring and summer. This observation corresponds well with the idea that ammonia availability is a key factor in thaumarchaeotal niche determination. In the surface waters of the southern North Sea, we observed a spatial variability in HPH crenarchaeol, thaumarchaeotal 16S rRNA gene abundance and transcriptional activity that corresponded well with the different water masses present. In bottom waters, a clear differentiation based on water masses was not observed; instead, we suggest that observed differences in thaumarchaeotal abundance with depth may be related to resuspension from the sediment. This could be due to suspension of benthic Thaumarchaeota to the water column or due to delivery of e.g. resuspended sediment or ammonium to the water column, which could be utilized by pelagic Thaumarchaeota. This study has shown that the seasonality of Thaumarchaeota in water and sediment is different and highlights the importance of water masses, currents and sedimentary processes in determining the spatial abundance of Thaumarchaeota in the southern North Sea.

scholarly journals Diversity and distribution of marine heterotrophic bacteria from a large culture collection

2020 ◽  
Author(s):  
Isabel Sanz-Sáez ◽  
Guillem Salazar ◽  
Elena Lara ◽  
Marta Royo-Llonch ◽  
Elisabet L. Sà ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Column ◽  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
Culture Collection ◽  
The Arctic ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
The North

Abstract BackgroundIsolation of marine microorganisms is fundamental to gather information about their physiology, ecology and genomic content. To date, most of the bacterial isolation efforts have focused on the photic ocean leaving the deep ocean less explored. We have created a marine culture collection of heterotrophic bacteria (MARINHET) using a standard marine medium comprising a total of 1561 bacterial strains, and covering a variety of oceanographic regions from different seasons and years, from 2009 to 2015. Specifically, our marine collection includes isolates from both photic (817) and aphotic layers (744), including the oxygen minimum zone (OMZ, 362) and the bathypelagic (382), from the North Western Mediterranean Sea, the North and South Atlantic Ocean, the Indian, the Pacific, and the Arctic Oceans. With this study, we describe the taxonomy, the phylogenetic diversity and the biogeography of a fraction of the marine culturable microorganisms to enhance our knowledge about which heterotrophic marine isolates are recurrently retrieved across oceans and along all the water column. ResultsThe partial sequencing of the 16S rRNA gene of all isolates revealed that they mainly affiliate with the classes Alphaproteobacteria (35.9%), Gammaproteobacteria (38.6%), and phylum Bacteroidetes (16.5%). In addition, Alteromonas and Erythrobacter genera were found the most common heterotrophic bacteria in the ocean growing in solid agar medium. When comparing photic, OMZ, and bathypelagic isolates sequences, a 37% of them were 100% identical. This percentage increased up to 59% when the comparison was restricted between photic and aphotic sequences (OMZ and bathypelagic together) indicating the ubiquity of some bacterial isolates along the water column. Finally, we isolated three strains related with the genus Mesonia sp. that may represent new species since their whole 16S rRNA gene shared less than 95% sequence similarity with any other culture representative. ConclusionsOverall, this study highlights the relevance of culture dependent studies, with focus on marine isolated bacteria from different oceanographic regions and depths, to provide a more comprehensive view of marine microbial diversity.

scholarly journals Different seasonality of pelagic and benthic Thaumarchaeota in the North Sea

2013 ◽  
Vol 10 (11) ◽  
pp. 7195-7206 ◽  
Author(s):  
N. J. Bale ◽  
L. Villanueva ◽  
E. C. Hopmans ◽  
S. Schouten ◽  
J. S. Sinninghe Damsté
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Column ◽  
North Sea ◽  
Winter Season ◽  
Water Masses ◽  
Rrna Gene ◽  
Southern North Sea ◽  
The North ◽  
Key Factor

Abstract. We have examined the spatial and seasonal distribution of Thaumarchaeota in the water column and sediment of the southern North Sea using the specific intact polar lipid (IPL) hexose-phosphohexose (HPH) crenarchaeol, as well as thaumarchaeotal 16S rRNA gene abundances and expression. In the water column, a higher abundance of Thaumarchaeota was observed in the winter season than in the summer, which is in agreement with previous studies, but this was not the case in the sediment where Thaumarchaeota were most abundant in spring and summer. This observation corresponds well with the idea that ammonia availability is a key factor in thaumarchaeotal niche determination. In the surface waters of the southern North Sea, we observed a spatial variability in HPH crenarchaeol, thaumarchaeotal 16S rRNA gene abundance and transcriptional activity that corresponded well with the different water masses present. In bottom waters, a clear differentiation based on water masses was not observed; instead, we suggest that observed differences in thaumarchaeotal abundance with depth may be related to resuspension from the sediment. This could be due to suspension of benthic Thaumarchaeota to the water column or due to delivery of e.g. resuspended sediment or ammonium to the water column, which could be utilized by pelagic Thaumarchaeota. This study has shown that the seasonality of Thaumarchaeota in water and sediment is different and highlights the importance of water masses, currents and sedimentary processes in determining the spatial abundance of Thaumarchaeota in the southern North Sea.

scholarly journals Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

2014 ◽  
Vol 80 (12) ◽  
pp. 3749-3756 ◽  
Author(s):  
Z. Cardman ◽  
C. Arnosti ◽  
A. Durbin ◽  
K. Ziervogel ◽  
C. Cox ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Chondroitin Sulfate ◽  
Water Column ◽  
Rrna Gene ◽  
Content Type ◽  
Xylan Hydrolysis ◽  
Detection Frequency ◽  
Arctic Fjord

ABSTRACTIn Arctic marine bacterial communities, members of the phylumVerrucomicrobiaare consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of theVerrucomicrobia, together withFlavobacteriaand smaller proportions ofAlpha- andGammaproteobacteria, constituted the most frequently detected bacterioplankton community members in 16S rRNA gene-based clone library analyses of the water column. Parallel measurements in the water column of the activities of six endo-acting polysaccharide hydrolases showed that chondroitin sulfate, laminarin, and xylan hydrolysis accounted for most of the activity. SeveralVerrucomicrobiawater column phylotypes were affiliated with previously sequenced, glycoside hydrolase-rich genomes of individualVerrucomicrobiacells that bound fluorescently labeled laminarin and xylan and therefore constituted candidates for laminarin and xylan hydrolysis. In sediments, the bacterial community was dominated by different lineages ofVerrucomicrobia,Bacteroidetes, andProteobacteriabut also included members of multiple phylum-level lineages not observed in the water column. This community hydrolyzed laminarin, xylan, chondroitin sulfate, and three additional polysaccharide substrates at high rates. Comparisons with data from the same fjord in the previous summer showed that the bacterial community in Smeerenburgfjord changed in composition, most conspicuously in the changing detection frequency ofVerrucomicrobiain the water column. Nonetheless, in both years the community hydrolyzed the same polysaccharide substrates.

scholarly journals Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

2007 ◽  
Vol 53 (3) ◽  
pp. 384-398 ◽  
Author(s):  
Sander K. Heijs ◽  
Ralf R. Haese ◽  
Paul W. J. J. van der Wielen ◽  
Larry J. Forney ◽  
Jan Dirk van Elsas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Methane Oxidation ◽  
Anaerobic Methane Oxidation ◽  
Cold Seep ◽  
Rrna Gene ◽  
Clone Libraries

scholarly journals Methylothermus subterraneus sp. nov., a moderately thermophilic methanotroph isolated from a terrestrial subsurface hot aquifer

2011 ◽  
Vol 61 (11) ◽  
pp. 2646-2653 ◽  
Author(s):  
Hisako Hirayama ◽  
Yohey Suzuki ◽  
Mariko Abe ◽  
Masayuki Miyazaki ◽  
Hiroko Makita ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Type I ◽  
Rrna Gene Sequence ◽  
Intracytoplasmic Membrane ◽  
Moderately Thermophilic

A novel methane-oxidizing bacterium, strain HTM55T, was isolated from subsurface hot aquifer water from a Japanese gold mine. Strain HTM55T was a Gram-negative, aerobic, motile, coccoid bacterium with a single polar flagellum and the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain HTM55T was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 37–65 °C (optimum 55–60 °C). The isolate grew at pH 5.2–7.5 (optimum 5.8–6.3) and with 0–1 % NaCl (optimum 0–0.3 %). The ribulose monophosphate pathway was operative for carbon assimilation. The DNA G+C content was 54.4 mol% and the major fatty acids were C16 : 0 (52.0 %) and C18 : 1ω7c (34.8 %). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HTM55T was closely related to Methylothermus thermalis MYHTT (99.2 % 16S rRNA gene sequence similarity), which is within the class Gammaproteobacteria. However, DNA–DNA relatedness between strain HTM55T and Methylothermus thermalis MYHTT was ≤39 %. On the basis of distinct phylogenetic, chemotaxonomic and physiological characteristics, strain HTM55T represents a novel species of the genus Methylothermus, for which the name Methylothermus subterraneus sp. nov. is proposed. The type strain is HTM55T ( = JCM 13664T = DSM 19750T).

scholarly journals Cyanobacterial communities on Qiyi glacier, Qilian Shan, China

2010 ◽  
Vol 51 (56) ◽  
pp. 135-144 ◽  
Author(s):  
Takahiro Segawa ◽  
Nozomu Takeuchi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Western China ◽  
The Arctic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Community Based ◽  
Glacier Surface ◽  
Snow And Ice

AbstractCyanobacterial communities on a glacier in the Qilian Shan, western China, were investigated using microscopic as well as 16S rRNA and internal transcribed spacer gene analyses. Microscopy revealed that there were abundant cyanobacteria on the entire glacier surface and their community consisted mainly of three morphological types. Low-cycle 16S rRNA gene sequences from six clone libraries were grouped into a total of eight cyanobacterial operational taxonomic units (OTUs), defined as 16S rRNA sequences with similarity of 99%. Although the cyanobacterial community based on morphological types displayed no significant differences among the study sites on the glacier, the community based on OTU groups varied among sites. This inconsistency may be due to simple morphology which might hide a large genetic variability. Phylogenetic analysis revealed that the OTU groups included the orders Oscillatoriales, Chroococcales and unclassified, and the majority of OTUs were Oscillatoriales. From the source environments of the cyanobacterial 16S rRNA gene sequences of each OTU on the glacier estimated by BLAST search (>97% similarity), 39.9% were from soil, 38.2% from fresh water and 1.7% from snow and ice environments. Based on geographical records in the database, all cyanobacterial OTUs were matched to those recorded from the Arctic and Antarctica. The results suggest that the cyanobacterial communities on the glacier are common in cold regions of the world and are likely not to be specialized members of the snow and ice biota but also inhabitants of soil and freshwater environments.

scholarly journals Lutibacter citreus sp. nov., isolated from Arctic surface sediment

2020 ◽  
Vol 70 (5) ◽  
pp. 3154-3161 ◽  
Author(s):  
Zhao-Zhong Du ◽  
Liu-Yan Zhou ◽  
Tao-Jie Wang ◽  
Hui-Rong Li ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Surface Sediment ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
The Arctic ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated 1KV19T, was isolated from a surface sediment sample collected near a bay in the Arctic. Growth of strain 1KV19T occurred in 1–4 % (w/v) NaCl (optimum, 2 %), at 4–35 °C (optimum, 25–30 °C) and at pH 6.5–8.0 (optimum, pH 7.0–7.5). The phylogenetic trees based on the 16S rRNA gene sequences showed that strain 1KV19T was associated with the genus Lutibacter and had the highest 16S rRNA gene sequence similarity to Lutibacter oceani 325-5T with 98.1 % similarity. Similarity values between strain 1KV19T and the type strains of other Lutibacter species were in the range 95.9–97.6 %. The average nucleotide identity and digital DNA–DNA hybridization values between strain 1KV19T and related species of the genus Lutibacter were 76.4–79.1 and 19.9–22.3 %, respectively. The major cellular fatty acids of strain 1KV19T were iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 1 H. The respiratory quinone was MK-6. The major polar lipids of strain 1KV19T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The phenotypic, genotypic and chemotaxonomic differences between strain 1KV19T and its phylogenetic relatives indicate that strain 1KV19T should be regarded as representing a novel species in the genus Lutibacter , for which the name Lutibacter citreus sp. nov. is proposed. The type strain is 1KV19T (=KCTC 62595T=MCCC 1H00307T).

scholarly journals Methanotroph Diversity in Landfill Soil: Isolation of Novel Type I and Type II Methanotrophs Whose Presence Was Suggested by Culture-Independent 16S Ribosomal DNA Analysis

1999 ◽  
Vol 65 (11) ◽  
pp. 4887-4897 ◽  
Author(s):  
Mark G. Wise ◽  
J Vaun McArthur ◽  
Lawrence J. Shimkets
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Ribosomal Dna ◽  
Rrna Gene ◽  
Type I ◽  
Type Ii ◽  
Partial Sequencing ◽  
16S Ribosomal Dna ◽  
Culture Independent ◽  
The 16S Rrna Gene

ABSTRACT The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4.8 versus 6.8), air/CH4/CO2 headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1× nitrate minimal salts [NMS] versus 0.2× NMS). Screening of the isolates showed that the nutrient-rich 1× NMS selected for type I methanotrophs, while the nutrient-poor 0.2× NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobiumgroup, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly publishedMethylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.

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