scholarly journals Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks

2021 ◽  
Author(s):  
Ömer K. Coskun ◽  
Aurèle Vuillemin ◽  
Florence Schubotz ◽  
Frieder Klein ◽  
Susanna E. Sichel ◽  
...  
Keyword(s):  
Subduction Zones ◽  
Carbon Assimilation ◽  
Oceanic Lithosphere ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ultramafic Rocks ◽  
Microbial Life ◽  
Order Of Magnitude ◽  
Mid Atlantic Ridge

AbstractThermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.

scholarly journals Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

2012 ◽  
Vol 79 (2) ◽  
pp. 424-433 ◽  
Author(s):  
Maialen Barret ◽  
Nathalie Gagnon ◽  
Martin L. Kalmokoff ◽  
Edward Topp ◽  
Yris Verastegui ◽  
...  
Keyword(s):  
Storage Tank ◽  
Swine Manure ◽  
Carbon Assimilation ◽  
Methanogenic Archaea ◽  
Methane Emissions ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Manure Storage

ABSTRACTMethane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-13C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplifiedmcrAgenes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of13C into DNA was detectable atin situacetate concentrations (∼7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the13C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of themcrAand 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded toMethanoculleusspp. Our results demonstrate that uncultivated methanogenic archaea related toMethanoculleusspp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested thatMethanoculleusspp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.

scholarly journals Biphenyl-Metabolizing Bacteria in the Rhizosphere of Horseradish and Bulk Soil Contaminated by Polychlorinated Biphenyls as Revealed by Stable Isotope Probing

2009 ◽  
Vol 75 (20) ◽  
pp. 6471-6477 ◽  
Author(s):  
Ondrej Uhlik ◽  
Katerina Jecna ◽  
Martina Mackova ◽  
Cestmir Vlcek ◽  
Miluse Hroudova ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
Polychlorinated Biphenyls ◽  
Stable Isotope Probing ◽  
Amino Acid Sequences ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Soil Environment ◽  
Α Subunits

ABSTRACT DNA-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (Armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (PCBs) compared to members of the microbial community in initial, uncultivated bulk soil. On the basis of early and recurrent detection of their 16S rRNA genes in clone libraries constructed from [13C]DNA, Hydrogenophaga spp. appeared to dominate biphenyl catabolism in the horseradish rhizosphere soil, whereas Paenibacillus spp. were the predominant biphenyl-utilizing bacteria in the initial bulk soil. Other bacteria found to derive carbon from biphenyl in this nutrient-amended microcosm-based study belonged mostly to the class Betaproteobacteria and were identified as Achromobacter spp., Variovorax spp., Methylovorus spp., or Methylophilus spp. Some bacteria that were unclassified at the genus level were also detected, and these bacteria may be members of undescribed genera. The deduced amino acid sequences of the biphenyl dioxygenase α subunits (BphA) from bacteria that incorporated [13C]into DNA in 3-day incubations of the soils with [13C]biphenyl are almost identical to that of Pseudomonas alcaligenes B-357. This suggests that the spectrum of the PCB congeners that can be degraded by these enzymes may be similar to that of strain B-357. These results demonstrate that altering the soil environment can result in the participation of different bacteria in the metabolism of biphenyl.

Distribution and evolution of uranium in the oceanic lithosphere

1979 ◽  
Vol 291 (1381) ◽  
pp. 423-431 ◽  
Keyword(s):  
Sea Water ◽  
Oceanic Lithosphere ◽  
Uranium Content ◽  
Major And Trace Elements ◽  
Ultramafic Rocks ◽  
Layer 2 ◽  
Secondary Enrichment ◽  
Layer 4 ◽  
Mid Atlantic Ridge ◽  
Fractionation Trend

Induced fission track techniques permit us to determine quantitatively the microscopic distribution of uranium in rocks, in their constituent minerals, and in percolating fluids. Both primary magmatic variations and secondary mobilization of uranium can be discerned. Concentrations of uranium in phenocrysts and fresh glasses of oceanic basalts and gabbros are very low (2-80 parts/10 9 ) and are comparable to concentrations in the same minerals of the associated ultramafic rocks. Variations with depth in D.S.D.P. holes show several distinct cyclic variations of uranium, accompanied by parallel trends in some major and trace elements. In Hole 332B (mid-Atlantic ridge, 36 °N), uranium and other elements can be shown to fall into two distinct groupings, each group following its own characteristic fractionation trend, suggesting that two distinct magmas differentiated independently beneath the median valley, the two magmas alternating in their contribution to the formation of oceanic layer 2. Earlier investigations of the uranium distribution in surface pillows and other dredged rocks exposed to sea water had shown that, owing to halmyrolysis, the uranium concentration increases systematically with distance from the axis of a midoceanic ridge. Subsequent investigations on rocks drilled from horizons deeper into oceanic layer 2 indicate that secondary enrichment or redistribution of uranium is confined to specific zones of altered basalt, near fractures, pillow and flow margins, and especially along horizontal planes of breccias and sediments in between massive flow where convective water circulation is thought to occur. Ultramafic rocks from the base of layer 3 and top of layer 4 are also enriched in uranium when hydrated by sea water during the process of serpentinization. A combination of these processes may double the uranium content of an oceanic lithospheric plate between the time of its formation and its eventual subduction.

scholarly journals Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

2013 ◽  
Vol 80 (5) ◽  
pp. 1684-1691 ◽  
Author(s):  
Baozhan Wang ◽  
Yan Zheng ◽  
Rong Huang ◽  
Xue Zhou ◽  
Dongmei Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
Buoyant Density ◽  
Stable Isotope Probing ◽  
Acidic Soil ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTAll cultivated ammonia-oxidizing archaea (AOA) within theNitrososphaeracluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence ofNitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth ofNitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis ofamoAgenes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that13CO2assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both13C-labeledamoAand 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strainsNitrososphaera viennensisEN76 and JG1 within theNitrososphaeracluster. Our results provide strong evidence for the adaptive growth ofNitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

scholarly journals Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)

2018 ◽  
pp. 284
Author(s):  
PARASKEVI POLYMENAKOU ◽  
MANOLIS MANDALAKIS ◽  
THANOS DAILIANIS ◽  
CHARALAMPOS DIMITRIADIS ◽  
MATEJ MEDVECKY ◽  
...  
Keyword(s):  
Room Temperature ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Limited Information ◽  
Preliminary Assessment ◽  
Microbial Life ◽  
Incertae Sedis ◽  
Marine Caves ◽  
Different Types ◽  
Anaerobic Microbial Community

Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation.

scholarly journals Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3527-3534 ◽  
Author(s):  
Ashraf Khalifa ◽  
Chol Gyu Lee ◽  
Takuya Ogiso ◽  
Chihoko Ueno ◽  
Dayéri Dianou ◽  
...  
Keyword(s):  
Type Strain ◽  
Carbon Assimilation ◽  
Membrane System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Type I ◽  
Intracytoplasmic Membrane ◽  
Respiratory Quinone ◽  
Rice Rhizosphere ◽  
The Family

An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus–Methylocaldum–Methyloparacoccus–Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T).

scholarly journals Origin and Diversity of Metabolically Active Gut Bacteria from Laboratory-Bred Larvae of Manduca sexta (Sphingidae, Lepidoptera, Insecta)

2008 ◽  
Vol 74 (23) ◽  
pp. 7189-7196 ◽  
Author(s):  
Nicole Brinkmann ◽  
Rainer Martens ◽  
Christoph C. Tebbe
Keyword(s):  
16S Rrna ◽  
Manduca Sexta ◽  
Metabolic Activity ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Cells ◽  
Rt Pcr ◽  
Tobacco Leaves ◽  
Active Bacteria

ABSTRACT Cultivation-independent analyses based on genetic profiling of partial bacterial 16S rRNA genes by PCR-single-strand conformation polymorphism (PCR-SSCP), reverse transcriptase (RT)-PCR-SSCP of the 16S rRNA itself, and stable isotope probing (SIP), followed by RT-PCR-SSCP, were applied to characterize the diversity of metabolically active bacteria in the larval gut of Manduca sexta bred on tobacco leaves under greenhouse conditions. For SIP, hatching larvae were fed with leaves from tobacco plants grown in a 13CO2-enriched atmosphere. Dominant SSCP bands were sequenced and phylogenetically analyzed. Only one major gut colonizer, an Enterococcus relative, was detected; it occurred in the heavy RNA fraction, demonstrating its metabolic activity, and it originated from eggs, where its metabolic activity was also indicated by rRNA-based SSCP profiles. In contrast, a Citrobacter sedlakii relative was detected on eggs by DNA-SSCP, but rRNA-SSCP and SIP-rRNA-SSCP were negative, suggesting that these bacterial cells were inactive. A Burkholderia relative was dominant and metabolically active on the tobacco leaves but inactive inside the gut, where it was also quantitatively reduced, as suggested by lower band intensities in the DNA-based SSCP profiles. SIP-RNA-SSCP detected another metabolically active gut bacterium (Enterobacter sp.) and more bacteria in the light RNA fraction, indicating low or no metabolic activity of the latter inside the gut. We conclude that the larval gut supported only a low diversity of metabolically active bacteria.

scholarly journals Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

2016 ◽  
Vol 82 (8) ◽  
pp. 2363-2371 ◽  
Author(s):  
Kaitlin C. Esson ◽  
Xueju Lin ◽  
Deepak Kumaresan ◽  
Jeffrey P. Chanton ◽  
J. Colin Murrell ◽  
...  
Keyword(s):  
Dry Weight ◽  
Amplicon Sequencing ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Type I ◽  
Type Ii ◽  
Content Type ◽  
Methane Consumption ◽  
Field Samples

ABSTRACTThe objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil−1day−1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4%in situto 25 to 36% after 8 to 14 days. Phylogenetic analysis of the13C-enriched DNA fractions revealed that the active methanotrophs were dominated by the generaMethylocystis(type II;Alphaproteobacteria),Methylomonas, andMethylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed forpmoAin surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNApmoAamplicons from field samples confirmed that the dominant active methanotrophs wereMethylocystisandMethylomonas. Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the generaMethylomonasandMethylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.

scholarly journals Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

2015 ◽  
Vol 81 (14) ◽  
pp. 4607-4615 ◽  
Author(s):  
Xiaoqing Wang ◽  
Christine E. Sharp ◽  
Gareth M. Jones ◽  
Stephen E. Grasby ◽  
Allyson L. Brady ◽  
...  
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
Soil Bacteria ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Degrading Bacteria ◽  
Aerobic Soil

ABSTRACTThe exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced byGluconacetobacter xylinusor the EPS produced byBeijerinckia indica. The latter is a heteropolysaccharide comprised primarily ofl-guluronic acid,d-glucose, andd-glycero-d-mannoheptose.13C-labeled EPS and13C-labeled cellulose were purified from bacterial cultures grown on [13C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from13C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However,B. indicaEPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylumPlanctomycetes. In one incubation, members of thePlanctomycetesmade up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo- or monosaccharides, the predominance ofPlanctomycetessuggested that they were primary degraders of EPS. Other bacteria assimilatingB. indicaEPS included members of theVerrucomicrobia, candidate division OD1, and theArmatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species.

Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria

2014 ◽  
Vol 60 (7) ◽  
pp. 469-476 ◽  
Author(s):  
Lee J. Pinnell ◽  
Eric Dunford ◽  
Patrick Ronan ◽  
Martina Hausner ◽  
Josh D. Neufeld
Keyword(s):  
Glycoside Hydrolase ◽  
Multiple Displacement Amplification ◽  
Arctic Tundra ◽  
Stable Isotope Probing ◽  
Glycoside Hydrolases ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Metagenomic Analysis ◽  
Rrna Genes ◽  
Cellulolytic Bacteria

Bacteria responsible for cellulose hydrolysis in situ are poorly understood, largely because of the relatively recent development of cultivation-independent methods for their detection and characterization. This study combined DNA stable-isotope probing (DNA-SIP) and metagenomics for identifying active bacterial communities that assimilated carbon from glucose and cellulose in Arctic tundra microcosms. Following DNA-SIP, bacterial fingerprint analysis of gradient fractions confirmed isotopic enrichment. Sequenced fingerprint bands and clone library analysis of 16S rRNA genes identified active bacterial taxa associated with cellulose-associated labelled DNA, including Bacteroidetes (Sphingobacteriales), Betaproteobacteria (Burkholderiales), Alphaproteobacteria (Caulobacteraceae), and Chloroflexi (Anaerolineaceae). We also compared glycoside hydrolase metagenomic profiles from bulk soil and heavy DNA recovered from DNA-SIP incubations. Active populations consuming [13C]glucose and [13C]cellulose were distinct, based on ordinations of light and heavy DNA. Metagenomic analysis demonstrated a ∼3-fold increase in the relative abundance of glycoside hydrolases in DNA-SIP libraries over bulk-soil libraries. The data also indicate that multiple displacement amplification introduced bias into the resulting metagenomic analysis. This research identified DNA-SIP incubation conditions for glucose and cellulose that were suitable for Arctic tundra soil and confirmed that DNA-SIP enrichment can increase target gene frequencies in metagenomic libraries.

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