Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

Kohrs, Fabian; Heyer, Robert; Magnussen, Anke; Benndorf, Dirk; Muth, Thilo; Behne, Alexander; Rapp, Erdmann; Kausmann, Robert; Heiermann, Monika; Klocke, Michael; Reichl, Udo

doi:10.1016/j.anaerobe.2013.11.009

Cited by 46 publications

(66 citation statements)

References 43 publications

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“…Later, the rapidly decreasing sequencing cost and the prevalence of NGS technologies other than 454 pyrosequencing allowed for more extensive applications of HTS-based metagenomics approaches, including 16S rRNA gene amplicons sequencing and metagenome for novel microbial insights into the anaerobic digestion processes operated for bioenergy production (e.g., methane, biohydrogen, bioethanol, fatty acids) and/or pollution control (e.g., refractory compounds, bacterial pathogens, antibiotics resistance genes). A few pioneering studies even applied metatranscriptome (Xia et al 2014;Zakrzewski et al 2012) or metaproteome (Lü et al 2013;Kohrs et al 2013;Hanreich et al 2013;Hanreich et al 2012;Abram et al 2011;Heyer et al 2013;Wu et al 2013) to gain some preliminary insights into the gene expression and active enzymes in anaerobic digestion processes.…”

Section: Applications Of Metagenomics In Anaerobic Technology Studiesmentioning

confidence: 99%

Application of Metagenomics in Environmental Anaerobic Technology

Ju¹,

Fang²,

Zhang³

2015

Anaerobic Biotechnology

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Anaerobic technology has been applied for the treatment of solid wastes and wastewater since the 1880s. This chapter reviews the most recent advance in molecular microbial characterization techniques, i.e., metagenomics, as well as its applications in anaerobic technology, from the exploration of the intriguing science of anaerobes to industrial engineering applications. With the rapidly decreasing cost of high-throughput sequencing technologies and timely updating of state-of-the-art bioinformatics analysis tools, metagenomics has revolutionized the study of microbiology and demonstrated the great potential of the development of novel microbial resources (e.g., industrial biomolecules and enzymes and biodegradation genes), as it discloses unprecedented genetic information of uncultivated microorganisms at an amazingly fast rate. This chapter gives a detailed introduction to the technical procedures of metagenomics, from preliminary molecular experiments to high-throughput sequencing, as well as its application in environmental anaerobic technology.

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Section: Applications Of Metagenomics In Anaerobic Technology Studiesmentioning

confidence: 99%

Application of Metagenomics in Environmental Anaerobic Technology

Ju¹,

Fang²,

Zhang³

2015

Anaerobic Biotechnology

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“…For example, it is known that fermentation of 52.85 g/L of rice straw at 39.23 °C and pH 10.0 leads to an increase in the families Ruminococcaceae, Bacteroidaceae, Porphyromonadaceae and Lachnospiraceae [26]; or that the acidification of alginate correlates with high titres of Bacteroides - and Clostridium -related microorganisms [27]. Proteomics has been used to study standard, one-step digestion plants without separated acidification [9, 10, 28], but there are no detailed proteomics studies of a separated acidification stage to date. In order to bridge this gap and to finely characterize one of the most important phases of the biogas production process, the dynamic behaviour of grass acidification processes at mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was monitored through both proteomics and 16S-rDNA analysis.…”

Section: Introductionmentioning

confidence: 99%

From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

Abendroth

Simeonov²,

Peretó

et al. 2017

Biotechnol Biofuels

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BackgroundSeparating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time.ResultsHigh-strength liquor from acidified grass biomass exhibited a low biodiversity, which differed greatly depending on temperature. It was dominated by Bacteroidetes and Firmicutes at 37 °C, and by Firmicutes and Proteobacteria at 55 °C. At the methane stage, Methanosaeta, Methanomicrobium and Methanosarcina proved to be highly sensitive to environmental changes as their abundance in the seed sludges dropped dramatically after transferring the seed sludges from the respective reactors into the experimental setup. Further, an increase in Actinobacteria coincided with reduced biogas production at the end of the experiment. Over 1700 proteins were quantified from the first cycle of acidification samples using label-free quantitative proteome analysis and searching protein databases. The most abundant proteins included an almost complete set of glycolytic enzymes indicating that the microbial population is basically engaged in the degradation and catabolism of sugars. Differences in protein abundances clearly separated samples into two clusters corresponding to culture temperature. More differentially expressed proteins were found under mesophilic (120) than thermophilic (5) conditions.ConclusionOur results are the first multi-omics characterisation of a two-stage biogas production system with separated acidification and suggest that screening approaches targeting specific taxa such as Methanosaeta, Methanomicrobium and Methanosarcina could be useful diagnostic tools as indicators of environmental changes such as temperature or oxidative stress or, as in the case of Actinobacteria, they could be used as a proxy of the gas production potential of anaerobic digesters. Metaproteome analyses only detected significant expression differences in mesophilic samples, whereas thermophilic samples showed more stable protein composition with an abundance of chaperones suggesting a role in protein stability under thermal stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0859-0) contains supplementary material, which is available to authorized users.

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“…The response time on RNA, protein, or metabolite level to changes in operational parameters is much faster than on DNA level, especially for the slow growing methanogens [28]. This allows the possibility for a more accurate measurement of the microbial community structure and activity dynamics, which could entail a more specific adjustment of selective operational parameters, such as pH or organic loading rate [29, 30]. …”

Section: Introductionmentioning

confidence: 99%

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

Vrieze

Regueiro

Props

et al. 2016

Biotechnol Biofuels

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BackgroundThe microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated.ResultsThe application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation.ConclusionsThis research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0652-5) contains supplementary material, which is available to authorized users.

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Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants

Cited by 46 publications

References 43 publications

Application of Metagenomics in Environmental Anaerobic Technology

Application of Metagenomics in Environmental Anaerobic Technology

From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

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