scholarly journals Basin-scale variability of microbial methanol uptake in the Atlantic Ocean

2018 ◽  
Author(s):  
Stephanie L. Sargeant ◽  
J. Colin Murrell ◽  
Philip D. Nightingale ◽  
Joanna L. Dixon
Keyword(s):  
16S Rrna ◽  
Atlantic Ocean ◽  
Carbon Assimilation ◽  
Inverse Correlation ◽  
Rrna Gene ◽  
Oxidation Rates ◽  
16S Rrna Pyrosequencing ◽  
Basin Scale ◽  
Biogeochemical Provinces ◽  
Depth Stratification

Abstract. Methanol is a climate active gas and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere and seawater. Marine methylotrophs are aerobic bacteria that utilise methanol from seawater as a source of carbon (assimilation) and/or energy (dissimilation). A few spatially limited studies have previously reported methanol oxidation rates in seawater; however the basin-wide ubiquity of marine microbial methanol utilisation remains unknown. This study uniquely combines seawater 14C labelled methanol tracer studies with 16S rRNA pyrosequencing to investigate variability in microbial methanol dissimilation and known methanol utilising bacteria throughout a meridional transect of the Atlantic Ocean between 47° N to 39° S. Microbial methanol dissimilation varied between 0.05–1.68 nmol l−1 h−1 in the top 200 m of the Atlantic Ocean and showed significant variability between biogeochemical provinces. The highest rates of methanol dissimilation were found in the northern subtropical gyre (average 0.99 ± 0.41 nmol l−1 h−1), which were up to eight times greater than other Atlantic regions. Microbial methanol dissimilation rates displayed a significant inverse correlation with heterotrophic bacterial production (determined using 3H-leucine). Despite significant depth stratification of bacterial communities, methanol dissimilation rates showed much greater variability between oceanic provinces compared to depth. There were no significant differences in rates between samples collected under light and dark environmental conditions. The variability in the numbers of SAR11 (16S rRNA gene sequences) were estimated to explain approximately 50 % of the changes in microbial methanol dissimilation rates. We estimate that SAR11 cells in the Atlantic Ocean account for between 0.3–59 % of the rates of methanol dissimilation in Atlantic waters, compared to

scholarly journals Basin-scale variability of microbial methanol uptake in the Atlantic Ocean

2018 ◽  
Vol 15 (16) ◽  
pp. 5155-5167 ◽  
Author(s):  
Stephanie L. Sargeant ◽  
J. Colin Murrell ◽  
Philip D. Nightingale ◽  
Joanna L. Dixon
Keyword(s):  
16S Rrna ◽  
Atlantic Ocean ◽  
Current Knowledge ◽  
Inverse Correlation ◽  
Substantial Contribution ◽  
Rrna Gene ◽  
Methanol Production ◽  
Oxidation Rates ◽  
16S Rrna Pyrosequencing ◽  
Basin Scale

Abstract. Methanol is a climate-active gas and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere and seawater. Marine methylotrophs are aerobic bacteria that utilise methanol from seawater as a source of carbon (assimilation) and/or energy (dissimilation). A few spatially limited studies have previously reported methanol oxidation rates in seawater; however, the basin-wide ubiquity of marine microbial methanol utilisation remains unknown. This study uniquely combines seawater 14C labelled methanol tracer studies with 16S rRNA pyrosequencing to investigate variability in microbial methanol dissimilation and known methanol-utilising bacteria throughout a meridional transect of the Atlantic Ocean between 47° N to 39° S. Microbial methanol dissimilation varied between 0.05 and 1.68 nmol L−1 h−1 in the top 200 m of the Atlantic Ocean and showed significant variability between biogeochemical provinces. The highest rates of methanol dissimilation were found in the northern subtropical gyre (average 0.99±0.41 nmol L−1 h−1), which were up to 8 times greater than other Atlantic regions. Microbial methanol dissimilation rates displayed a significant inverse correlation with heterotrophic bacterial production (determined using 3H-leucine). Despite significant depth stratification of bacterial communities, methanol dissimilation rates showed much greater variability between oceanic provinces compared to depth. There were no significant differences in rates between samples collected under light and dark environmental conditions. The variability in the numbers of SAR11 (16S rRNA gene sequences) were estimated to explain approximately 50 % of the changes in microbial methanol dissimilation rates. We estimate that SAR11 cells in the Atlantic Ocean account for between 0.3 % and 59 % of the rates of methanol dissimilation in Atlantic waters, compared to < 0.01 %–2.3 % for temperate coastal waters. These results make a substantial contribution to our current knowledge and understanding of the utilisation of methanol by marine microbial communities, but highlight the lack of understanding of in situ methanol production mechanisms.

scholarly journals Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis

2018 ◽  
Author(s):  
Raúl Miranda-CasoLuengo ◽  
Junnan Lu ◽  
Erin J. Williams ◽  
Aleksandra A. Miranda-CasoLuengo ◽  
Stephen D. Carrington ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Diversity ◽  
Reproductive Tract ◽  
Fragment Length Polymorphism ◽  
Rrna Gene ◽  
Microbial Succession ◽  
Delayed Differentiation ◽  
Early Postpartum ◽  
16S Rrna Pyrosequencing ◽  
The 16S Rrna Gene

AbstractBacterial infection of the uterus is a normal event after parturition. While the healthy cow achieves uterine clearance early postpartum, cows unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA Pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This microbial succession is likely associated to early clearance in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession in cows developing endometritis at 7 DPP.

scholarly journals Tree phyllospheres are a habitat for diverse populations of CO-oxidising bacteria

2021 ◽  
Author(s):  
Jess L. Palmer ◽  
Sally Hilton ◽  
Emma Picot ◽  
Gary D. Bending ◽  
Hendrik Schäfer
Keyword(s):  
Carbon Monoxide ◽  
16S Rrna ◽  
Urban Areas ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Co Dehydrogenase ◽  
Diverse Range ◽  
Oxidation Rates ◽  
Genes Encoding ◽  
Phyllosphere Bacteria

AbstractBackgroundCarbon monoxide (CO) is a naturally occurring and ubiquitous trace gas in the atmosphere. As a product of combustion processes, it can reach concentrations in the mg/m3 range in urban areas, contributing to air pollution. Aerobic CO-degrading microorganisms have been identified previously and are thought to remove ~370 Tg of CO in soils and oceans per year. Based on the presence of genes encoding subunits of the enzyme carbon monoxide dehydrogenase in metagenomes, a large fraction of soil bacteria may have the potential for CO degradation. The activity and diversity of CO-degrading microorganisms in above ground habitats such as the phyllosphere has not been addressed, however, and their potential role in global CO cycling remains unknown.ResultsMonitoring of CO-degradation in leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Leaf washes of I. aquifolium had significantly higher CO oxidation rates than those of C. monogyna. A diverse range of bacterial taxa were identified as candidate CO-oxidising taxa based on high-throughput sequencing and multivariate statistical analysis of 16S rRNA amplicon data, as well as functional diversity analysis based on coxL, the gene encoding the large subunit of CO-dehydrogenase. Candidate CO-oxidising taxa included a range of Rhizobiales and Burkholderiales, of which the Burkholderiales OTUs were abundant colonisers of the phyllosphere at the time of sampling, as indicated by 16S rRNA gene sequencing. In addition, an estimated 12.4% of leaf OTUs in samples of this study contained coxL homologues, based on their predicted genomes. We also mined data of publicly available phyllosphere metagenomes for genes encoding subunits of CO-dehydrogenase which indicated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidising Phyllobacteriaceae strain was isolated from phyllosphere samples which contains genes encoding both CODH as well as a RuBisCO.ConclusionsThe phyllosphere, a vast microbial habitat, supports diverse and potentially abundant CO-oxidising bacteria. These findings identify tree phyllosphere bacteria as a potential sink for atmospheric CO and highlight the need for a more detailed assessment of phyllosphere microbial communities in the global cycle of CO.

scholarly journals Methanotroph community structure and processes in an inland river affected by natural gas macro-seeps

2021 ◽  
Vol 97 (10) ◽  
Author(s):  
Ryan M Burrows ◽  
Jodie van de Kamp ◽  
Levente Bodrossy ◽  
Michael Venarsky ◽  
Jack Coates-Marnane ◽  
...  
Keyword(s):  
Natural Gas ◽  
16S Rrna ◽  
Temporal Variation ◽  
Methane Oxidation ◽  
Gene Analysis ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Oxidation Rates ◽  
Inland River ◽  
Eastern Australia

ABSTRACT Methane availability in freshwaters is usually associated with spatial-temporal variation in methanogenesis. Unusually, however, natural gas macro-seeps occur along the Condamine River in eastern Australia which elevate ambient water-column methane concentrations more than 3,000 times. We quantified the spatial-temporal variation in methane oxidation rates and the total microbial and methanotroph community composition (through the amplification and sequencing of 16S rRNA and particulate methane monooxygenase (pmoA) genes), and the factors mediating this variation, in reaches with and without macro-seeps. Sediment methane oxidation rates were, on average, 29 times greater, and the abundance of methanotrophs significantly higher, in the vicinity of methane macro-seeps compared to non-seep sites. Methylocystis was the most abundant methanotroph group at all sites, but type Ib methanotrophs showed the steepest increase in abundance at seep sites. pmoA gene analysis identified these as clade 501, while 16S rRNA gene analysis identified these as the closely related genus Methylocaldum. Sediment methane oxidation rates and the relative abundance and composition of benthic microbial communities were primarily influenced by methane availability which was in turn related to variation in river discharge. Methane-derived carbon may be an important energy source for the aquatic food webs in reaches affected by natural gas macro-seeps.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Marine mammals are natural hosts of Oceanivirga salmonicida, a bacterial pathogen of Atlantic salmon

2020 ◽  
Vol 139 ◽  
pp. 161-174
Author(s):  
R Palmer ◽  
GTA Fleming ◽  
S Glaeser ◽  
T Semmler ◽  
A Flamm ◽  
...  
Keyword(s):  
16S Rrna ◽  
Atlantic Salmon ◽  
16S Rrna Gene ◽  
Marine Mammals ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Common Dolphin ◽  
Stenella Coeruleoalba ◽  
Striped Dolphin ◽  
Natural Hosts

During 1992 and 1993, a bacterial disease occurred in a seawater Atlantic salmon Salmo salar farm, causing serious mortalities. The causative agent was subsequently named as Oceanivirga salmonicida, a member of the Leptotrichiaceae. Searches of 16S rRNA gene sequence databases have shown sequence similarities between O. salmonicida and uncultured bacterial clones from the digestive tracts of marine mammals. In the current study, oral samples were taken from stranded dolphins (common dolphin Delphinus delphis, striped dolphin Stenella coeruleoalba) and healthy harbour seals Phoca vitulina. A bacterium with growth characteristics consistent with O. salmonicida was isolated from a common dolphin. The isolate was confirmed as O. salmonicida, by comparisons to the type strain, using 16S rRNA gene, gyrB, groEL, and recA sequence analyses, average nucleotide identity analysis, and MALDI-TOF mass spectrometry. Metagenomic analysis indicated that the genus Oceanivirga represented a significant component of the oral bacterial microbiomes of the dolphins and seals. However, sequences consistent with O. salmonicida were only found in the dolphin samples. Analyses of marine mammal microbiome studies in the NCBI databases showed sequences consistent with O. salmonicida from the common dolphin, striped dolphin, bottlenose dolphin Tursiops truncatus, humpback whale Megaptera novaeangliae, and harbour seal. Sequences from marine environmental studies in the NCBI databases showed no sequences consistent with O. salmonicida. The findings suggest that several species of marine mammals are natural hosts of O. salmonicida.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

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