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      Selecting for lactic acid producing and utilising bacteria in anaerobic enrichment cultures

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          Abstract

          Lactic acid‐producing bacteria are important in many fermentations, such as the production of biobased plastics. Insight in the competitive advantage of lactic acid bacteria over other fermentative bacteria in a mixed culture enables ecology‐based process design and can aid the development of sustainable and energy‐efficient bioprocesses. Here we demonstrate the enrichment of lactic acid bacteria in a controlled sequencing batch bioreactor environment using a glucose‐based medium supplemented with peptides and B vitamins. A mineral medium enrichment operated in parallel was dominated by Ethanoligenens species and fermented glucose to acetate, butyrate and hydrogen. The complex medium enrichment was populated by Lactococcus, Lactobacillus and Megasphaera species and showed a product spectrum of acetate, ethanol, propionate, butyrate and valerate. An intermediate peak of lactate was observed, showing the simultaneous production and consumption of lactate, which is of concern for lactic acid production purposes. This study underlines that the competitive advantage for lactic acid‐producing bacteria primarily lies in their ability to attain a high biomass specific uptake rate of glucose, which was two times higher for the complex medium enrichment when compared to the mineral medium enrichment. The competitive advantage of lactic acid production in rich media can be explained using a resource allocation theory for microbial growth processes.

          Abstract

          The supplementation of peptides and B vitamins to an ecosystem where glucose was fermented directs the glucose to lactate and ethanol. Enriching with glucose and a mineral medium, acetate, butyrate and hydrogen was the dominant product pathway. This is likely caused by proteome optimisation of lactic acid bacteria. Also, lactate was only fermented in the presence of B vitamins and peptides. We demonstrate the rate efficiency trade off in fermentative ecosystems and pave the way for directing product formation.

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          Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

          The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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            Lactic acid bacteria as functional starter cultures for the food fermentation industry

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              Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation.

              The review describes four flavin-containing cytoplasmatic multienzyme complexes from anaerobic bacteria and archaea that catalyze the reduction of the low potential ferredoxin by electron donors with higher potentials, such as NAD(P)H or H(2) at ≤ 100 kPa. These endergonic reactions are driven by concomitant oxidation of the same donor with higher potential acceptors such as crotonyl-CoA, NAD(+) or heterodisulfide (CoM-S-S-CoB). The process called flavin-based electron bifurcation (FBEB) can be regarded as a third mode of energy conservation in addition to substrate level phosphorylation (SLP) and electron transport phosphorylation (ETP). FBEB has been detected in the clostridial butyryl-CoA dehydrogenase/electron transferring flavoprotein complex (BcdA-EtfBC), the multisubunit [FeFe]hydrogenase from Thermotoga maritima (HydABC) and from acetogenic bacteria, the [NiFe]hydrogenase/heterodisulfide reductase (MvhADG-HdrABC) from methanogenic archaea, and the transhydrogenase (NfnAB) from many Gram positive and Gram negative bacteria and from anaerobic archaea. The Bcd/EtfBC complex that catalyzes electron bifurcation from NADH to the low potential ferredoxin and to the high potential crotonyl-CoA has already been studied in some detail. The bifurcating protein most likely is EtfBC, which in each subunit (βγ) contains one FAD. In analogy to the bifurcating complex III of the mitochondrial respiratory chain and with the help of the structure of the human ETF, we propose a conformational change by which γ-FADH(-) in EtfBC approaches β-FAD to enable the bifurcating one-electron transfer. The ferredoxin reduced in one of the four electron bifurcating reactions can regenerate H(2) or NADPH, reduce CO(2) in acetogenic bacteria and methanogenic archaea, or is converted to ΔμH(+)/Na(+) by the membrane-associated enzyme complexes Rnf and Ech, whereby NADH and H(2) are recycled, respectively. The mainly bacterial Rnf complexes couple ferredoxin oxidation by NAD(+) with proton/sodium ion translocation and the more diverse energy converting [NiFe]hydrogenases (Ech) do the same, whereby NAD(+) is replaced by H(+). Many organisms also use Rnf and Ech in the reverse direction to reduce ferredoxin driven by ΔμH(+)/Na(+). Finally examples are shown, in which the four bifurcating multienzyme complexes alone or together with Rnf and Ech are integrated into energy metabolisms of nine anaerobes. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.
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                Author and article information

                Contributors
                julesrombouts@gmail.com
                m.c.m.vanloosdrecht@tudelft.nl
                Journal
                Biotechnol Bioeng
                Biotechnol. Bioeng
                10.1002/(ISSN)1097-0290
                BIT
                Biotechnology and Bioengineering
                John Wiley and Sons Inc. (Hoboken )
                0006-3592
                1097-0290
                18 February 2020
                May 2020
                : 117
                : 5 ( doiID: 10.1002/bit.v117.5 )
                : 1281-1293
                Affiliations
                [ 1 ] Department of Biotechnology Delft University of Technology Delft The Netherlands
                [ 2 ] Department of Chemical Engineering, Institute of Technology Universidade de Santiago Compostela Santiago de Compostela Spain
                Author notes
                [*] [* ] Correspondence Julius Laurens Rombouts and Mark Cornelis Maria van Loosdrecht, Delft University of technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.

                Email: julesrombouts@ 123456gmail.com (JLR) and m.c.m.vanloosdrecht@ 123456tudelft.nl (MCML)

                Author information
                http://orcid.org/0000-0002-5829-0050
                http://orcid.org/0000-0001-8227-6665
                http://orcid.org/0000-0002-6313-1652
                http://orcid.org/0000-0001-7612-7794
                http://orcid.org/0000-0003-0658-4775
                Article
                BIT27301
                10.1002/bit.27301
                7187302
                32034763
                0422fbdb-ef2a-4f1a-a357-946e2a5972e5
                © 2020 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 19 November 2019
                : 27 January 2020
                : 07 February 2020
                Page count
                Figures: 6, Tables: 1, Pages: 13, Words: 9111
                Funding
                Funded by: Nederlandse Organisatie voor Wetenschappelijk Onderzoek , open-funder-registry 10.13039/501100003246;
                Award ID: 024.002.002
                Funded by: Spanish Ministry of Education
                Award ID: FPU14/05457
                Categories
                Article
                ARTICLES
                Biofuels and Environmental Biotechnology
                Custom metadata
                2.0
                May 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.1 mode:remove_FC converted:28.04.2020

                Biotechnology
                enrichment cultures,kinetics,lactic acid bacteria,microbial ecology,resource allocation

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