Publications by authors named "Chrats Melkonian"

4 Publications

  • Page 1 of 1

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.

Commun Biol 2021 May 5;4(1):530. Epub 2021 May 5.

Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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http://dx.doi.org/10.1038/s42003-021-01948-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8099898PMC
May 2021

New Insights Into Cinnamoyl Esterase Activity of .

Front Microbiol 2019 8;10:2597. Epub 2019 Nov 8.

Escola Superior de Biotecnologia, Centro de Biotecnologia e Química Fina, Universidade Católica Portuguesa, Porto, Portugal.

Some strains of possess cinnamoyl esterase activity that can be relevant in the malolactic stage of wine production liberating hydroxycinnamic acids that are precursors of volatile phenols responsible for sensory faults. The objective of this study was to better understand the basis of the differential activity between strains. After initial screening, five commercial strains of were selected, three were found to exhibit cinnamoyl esterase activity (CE+) and two not (CE-). Although the use of functional annotation of genes revealed genotypic variations between the strains, no specific genes common only to the three CE+ strains could explain the different activities. Pasteurized wine was used as a natural source of tartrate esters in growth and metabolism experiments conducted in MRS medium, whilst commercial -caftaric acid was used as substrate for enzyme assays. Detoxification did not seem to be the main biological mechanism involved in the activity since unlike its phenolic cleavage products and their immediate metabolites (caffeic acid and 4-ethylcatechol), -caftaric acid was not toxic toward . In the case of the two CE+ strains Oenos and CiNe, wine-exposed samples showed a more rapid degradation of -caftaric acid than the unexposed ones. The CE activity was present in all cell-free extracts of both wine-exposed and unexposed strains, except in the cell-free extracts of the CE- strain CH11. This activity may be constitutive rather than induced by exposure to tartrate esters. -caftaric acid was totally cleaved to -caffeic acid by cell-free extracts of the three CE+ strains, whilst cell-free extracts of the CE- strain CH16 showed significantly lower activity, although higher for the strains in experiments with no prior wine exposure. The EstB28 esterase gene, found in the genomes of the 5 strains, did not reveal any difference on the upstream regulation and transport functionality between the strains. This study highlights the complexity of the basis of this activity in wine related population. Variable cinnamoyl esterases or/and membrane transport activities in the strains analyzed and a possible implication of wine molecules could explain this phenomenon.
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http://dx.doi.org/10.3389/fmicb.2019.02597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857119PMC
November 2019

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture.

Front Microbiol 2019 25;10:1347. Epub 2019 Jun 25.

Systems Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands.

Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that , a dominant organism in kefir, stands out among the because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated in malolactic fermentation. We observed that thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, together with , and genera had the highest number of genes involved in biosynthesis of amino acids.
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http://dx.doi.org/10.3389/fmicb.2019.01347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6603220PMC
June 2019

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous Fermentation of Riesling Must.

Front Microbiol 2019 9;10:697. Epub 2019 Apr 9.

Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

Although there is an extensive tradition of research into the microbes that underlie the winemaking process, much remains to be learnt. We combined the high-throughput sequencing (HTS) tools of metabarcoding and metagenomics, to characterize how microbial communities of Riesling musts sampled at four different vineyards, and their subsequent spontaneously fermented derivatives, vary. We specifically explored community variation relating to three points: (i) how microbial communities vary by vineyard; (ii) how community biodiversity changes during alcoholic fermentation; and (iii) how microbial community varies between musts that successfully complete alcoholic fermentation and those that become 'stuck' in the process. Our metabarcoding data showed a general influence of microbial composition at the vineyard level. Two of the vineyards (4 and 5) had strikingly a change in the differential abundance of . We therefore additionally performed shotgun metagenomic sequencing on a subset of the samples to provide preliminary insights into the potential relevance of this observation, and used the data to both investigate functional potential and reconstruct draft genomes (bins). At these two vineyards, we also observed an increase in non-Saccharomycetaceae fungal functions, and a decrease in bacterial functions during the early fermentation stage. The binning results yielded 11 coherent bins, with both vineyards sharing the yeast bins and . Read recruitment and functional analysis of this data revealed that during fermentation, a high abundance of might serve as a biocontrol agent against bacteria, via a putative iron depletion pathway, and this in turn could help dominate the fermentation. During alcoholic fermentation, we observed a general decrease in biodiversity in both the metabarcoding and metagenomic data. Unexpected behavior was observed in vineyard 4 according to metagenomic analyses based on reference-based read mapping. Analysis of open reading frames using these data showed an increase of functions assigned to class Actinobacteria in the end of fermentation. Therefore, we hypothesize that bacteria might sit-and-wait until activity slows down. Complementary approaches to annotation instead of relying a single database provide more coherent information true species. Lastly, our metabarcoding data enabled us to identify a relationship between stuck fermentations and abundance. Given that robust chemical analysis indicated that although the stuck samples contained residual glucose, all fructose had been consumed, we hypothesize that this was because fructophilic , rather than , dominated these fermentations. Overall, our results showcase the different ways in which metagenomic analyses can improve our understanding of the wine alcoholic fermentation process.
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http://dx.doi.org/10.3389/fmicb.2019.00697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6465770PMC
April 2019