scholarly journals Anaerobic Oxidization of Methane in a Minerotrophic Peatland: Enrichment of Nitrite-Dependent Methane-Oxidizing Bacteria

2012 ◽  
Vol 78 (24) ◽  
pp. 8657-8665 ◽  
Author(s):  
Baoli Zhu ◽  
Gijs van Dijk ◽  
Christian Fritz ◽  
Alfons J. P. Smolders ◽  
Arjan Pol ◽  
...  
Keyword(s):  
16S Rrna ◽  
Transition Zone ◽  
Anaerobic Oxidation Of Methane ◽  
Potential Contribution ◽  
Content Type ◽  
Cell Numbers ◽  
Oxidation Of Methane ◽  
Methane Oxidizing Bacteria ◽  
Minerotrophic Peatland

ABSTRACTThe importance of anaerobic oxidation of methane (AOM) as a methane sink in freshwater systems is largely unexplored, particularly in peat ecosystems. Nitrite-dependent anaerobic methane oxidation (n-damo) was recently discovered and reported to be catalyzed by the bacterium “CandidatusMethylomirabilis oxyfera,” which is affiliated with the NC10 phylum. So far, several “Ca. Methylomirabilis oxyfera” enrichment cultures have been obtained using a limited number of freshwater sediments or wastewater treatment sludge as the inoculum. In this study, using stable isotope measurements and porewater profiles, we investigated the potential of n-damo in a minerotrophic peatland in the south of the Netherlands that is infiltrated by nitrate-rich ground water. Methane and nitrate profiles suggested that all methane produced was oxidized before reaching the oxic layer, and NC10 bacteria could be active in the transition zone where countergradients of methane and nitrate occur. Quantitative PCR showed high NC10 bacterial cell numbers at this methane-nitrate transition zone. This soil section was used to enrich the prevalent NC10 bacteria in a continuous culture supplied with methane and nitrite at anin situpH of 6.2. An enrichment of nitrite-reducing methanotrophic NC10 bacteria was successfully obtained. Phylogenetic analysis of retrieved 16S rRNA andpmoAgenes showed that the enriched bacteria were very similar to the ones foundin situand constituted a new branch of NC10 bacteria with an identity of less than 96 and 90% to the 16S rRNA andpmoAgenes of “Ca. Methylomirabilis oxyfera,” respectively. The results of this study expand our knowledge of the diversity and distribution of NC10 bacteria in the environment and highlight their potential contribution to nitrogen and methane cycles.

scholarly journals Simultaneous Nitrite-Dependent Anaerobic Methane and Ammonium Oxidation Processes

2011 ◽  
Vol 77 (19) ◽  
pp. 6802-6807 ◽  
Author(s):  
Francisca A. Luesken ◽  
Jaime Sánchez ◽  
Theo A. van Alen ◽  
Janeth Sanabria ◽  
Huub J. M. Op den Camp ◽  
...  
Keyword(s):  
Enrichment Culture ◽  
Anammox Bacteria ◽  
Anaerobic Oxidation Of Methane ◽  
Ammonium Oxidation ◽  
Content Type ◽  
Oxidation Of Methane ◽  
Activity Measurements ◽  
Near Future ◽  
Damo Bacteria

ABSTRACTNitrite-dependent anaerobic oxidation of methane (n-damo) and ammonium (anammox) are two recently discovered processes in the nitrogen cycle that are catalyzed by n-damo bacteria, including “CandidatusMethylomirabilis oxyfera,” and anammox bacteria, respectively. The feasibility of coculturing anammox and n-damo bacteria is important for implementation in wastewater treatment systems that contain substantial amounts of both methane and ammonium. Here we tested this possible coexistence experimentally. To obtain such a coculture, ammonium was fed to a stable enrichment culture of n-damo bacteria that still contained some residual anammox bacteria. The ammonium supplied to the reactor was consumed rapidly and could be gradually increased from 1 to 20 mM/day. The enriched coculture was monitored by fluorescencein situhybridization and 16S rRNA andpmoAgene clone libraries and activity measurements. After 161 days, a coculture with about equal amounts of n-damo and anammox bacteria was established that converted nitrite at a rate of 0.1 kg-N/m3/day (17.2 mmol day−1). This indicated that the application of such a coculture for nitrogen removal may be feasible in the near future.

scholarly journals Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

2011 ◽  
Vol 77 (24) ◽  
pp. 8635-8647 ◽  
Author(s):  
Man-Young Jung ◽  
Soo-Je Park ◽  
Deullae Min ◽  
Jin-Seog Kim ◽  
W. Irene C. Rijpstra ◽  
...  
Keyword(s):  
16S Rrna ◽  
Agricultural Soil ◽  
Ammonia Oxidizing Bacteria ◽  
Sequence Comparisons ◽  
Soil Nitrification ◽  
Content Type ◽  
Group I ◽  
Single Sequence

ABSTRACTSoil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizingArchaeafrom soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescencein situhybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaealamoAgenes featured a single sequence each. No bacterialamoAgenes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of13C intoArchaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “CandidatusNitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2%amoAgene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “CandidatusNitrosoarchaeum koreensis.”

scholarly journals Equine Stomachs Harbor an Abundant and Diverse Mucosal Microbiota

2012 ◽  
Vol 78 (8) ◽  
pp. 2522-2532 ◽  
Author(s):  
G. A. Perkins ◽  
H. C. den Bakker ◽  
A. J. Burton ◽  
H. N. Erb ◽  
S. P. McDonough ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
16S Rrna ◽  
Gastric Disease ◽  
Close Apposition ◽  
Content Type ◽  
Biopsy Specimens ◽  
Dominant Bacteria ◽  
Cluster 2

ABSTRACTLittle is known about the gastric mucosal microbiota in healthy horses, and its role in gastric disease has not been critically examined. The present study used a combination of 16S rRNA bacterial tag-encoded pyrosequencing (bTEFAP) and fluorescencein situhybridization (FISH) to characterize the composition and spatial distribution of selected gastric mucosal microbiota of healthy horses. Biopsy specimens of the squamous, glandular, antral, and any ulcerated mucosa were obtained from 6 healthy horses by gastroscopy and from 3 horses immediately postmortem. Pyrosequencing was performed on biopsy specimens from 6 of the horses and yielded 53,920 reads in total, with 631 to 4,345 reads in each region per horse. The microbiome segregated into two distinct clusters comprised of horses that were stabled, fed hay, and sampled at postmortem (cluster 1) and horses that were pastured on grass, fed hay, and biopsied gastroscopically after a 12-h fast (cluster 2). The types of bacteria obtained from different anatomic regions clustered by horse rather than region. The dominant bacteria in cluster 1 wereFirmicutes(>83% reads/sample), mainlyStreptococcusspp.,Lactobacillusspp. and,Sarcinaspp. Cluster 2 was more diverse, with predominantlyProteobacteria,Bacteroidetes, andFirmicutes, consisting ofActinobacillusspp.Moraxellaspp.,Prevotellaspp., andPorphyromonasspp.Helicobactersp. sequences were not identified in any of 53,920 reads. FISH (n= 9) revealed bacteria throughout the stomach in close apposition to the mucosa, with significantly moreStreptococcusspp. present in the glandular region of the stomach. The equine stomach harbors an abundant and diverse mucosal microbiota that varies by individual.

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 Anaerobic oxidation of methane: an underappreciated aspect of methane cycling in peatland ecosystems?

2010 ◽  
Vol 7 (5) ◽  
pp. 7945-7983 ◽  
Author(s):  
K. A. Smemo ◽  
J. B. Yavitt
Keyword(s):  
Large Body ◽  
Conclusive Evidence ◽  
Future Research ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Ch4 Oxidation ◽  
Oxidation Of Methane ◽  
Ch4 Production

Abstract. Despite a large body of literature on microbial anaerobic oxidation of methane (AOM) in marine sediments and saline waters and its importance to the global methane (CH4) cycle, until recently little work has addressed the potential occurrence and importance of AOM in non-marine systems. This is particularly true for peatlands, which represent both a massive sink for atmospheric CO2 and a significant source of atmospheric CH4. Our knowledge of this process in peatlands is inherently limited by the methods used to study CH4 dynamics in soil and sediment and the assumption that there are no anaerobic sinks for CH4 in these systems. Studies suggest that AOM is CH4-limited and difficult to detect in potential CH4 production assays against a background of CH4 production. In situ rates also might be elusive due to background rates of aerobic CH4 oxidation and the difficulty in separating net and gross process rates. Conclusive evidence for the electron acceptor in this process has not been presented. Nitrate and sulfate are both plausible and favorable electron acceptors, as seen in other systems, but there exist theoretical issues related to the availability of these ions in peatlands and only circumstantial evidence suggests that these pathways are important. Iron cycling is important in many wetland systems, but recent evidence does not support the notion of CH4 oxidation via dissimilatory Fe(III) reduction or a CH4 oxidizing archaea in consortium with an Fe(III) reducer. Calculations based on published rates demonstrate that AOM might be a significant and underappreciated constraint on the global CH4 cycle, although much about the process in unknown, in vitro rates may not relate well to in situ rates, and projections based on those rates are fraught with uncertainty. We suggest electron transfer mechanisms, C flow and pathways, and quantifying in situ peatland AOM rates as the highest priority topics for future research.

scholarly journals Anaerobic methanotrophic communities thrive in deep submarine permafrost

2017 ◽  
Author(s):  
Matthias Winkel ◽  
Julia Mitzscherling ◽  
Pier P. Overduin ◽  
Fabian Horn ◽  
Maria Winterfeld ◽  
...  
Keyword(s):  
Low Temperatures ◽  
Marker Genes ◽  
Anaerobic Oxidation Of Methane ◽  
Oxidation Of Methane ◽  
Iron Manganese ◽  
Archaeal Communities ◽  
Permafrost Sediments ◽  
Methane Concentrations ◽  
Methanotrophic Communities

AbstractThawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic (ANME-2a/b, ANME-2d) assemblages in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in AOM we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential anaerobic oxidation of methane (AOM) coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate AOM communities in submarine permafrost sediments potentially active at low temperatures. Extrapolating potential AOM rates, when scaled to the total area of expected submarine permafrost thaw, reveals that methane could be consumed at rates between 8 and 120 Tg C per year, which is comparable to other AOM habitats such as seeps, continental SMTZ and wetlands. We thus propose that AOM is active where submarine permafrost thaws and needs to be accounted for in global methane budgets.

scholarly journals Anaerobic Oxidation of Methane Coupled to Nitrite Reduction by Halophilic Marine NC10 Bacteria

2015 ◽  
Vol 81 (16) ◽  
pp. 5538-5545 ◽  
Author(s):  
Zhanfei He ◽  
Sha Geng ◽  
Chaoyang Cai ◽  
Shuai Liu ◽  
Yan Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Methane Oxidation ◽  
Nitrite Reduction ◽  
Substrate Affinity ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Activity ◽  
Optimal Salinity ◽  
Oxidation Of Methane

ABSTRACTAnaerobic oxidation of methane (AOM) coupled to nitrite reduction is a novel AOM process that is mediated by denitrifying methanotrophs. To date, enrichments of these denitrifying methanotrophs have been confined to freshwater systems; however, the recent findings of 16S rRNA andpmoAgene sequences in marine sediments suggest a possible occurrence of AOM coupled to nitrite reduction in marine systems. In this research, a marine denitrifying methanotrophic culture was obtained after 20 months of enrichment. Activity testing and quantitative PCR (qPCR) analysis were then conducted and showed that the methane oxidation activity and the number of NC10 bacteria increased correlatively during the enrichment period. 16S rRNA gene sequencing indicated that only bacteria in group A of the NC10 phylum were enriched and responsible for the resulting methane oxidation activity, although a diverse community of NC10 bacteria was harbored in the inoculum. Fluorescencein situhybridization showed that NC10 bacteria were dominant in the enrichment culture after 20 months. The effect of salinity on the marine denitrifying methanotrophic culture was investigated, and the apparent optimal salinity was 20.5‰, which suggested that halophilic bacterial AOM coupled to nitrite reduction was obtained. Moreover, the apparent substrate affinity coefficients of the halophilic denitrifying methanotrophs were determined to be 9.8 ± 2.2 μM for methane and 8.7 ± 1.5 μM for nitrite.

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 Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

2016 ◽  
Vol 113 (28) ◽  
pp. E4069-E4078 ◽  
Author(s):  
Roland Hatzenpichler ◽  
Stephanie A. Connon ◽  
Danielle Goudeau ◽  
Rex R. Malmstrom ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Bacterial Consortia ◽  
Symbiotic Relationships ◽  
Oxidation Of Methane ◽  
Translational Activity ◽  
Rrna Gene Sequencing

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.

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