scholarly journals Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments

2019 ◽  
Author(s):  
Guangyi Su ◽  
Jakob Zopfi ◽  
Haoyi Yao ◽  
Lea Steinle ◽  
Helge Niemann ◽  
...  
Keyword(s):  
Lake Sediments ◽  
16S Rrna Gene Sequencing ◽  
Electron Acceptors ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Sequencing Data ◽  
Oxidation Of Methane ◽  
Freshwater Habitats ◽  
Rrna Gene Sequencing

AbstractAnaerobic oxidation of methane (AOM) by methanotrophic archaea is an important sink of this greenhouse gas in marine sediments. However, evidence for AOM in freshwater habitats is rare, and little is known about the pathways, electron acceptors and microbes involved. Here, we show that AOM occurs in anoxic sediments of a lake in southern Switzerland (Lake Cadagno). Combined AOM-rate and 16S rRNA gene-sequencing data suggest thatCandidatusMethanoperedens archaea are responsible for the observed methane oxidation. Members of the Methanoperedenaceae family were previously reported to conduct nitrate- or iron/manganese-dependent AOM. However, we demonstrate for the first time that the methanotrophic archaea do not necessarily rely upon these oxidants as terminal electron acceptors directly, but mainly perform canonical sulfate-dependent AOM, which under sulfate-starved conditions can be supported by metal (Mn, Fe) oxides through oxidation of reduced sulfur species to sulfate. The correspondence of high abundances of Desulfobulbaceae andCandidatusMethanoperedens at the same sediment depth confirm the interdependence of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria. The relatively high abundance and widespread distribution ofCandidatusMethanoperedens in lake sediments highlight their potentially important role in mitigating methane emissions from terrestrial freshwater environments to the atmosphere, analogous to ANME-1, -2 and -3 in marine settings.

scholarly journals Anaerobic Oxidation of Methane in Sediments of Lake Constance, an Oligotrophic Freshwater Lake

2011 ◽  
Vol 77 (13) ◽  
pp. 4429-4436 ◽  
Author(s):  
Jörg S. Deutzmann ◽  
Bernhard Schink
Keyword(s):  
Methane Oxidation ◽  
Electron Acceptors ◽  
Molecular Techniques ◽  
Freshwater Lake ◽  
Lake Constance ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Terminal Electron Acceptor ◽  
Oxidation Of Methane ◽  
Freshwater Habitats

ABSTRACTAnaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor has been reported for various environments, including freshwater habitats, and also, nitrate and nitrite were recently shown to act as electron acceptors for methane oxidation in eutrophic freshwater habitats. Radiotracer experiments with sediment material of Lake Constance, an oligotrophic freshwater lake, were performed to follow14CO2formation from14CH4in sediment incubations in the presence of different electron acceptors, namely, nitrate, nitrite, sulfate, or oxygen. Whereas14CO2formation without and with sulfate addition was negligible, addition of nitrate increased14CO2formation significantly, suggesting that AOM could be coupled to denitrification. Nonetheless, denitrification-dependent AOM rates remained at least 1 order of magnitude lower than rates of aerobic methane oxidation. Using molecular techniques, putative denitrifying methanotrophs belonging to the NC10 phylum were detected on the basis of thepmoAand 16S rRNA gene sequences. These findings show that sulfate-dependent AOM was insignificant in Lake constant sediments. However, AOM can also be coupled to denitrification in this oligotrophic freshwater habitat, providing first indications that this might be a widespread process that plays an important role in mitigating methane emissions.

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.

The evolvement of anaerobic oxidation of methane in fresh water sediments

2020 ◽  
Author(s):  
Hanni Vigderovich ◽  
Werner Eckert ◽  
Orit Sivan
Keyword(s):  
Lake Sediments ◽  
Marine Sediments ◽  
Electron Acceptors ◽  
Lake Kinneret ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Ongoing Research ◽  
Oxidation Of Methane ◽  
Anoxic Environments

<p>Methane is a potent greenhouse gas that is produced naturally via microbial processes in anoxic environments (i.e. marine and lake sediments). The release of methane to the atmosphere from sediments is controlled by its aerobic and anaerobic oxidation. Anaerobic oxidation of methane (AOM) consumes up to 90% of the produced methane in marine sediments and over half of the produced methane in freshwater sediments. The most common electron acceptor in marine sediments for AOM is sulfate, however, in freshwater lake sediments, where sulfate concentrations are low, other electron acceptors can take its place (i.e. iron/manganese/nitrate). In lake Kinneret (Israel), iron-coupled AOM was evident by in-situ sedimentary profiles and in fresh sediment slurry incubations. Here we present geochemical and molecular analyses results of slurry experiments of long-term incubated lake Kinneret sediments with labeled <sup>13</sup>C-methane, different potential electron acceptors and a few inhibitors. These experiments are part of an ongoing research to characterize the AOM processes in lake sediments, and indicate another possible type of AOM that has evolved in the long-term incubated lake sediments.</p>

scholarly journals Nitrate enhances anaerobic oxidation of methane in boreal lake sediments

2021 ◽  
Author(s):  
Antti J Rissanen ◽  
Tom Jilbert ◽  
Asko Simojoki ◽  
Rahul Mangayil ◽  
Sanni L Aalto ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Nitrate Reduction ◽  
Boreal Lakes ◽  
The Other ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Metagenomic Sequencing ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane ◽  
Boreal Lake

ABSTRACTThe importance of nitrate in promoting anaerobic oxidation of methane (AOM) in the sediments of boreal lakes is currently unknown. Here we investigated the extent to which sediment AOM is linked to nitrate reduction in a nitrate-rich, oligo-mesotrophic, boreal lake (Lake Pääjärvi, Finland). AOM potential of sediment slurries, collected from three profundal stations of the study lake, was measured at varying nitrate concentrations using 13C-labelling. This was coupled with analysis of vertical profiles of the sediment and porewater geochemistry and the microbial communities (16S rRNA gene and shotgun metagenomic sequencing). Sediment AOM potential was enhanced by nitrate at a shallow station with high contents of labile phytoplankton-derived organic matter (Station 1), but not at the other two stations. AOM was also much higher at Station 1 (2.0-6.8 nmol C cm-3 d-1) than at the other stations (0-0.3 nmol C cm-3 d-1). Accordingly, methanotrophic archaea (Candidatus Methanoperedens sp.) and bacteria (Methylococcales) had the highest relative abundance at Station 1. Furthermore, geochemical profiles indicated that AOM was potentially coupled with reduction of nitrate, iron, or sulfate at all stations. We conclude that AOM linked to nitrate reduction takes place in boreal lake sediments. However, our data cannot resolve whether nitrate affects the process directly, via enhancing nitrate reduction-mediated AOM, or indirectly, via enhancing AOM mediated by reduction of other electron acceptors.One sentence summaryAnaerobic oxidation of methane linked to nitrate reduction in boreal lake sediments

scholarly journals Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

2021 ◽  
Vol 12 ◽  
Author(s):  
Marc Crampon ◽  
Coralie Soulier ◽  
Pauline Sidoli ◽  
Jennifer Hellal ◽  
Catherine Joulian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Treated Wastewater ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

scholarly journals Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding

2021 ◽  
Vol 11 ◽  
Author(s):  
Yujie Hou ◽  
Xiong Zhang ◽  
Qinyan Zhou ◽  
Wenxing Hong ◽  
Ying Wang
Keyword(s):  
16S Rrna ◽  
Penaeus Monodon ◽  
Poor Performance ◽  
16S Rrna Gene Sequencing ◽  
Reference Database ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Significant Generalization ◽  
Rrna Gene Sequencing ◽  
Almost All

Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates topological structures of microbial co-occurrence networks with k-mer compositions of OTU sequences and embeds them into a lower-dimensional continuous latent space, while maximally preserving topological relationships among OTUs. The high imbalance among KEGG Orthology (KO) functions of microbes is recognized in our framework that usually yields poor performance. A hierarchical multitask learning module is used in HOPE to alleviate the challenge brought by the long-tailed distribution among classes. To test the performance of HOPE, we compare it with HOPE-one, HOPE-seq, and GraphSAGE, respectively, in three microbial metagenomic 16s rRNA sequencing datasets, including abalone gut, human gut, and gut of Penaeus monodon. Experiments demonstrate that HOPE outperforms baselines on almost all indexes in all experiments. Furthermore, HOPE reveals significant generalization ability. HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.

scholarly journals Manganese/iron‐supported sulfate‐dependent anaerobic oxidation of methane by archaea in lake sediments

2019 ◽  
Vol 65 (4) ◽  
pp. 863-875 ◽  
Author(s):  
Guangyi Su ◽  
Jakob Zopfi ◽  
Haoyi Yao ◽  
Lea Steinle ◽  
Helge Niemann ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Oxidation Of Methane

scholarly journals Anaerobic oxidation of methane alters sediment records of sulfur, iron and phosphorus in the Black Sea

2016 ◽  
Author(s):  
Matthias Egger ◽  
Peter Kraal ◽  
Tom Jilbert ◽  
Fatimah Sulu-Gambari ◽  
Célia J. Sapart ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Pore Water ◽  
Black Sea ◽  
The Black Sea ◽  
Anaerobic Oxidation Of Methane ◽  
Anaerobic Oxidation ◽  
Fe Oxide ◽  
Fe Oxides ◽  
Oxidation Of Methane ◽  
High Concentrations

Abstract. The surface sediments in the Black Sea are underlain by extensive deposits of iron (Fe) oxide-rich lake sediments that were deposited prior to the inflow of marine Mediterranean Sea waters ca. 9000 years ago. The subsequent downward diffusion of marine sulfate into the methane-bearing lake sediments has led to a multitude of diagenetic reactions in the sulfate-methane transition zone (SMTZ), including anaerobic oxidation of methane (AOM) with sulfate. While the sedimentary cycles of sulfur (S), methane and Fe in the SMTZ have been extensively studied, relatively little is known about the diagenetic alterations of the sediment record occurring below the SMTZ. Here we combine detailed geochemical analyses of the sediment and pore water with multicomponent diagenetic modeling to study the diagenetic alterations below the SMTZ at two sites in the western Black Sea. We focus on the dynamics of Fe, S and phosphorus (P) and demonstrate that diagenesis has strongly overprinted the sedimentary burial records of these elements. Our results show that sulfate-mediated AOM substantially enhances the downward diffusive flux of sulfide into the deep limnic deposits. During this downward sulfidization, Fe oxides, Fe carbonates and Fe phosphates (e.g. vivianite) are converted to sulfide phases, leading to an enrichment in solid phase S and the release of phosphate to the pore water. Below the sulfidization front, high concentrations of dissolved ferrous Fe (Fe2+) lead to sequestration of downward diffusing phosphate as authigenic vivianite, resulting in a transient accumulation of total P directly below the sulfidization front. Our model results further demonstrate that downward migrating sulfide becomes partly re-oxidized to sulfate due to reactions with oxidized Fe minerals, fueling a cryptic S cycle and thus stimulating slow rates of sulfate-driven AOM (~ 1–100 pmol cm−3 d−1) in the sulfate-depleted limnic deposits. However, this process is unlikely to explain the observed release of dissolved Fe2+ below the SMTZ. Instead, we suggest that besides organoclastic Fe oxide reduction, AOM coupled to the reduction of Fe oxides may also provide a possible mechanism for the high concentrations of Fe2+ in the pore water at depth. Our results reveal that methane plays a key role in the diagenetic alterations of Fe, S and P records in Black Sea sediments. The downward sulfidization into the limnic deposits is enhanced through sulfate-driven AOM with sulfate and AOM with Fe oxides may provide a deep source of dissolved Fe2+ that drives the sequestration of P in vivianite below the sulfidization front.

scholarly journals Modification of methane oxidation pathways during long-term incubations of methanic lake sediments

2021 ◽  
Author(s):  
Hanni Vigderovich ◽  
Werner Eckert ◽  
Michal Elul ◽  
Maxim Rubin-Blum ◽  
Marcus Elvert ◽  
...  
Keyword(s):  
Lake Sediments ◽  
Carbon Isotope ◽  
Iron Oxides ◽  
Methane Oxidation ◽  
Electron Acceptors ◽  
Anaerobic Oxidation Of Methane ◽  
Methanotrophic Bacteria ◽  
Oxidation Of Methane ◽  
Isotope Measurements

Abstract. Anaerobic oxidation of methane (AOM) is one of the major processes limiting the release of the greenhouse gas methane from natural environments. In Lake Kinneret sediments, iron-coupled AOM (Fe-AOM) was suggested to play a substantial role (10–15 % relative to methanogenesis) in the methanic zone (> 20 cm sediment depth), based on geochemical profiles and experiments on fresh sediments. Apparently, the oxidation of methane is mediated by a combination of mcr gene bearing archaea and aerobic bacterial methanotrophs. Here we aimed to investigate the survival of this complex microbial interplay under controlled conditions. We followed the AOM process during long-term (~18 months) anaerobic slurry experiments of these methanic sediments with two stages of incubations and additions of 13C-labeled methane, multiple electron acceptors and inhibitors. After these incubation stages carbon isotope measurements in the dissolved inorganic pool still showed considerable AOM (3–8 % relative to methanogenesis). Specific lipid carbon isotope measurements and metagenomic analyses indicate that after the prolonged incubation aerobic methanotrophic bacteria were no longer involved in the oxidation process, whereas mcr gene bearing archaea were most likely responsible for oxidizing the methane. Humic substances and iron oxides are likely electron acceptors to support this oxidation, whereas sulfate, manganese, nitrate, and nitrite did not support the AOM in these methanic sediments. Our results suggest in the natural lake sediments methanotrophic bacteria are responsible for part of the methane oxidation by the reduction of combined micro levels of oxygen and iron oxides in a cryptic cycle, while the rest of the methane is converted by reverse methanogenesis. After long-term incubation, the latter prevails without bacterial methanotropic activity and with a different iron reduction pathway.

scholarly journals The archives are half-empty: an assessment of the availability of microbial community sequencing data

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Stephanie D. Jurburg ◽  
Maximilian Konzack ◽  
Nico Eisenhauer ◽  
Anna Heintz-Buschart
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Data Reuse ◽  
Data Availability ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Data Archiving ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing

AbstractAs DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.

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