The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

Schlüter, Andreas; Bekel, Thomas; Diaz, Naryttza N.; Dondrup, Michael; Eichenlaub, Rudolf; Gartemann, Karl-Heinz; Krahn, Irene; Krause, Lutz; Krömeke, Holger; Kruse, Olaf; Mussgnug, Jan H.; Neuweger, Heiko; Niehaus, Karsten; Pühler, Alfred; Runte, Kai J.; Szczepanowski, Rafael; Tauch, Andreas; Tilker, Alexandra; Viehöver, Prisca; Goesmann, Alexander

doi:10.1016/j.jbiotec.2008.05.008

Cited by 308 publications

(254 citation statements)

References 87 publications

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“…Isotopic labelled substrates were exploited to identify the functional microbial groups catalysing the methanisation of cellulose using stable isotope probing (Li et al, 2009). Several metagenomic studies shed light on the identity of the functional groups and provided an extended catalogue of the catalytic potential (Krause et al, 2008;Schlü ter et al, 2008;Jaenicke et al, 2011;Rademacher et al, 2012). However, these approaches do not generate direct information on the expressed genes and associated metabolic processes.…”

Section: Introductionmentioning

confidence: 99%

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

Bize²,

et al. 2013

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Cellulose is the most abundant biopolymer on Earth. Optimising energy recovery from this renewable but recalcitrant material is a key issue. The metaproteome expressed by thermophilic communities during cellulose anaerobic digestion was investigated in microcosms. By multiplying the analytical replicates (65 protein fractions analysed by MS/MS) and relying solely on public protein databases, more than 500 non-redundant protein functions were identified. The taxonomic community structure as inferred from the metaproteomic data set was in good overall agreement with 16S rRNA gene tag pyrosequencing and fluorescent in situ hybridisation analyses. Numerous functions related to cellulose and hemicellulose hydrolysis and fermentation catalysed by bacteria related to Caldicellulosiruptor spp. and Clostridium thermocellum were retrieved, indicating their key role in the cellulose-degradation process and also suggesting their complementary action. Despite the abundance of acetate as a major fermentation product, key methanogenesis enzymes from the acetoclastic pathway were not detected. In contrast, enzymes from the hydrogenotrophic pathway affiliated to Methanothermobacter were almost exclusively identified for methanogenesis, suggesting a syntrophic acetate oxidation process coupled to hydrogenotrophic methanogenesis. Isotopic analyses confirmed the high dominance of the hydrogenotrophic methanogenesis. Very surprising was the identification of an abundant proteolytic activity from Coprothermobacter proteolyticus strains, probably acting as scavenger and/or predator performing proteolysis and fermentation. Metaproteomics thus appeared as an efficient tool to unravel and characterise metabolic networks as well as ecological interactions during methanisation bioprocesses. More generally, metaproteomics provides direct functional insights at a limited cost, and its attractiveness should increase in the future as sequence databases are growing exponentially.

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Section: Introductionmentioning

confidence: 99%

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

Bize²,

et al. 2013

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“…454 pyrosequencing is a widely accepted sequencing method, which was developed by Margulies et al (2005). Pyrosequencing has been used in microbial ecology in various habitats, such as in a biogas plant (Schlüter et al, 2008), in deep mines (Edwards et al, 2006), in a deep marine biosphere (Huber et al, 2007) and with deep chlorophyll maximum (Ghai et al, 2010). These studies supported that pyrosequencing facilitated greater understanding of microbial diversity.…”

Section: Introductionmentioning

confidence: 99%

Pyrosequencing reveals the dominance of methylotrophic methanogenesis in a coal bed methane reservoir associated with Eastern Ordos Basin in China

Guo

Liu

et al. 2012

International Journal of Coal Geology

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a b s t r a c t a r t i c l e i n f oIt is generally believed that biogenic coal bed methane (CBM) is an end product of coal biodegradation by methanogenic archaea and syntrophic bacteria. In this work, the archaeal and bacterial communities of CBM reservoir associated with Ordos Basin in China were investigated using 454 pyrosequencing. Sampling produced water, coal and rock in the reservoir, a total of 46,598 sequence reads were obtained. All archaea were methanogens with the genus Methanolobus predominating. The genus consisted of 81.18% of pyrosequencing reads in water sample and > 99% in coal and rock samples. Although the phylum Proteobacteria was the main component of all samples, bacterial communities in coal and rock samples were similar at the genus level, which were distinctly separated with water sample. The results strongly suggested that methylotrophic methanogenesis governed the biogenic CBM formation. The separation of microbial communities between water and coal, rock samples should be considered when investigating the process of coal biodegradation and the generation of new biogenic CBM.

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“…Because this process requires multiple enzymes because of the complex structure of plant cell walls, a consortium of organisms may be best suited for decomposition of cellulose-rich substrates (Ohkuma and Kudo, 1996;Schlü ter et al, 2008;Strickland et al, 2009). We detected bacteria associated with S. noctilio that can degrade a diversity of carbohydrates, including cellulose and putatively hemicellulose.…”

Section: Discussionmentioning

confidence: 99%

Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio

et al. 2011

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Sirex noctilio is an invasive wood-feeding wasp that threatens the world's commercial and natural pine forests. Successful tree colonization by this insect is contingent on the decline of host defenses and the ability to utilize the woody substrate as a source of energy. We explored its potential association with bacterial symbionts that may assist in nutrient acquisition via plant biomass deconstruction using growth assays, culture-dependent and -independent analysis of bacterial frequency of association and whole-genome analysis. We identified Streptomyces and c-Proteobacteria that were each associated with 94% and 88% of wasps, respectively. Streptomyces isolates grew on all three cellulose substrates tested and across a range of pH 5.6 to 9. On the basis of whole-genome sequencing, three Streptomyces isolates have some of the highest proportions of genes predicted to encode for carbohydrate-active enzymes (CAZyme) of sequenced Actinobacteria. c-Proteobacteria isolates grew on a cellulose derivative and a structurally diverse substrate, ammonia fiber explosion-treated corn stover, but not on microcrystalline cellulose. Analysis of the genome of a Pantoea isolate detected genes putatively encoding for CAZymes, the majority predicted to be active on hemicellulose and more simple sugars. We propose that a consortium of microorganisms, including the described bacteria and the fungal symbiont Amylostereum areolatum, has complementary functions for degrading woody substrates and that such degradation may assist in nutrient acquisition by S. noctilio, thus contributing to its ability to be established in forested habitats worldwide.

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The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

Cited by 308 publications

References 87 publications

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity

Pyrosequencing reveals the dominance of methylotrophic methanogenesis in a coal bed methane reservoir associated with Eastern Ordos Basin in China

Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio

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