Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic

Chaudhary, Prem Prashant; Wright, André‐Denis G.; Brablcová, Lenka; Buriánková, Iva; Bednařík, Adam; Rulı́k, Martin

doi:10.1007/s00284-014-0659-8

Cited by 10 publications

(6 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our previous study conducted on the Sitka stream also revealed phylotypes from the orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales (Brablcova et al., ; Buriankova et al., ; Chaudhary et al., ). A community profiling using denaturing gradient gel electrophoresis DGGE presented by Brablcova et al., () showed nine bands for Methanosarcinales, one band for Methanomicrobiales, and one band for Methanocellaceae.…”

Section: Discussionmentioning

confidence: 90%

“…Currently, there are seven orders of methanogenic archaea described in literature (Borrel et al., , ; Lang et al., ). However, our previous study conducted on the Sitka stream (Location IV) revealed only three major methanogenic groups using molecular techniques (denaturing gradient gel electrophoresis and cloning): Methanosarcinales, Methanomicrobiales, and Methanobacteriales (Brablcova, Buriankova, Badurova, Chaudhary, & Rulik, ; Buriankova et al., ; Chaudhary et al., ). Hence, we focused our attempts to verify these results with molecular fingerprinting and qPCR to cover these three groups; in addition, we want to expand our knowledge by comparing two different sites and two sampling occasions..…”

Section: Introductionmentioning

confidence: 95%

“…Methanosarcinales, Methanomicrobiales, and Methanobacteriales (Brablcova, Buriankova, Badurova, Chaudhary, & Rulik, 2014;Buriankova et al, 2013;Chaudhary et al, 2014). Hence, we focused our attempts to verify these results with molecular fingerprinting and qPCR to cover these three groups; in addition, we want to expand our knowledge by comparing two different sites and two sampling occasions..…”

mentioning

confidence: 99%

See 2 more Smart Citations

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites

2017

Self Cite

View full text Add to dashboard Cite

Studies on methanogenesis from freshwater sediments have so far primarily focused on lake sediments. To expand our knowledge on the community composition of methanogenic archaea in river sediments, we studied the abundance and diversity of methanogenic archaea at two localities along a vertical profile (top 50 cm) obtained from sediment samples from Sitka stream (the Czech Republic). In this study, we compare two sites which previously have been shown to have a 10‐fold different methane emission. Archaeal and methanogen abundance were analyzed by real‐time PCR and T‐RFLP. Our results show that the absolute numbers for the methanogenic community (qPCR) are relatively stable along a vertical profile as well as for both study sites. This was also true for the archaeal community and for the three major methanogenic orders in our samples (Methanosarcinales, Methanomicrobiales, and Methanobacteriales). However, the underlying community structure (T‐RFLP) reveals different community compositions of the methanogens for both locations as well as for different depth layers and over different sampling times. In general, our data confirm that Methanosarcinales together with Methanomicrobiales are the two dominant methanogenic orders in river sediments, while members of Methanobacteriales contribute a smaller community and Methanocellales are only rarely present in this sediment. Our results show that the previously observed 10‐fold difference in methane emission of the two sites could not be explained by molecular methods alone.

show abstract

Section: Discussionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 95%

mentioning

confidence: 99%

See 1 more Smart Citation

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites

2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…This can be reduced if combined with an oriented cloning and/or a fingerprinting technique (Mihajlovski et al 2008), which leads to an easiest selection of clones (based on restriction fragment length polymorphism (RFLP) for example). To our knowledge, there are few reports of the application of denaturing gradient gel electrophoresis (DGGE)/temporal temperature gel electrophoresis (TTGE) (Muyzer 1999) in studying human gut archaea or methanogens specifically (Abell et al 2006;Nam et al 2008), despite having already been extensively used for other environments (see for example Nakamura et al 2009;Chaudhary et al 2014). One major limitation of this technique relies on its inability to differentiate minor base pair differences in two sequences and thus may result in single band for different microbial strains.…”

Section: Cloning and Fingerprinting Techniquesmentioning

confidence: 97%

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Chaudhary

Gaci

Borrel

et al. 2015

Appl Microbiol Biotechnol

Self Cite

View full text Add to dashboard Cite

Until recently, human gut microbiota was believed to be colonized by few methanogenic archaeal species. Much higher microbial diversity within the human gut was revealed by the use of molecular approaches as compared to routine microbiological techniques, but still, a lot remains unknown. Molecular techniques has the advantage of being rapid, reproducible, and can be highly discriminative as compared to conventional culturing methods. Some of them provide both qualitative and quantitative information. However, the choice of method should be taken with care to avoid biases. The advent of next-generation sequencing gives much deeper information from which functional and ecological hypotheses can be drawn. In this review, molecular techniques that are currently used together with their possible future developments to study gut methanogenic communities are indicated along with their limitations and difficulties that are encountered during their implementation. Moreover, the high amount of metagenomics data from the human gut microbiome indicate that this environment could be a paradigm for new directions in methanogen diversity studies and help to develop new approaches for other environments as well. Concerning humans, this should help us to better understand the possible association of methanogens with some of the diseased conditions and their peculiar distribution among age groups in human.

show abstract

“…While the study of stream CO 2 biogeochemistry has received considerable attention over the last decade, the biogeochemistry of CH 4 (Crawford et al, 2014;Trimmer et al, 2015;Stanley et al, 2016) and specifically the microbial ecology of aerobic CH 4 oxidizing bacteria (MOB) in streams remains poorly understood (Trimmer et al, 2015(Trimmer et al, , 2010Stanley et al, 2016). Streams outgas substantial amounts of CH 4 originating from groundwater and methanogenesis within the streambed (Chaudhary et al, 2014;Stanley et al, 2016). Globally, streams and rivers may emit 26.8 Tg CH 4 per year, which is similar to the combined contribution of other natural CH 4 sources such as wildfires, termites, CH 4 hydrates, and permafrost (Stanley et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability

et al. 2020

View full text Add to dashboard Cite

Despite the recognition of streams and rivers as sources of methane (CH 4) to the atmosphere, the role of CH 4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH 4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream-and porewater CH 4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (V max), and CH 4 concentration at half V max (K S) increased with CH 4 supply. K S values in the micromolar range matched the CH 4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH 4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

show abstract

Dominance of Methanosarcinales Phylotypes and Depth-Wise Distribution of Methanogenic Community in Fresh Water Sediments of Sitka Stream from Czech Republic

Cited by 10 publications

References 54 publications

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites

Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability

Contact Info

Product

Resources

About