1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms

Murovec, Boštjan; Makuc, Damjan; Repinc, Sabina Kolbl; Prevoršek, Zala; Zavec, Domen; Šket, Robert; Pečnik, Klemen; Plavec, Janez; Stres, Blaž

doi:10.1016/j.jenvman.2018.05.068

Cited by 15 publications

(19 citation statements)

References 39 publications

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“…The process of lignin and cellulose decomposition in biological systems has attracted attention because their hydrolysis frequently limits plant biomass degradation and consequently, the processing of wastewaters, industrial organic sludge and residues containing a large proportion of plant biomass. Usually, anaerobic reactors must perform the whole digestion of input residues down to the end products of fermentations which represent the basic substrates used for methanogenesis (Acetate, CO 2 and H 2 and one-or two-C molecules such as methylamines, methanol, formate, as some examples) (Murovec et al, 2018). The complex metabolism results in a number of metabolites (Murovec et al, 2018) produced by highly active interactions between different groups of microorganisms which center their ecological niche in maintaining degradation of specific type of chemical bonds between or within complex molecules.…”

Section: Organic Carbon Processingmentioning

confidence: 99%

“…Usually, anaerobic reactors must perform the whole digestion of input residues down to the end products of fermentations which represent the basic substrates used for methanogenesis (Acetate, CO 2 and H 2 and one-or two-C molecules such as methylamines, methanol, formate, as some examples) (Murovec et al, 2018). The complex metabolism results in a number of metabolites (Murovec et al, 2018) produced by highly active interactions between different groups of microorganisms which center their ecological niche in maintaining degradation of specific type of chemical bonds between or within complex molecules. The sequential decomposition of major polymers involves many and diverse sets of microorganisms (Guo et al, 2015;Madigan et al, 2003).…”

Section: Organic Carbon Processingmentioning

confidence: 99%

“…Such cases force microorganisms to respond accordingly, increase their energetic expenditure and invest resources to fine-tune their protein makeup to their current environmental conditions. The lack of understanding of metabolic prerequisites of microorganisms in full-scale industrial anaerobic digesters may result in consequent borderline conditions with insufficient microbial activity towards methane production (Garuti et al, 2018;Murovec et al, 2018;Repinc et al, 2018).…”

Section: Perspectivesmentioning

confidence: 99%

“…Depending on the history, biogeography, and operational parameters of biogas reactors, crucial microbial constituents can fluctuate showing different abundance and level of activity as a consequence of, for instance, trace-element deficiency, long-term limitation of organic substrate or short-term overload (Murovec et al, 2018;Repinc et al, 2018;Sun et al, 2015). This variability builds up the diversity of both microorganisms and their enzymes implicated in the processes leading to methane and the complete mineralization of organic matter (i.e.…”

Section: Introductionmentioning

confidence: 99%

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Trace element enzymes in reactions essential for anaerobic digestion

González¹,

Stres²

2019

Trace Elements in Anaerobic Biotechnologies

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Trace elements play a very important role on the performance and stability of biogas digesters from a variety of biomass-containing residues, both natural or synthetic. Degradation of these complex chemical compounds occurs by the interaction of numerous microorganisms carrying out a series of pathways involving fermentative processes that ultimately lead to methane production. The purpose of this study was to provide an overview of the direct relationships existing among trace elements and enzyme activity which regulates the anaerobic digestion processes carried out by these microorganisms. Methanogenesis is one of the most trace-element enriched enzymatic pathways in biology. Trace elements are major key elements in the functioning of multiple enzymes reviewed within this work. Although exact trace-element requirements may differ slightly between pathways depending on composition and the microorganisms involved, there are some general trends characterizing the anaerobic digestion processes. Iron (Fe) is the most abundantly required metal, followed by nickel (Ni), cobalt (Co), molybdenum (Mo), tungsten (W), and zinc (Zn). In order to sustain the

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Section: Organic Carbon Processingmentioning

confidence: 99%

Section: Organic Carbon Processingmentioning

confidence: 99%

Section: Perspectivesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Trace element enzymes in reactions essential for anaerobic digestion

González¹,

Stres²

2019

Trace Elements in Anaerobic Biotechnologies

View full text Add to dashboard Cite

show abstract

“…Significant advances in nuclear magnetic resonance (NMR) sensitivity by the development of associated tools, such as cryoprobes that increase the sensitivity by around 20-fold, have opened the possibility of identifying and quantifying a broad range of natural compounds [17,18]. It has benefited the emergence of new fields such as microbial metabolomics [19,20], and in particular the study the exometabolomes of bacteria without requiring chemical extractions or derivatizations of the samples [3,21,22,23,24,25]. This non-destructive and highly reproducible technique can detect a wide range of structural diverse compounds at micromolar concentrations [26].…”

Section: Introductionmentioning

confidence: 99%

Exo-Metabolites of Phaseolus vulgaris-Nodulating Rhizobial Strains

et al. 2019

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Rhizobia are able to convert dinitrogen into biologically available forms of nitrogen through their symbiotic association with leguminous plants. This results in plant growth promotion, and also in conferring host resistance to different types of stress. These bacteria can interact with other organisms and survive in a wide range of environments, such as soil, rhizosphere, and inside roots. As most of these processes are molecularly mediated, the aim of this research was to identify and quantify the exo-metabolites produced by Rhizobium etli CFN42, Rhizobium leucaenae CFN299, Rhizobium tropici CIAT899, Rhizobium phaseoli Ch24-10, and Sinorhizobium americanum CFNEI156, by nuclear magnetic resonance (NMR). Bacteria were grown in free-living cultures using minimal medium containing sucrose and glutamate. Interestingly, we found that even when these bacteria belong to the same family (Rhizobiaceae) and all form nitrogen-fixing nodules on Phaseolus vulgaris roots, they exhibited different patterns and concentrations of chemical species produced by them.

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Evaluating line-broadening factors on a reference spectrum as a bucketing method for NMR based metabolomics

Wang

Maldonado‐Devincci

Lin

2020

Analytical Biochemistry

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Metabolomics based nuclear magnetic resonance (NMR) is widely used in disease mechanism analysis and drug discovery. One of the most important factors in NMR based metabolomics study is the accuracy of spectra bucketing which plays a critical role in data interpretation. Though various methods have been developed for automatic bucketing, the most popular approach is still the traditional rectangular bucketing method which is mainly due to the requirement of user expertise for the automatic bucketing methods. In this study, we developed a new automatic bucketing method that not only efficiently increases peak bucketing accuracy but also allows the bucketing process to be conveniently visualized and adjusted by the end-users. This method applied the line broadening (lb) factor to the average spectrum for a study set which serves as the reference spectrum, and the peak width of the reference spectrum was then set as the peak bucketing pattern. The approach to pick the bucket boundaries is simple but powerful after the line broadening factor was applied. The line broadening factors from 0 to 2 lb were tested using mouse fecal samples and the 1 lb method showed similar peak patterns and data interpretation results compared with a careful manual bucketing pattern. Besides this, the new method generated bucketing patterns could be easily visualized using the Amix software and revised by general users without excessive data science and NMR instrumentation expertise. In summary, our study showed a powerful and convenient tool in NMR peak auto bucketing with flexible visualization and adjustment ability for metabolomics studies.

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1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms

Cited by 15 publications

References 39 publications

Trace element enzymes in reactions essential for anaerobic digestion

Trace element enzymes in reactions essential for anaerobic digestion

Exo-Metabolites of Phaseolus vulgaris-Nodulating Rhizobial Strains

Evaluating line-broadening factors on a reference spectrum as a bucketing method for NMR based metabolomics

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