Methanogenic System of a Small Lowland Stream Sitka, Czech Republic

Rulk, Martin; Bednak, Adam; Mach, Vclav; Brablcov, Lenka; Burinkov, Iva; Badurov, Pavlna; Gratzov, Kristyna

doi:10.5772/52718

Cited by 9 publications

(25 citation statements)

References 81 publications

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“…It is interesting to note the one clone obtained for Methanocellaceae (Brablcova et al., ) originates from Location I, and only for this location, we could assign one TRF (238 bp) to Methanocellaceae for the 40–50 cm depth confirming the presence of this microbial order in the sediments of Location I. A microscopic study using FISH of Methanosarcinaceae, Methanosaetaceae as well as Methanobacteriaceae, not only revealed the presence of these three groups with each contributing roughly 10% to the total cell counts (DAPI counts) (Rulik et al., ), but also showed that the vertical distribution is quite stable.…”

Section: Discussionmentioning

confidence: 55%

“…Sitka stream is considered to be an undisturbed, 35 km long, lowland, third‐order stream originating in the Hrubý Jeseník Mountains, 650 m above sea level. Of the two localities studied, one (Location I) was situated in an upper forested area, whereas the second location (Location IV) was situated in agricultural landscape (further description of the sampling sites has been provided earlier (Hlavacova, Rulik, & Cap, ; Buriankova et al., ; Rulik et al., ; Brablcova et al., ). These two sites were selected on the basis of the different amount of methane production and methanogenic potential on the basis of earlier studies (Buriankova et al., , ).…”

Section: Methodsmentioning

confidence: 99%

“…Methane is one of the most potent greenhouse gases with a global warming potential 25 times higher than carbon dioxide. A significant contribution to the annual atmospheric methane flux (40%–50%) comes from freshwater sediments like lakes, wetlands, and rice paddy fields (Cicerone & Oremland, ; Conrad, ; Rulik et al., ). As the sediment depth increases, there is also a shift in the physical and chemical conditions, such as redox potential and dissolved oxygen, an increase in temperature and nutrient gradients, which constitutively provides a unique environment for the growth of metabolically diverse microorganisms (Chunleuchanon, Sooksawang, Teaumroong, & Boonkerd, ; Newberry et al., ; Orphan et al., ).…”

Section: Introductionmentioning

confidence: 99%

“…In a previous study, we already evaluated the methane emissions as well as the methanogenic potential of several sites of River Sitka (Rulik et al., ). In the present study, we focused on the methanogenic community composition of river sediment samples and compare the community composition of a low‐emitting site (Location I: 2.39 mg CH 4 m −2 water day −1 ) with that of a high‐emitting site (Location IV: 32.1 mg CH 4 m −2 water day −1 ) (Rulik et al., ).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

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

2017

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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.

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Section: Discussionmentioning

confidence: 55%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

2017

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“…These investigations helped to establish a broad understanding concerning microbial community's temporal and spatial distribution patterns. For example, a PCR‐DGGE/clone library study of the bacterial community in Sitka stream, Czech Republic found that most of the mcrA gene clones showed low affiliation with known species and probably represented genes of novel methanogenic archeal genera/species (Rulik et al., ). Another research in the Yangtze Delta (Huang, Xie, Yuan, Xu, & Lu, ), using the same technique found the number of total cultivable bacteria in an estuary reservoir was significantly lower than that of the main river.…”

Section: Introductionmentioning

confidence: 99%

Illumina sequencing‐based analysis of sediment bacteria community in different trophic status freshwater lakes

et al. 2017

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Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution. The results uncovered a 1,000‐fold increase in the total amount of sequences harvested and a reverse relationship between trophic level and the bacterial diversity in most seasons of a year. A total of 65 phyla, 221 classes, 436 orders, 624 families, and 864 genera were identified in the study area. Delta‐proteobacteria and gamma‐proteobacteria prevailed in spring/summer and winter, respectively, regardless trophic conditions; meanwhile, the two classes dominated in the eutrophication and mesotrophication lake regions, respectively, but exclusively in the Fall. For LEfSe analysis, bacterial taxon that showed the strongest seasonal or spatial variation, majority had the highest abundance in spring/summer or medium eutrophication region, respectively. Pearson's correlation analysis indicated that 5 major phyla and 18 sub‐phylogenetic groups showed significant correlation with trophic status. Canonical correspondence analysis further revealed that porewater NH 4 +‐N as well as sediment TOM and NO x‐N are likely the dominant environmental factors affecting bacterial community compositions.

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Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

et al. 2017

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About half of the global methane (CH ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.

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Methanogenic System of a Small Lowland Stream Sitka, Czech Republic

Cited by 9 publications

References 81 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

Illumina sequencing‐based analysis of sediment bacteria community in different trophic status freshwater lakes

Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems

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