Bacterial Fermentation

M��ller, Volker

doi:10.1002/9780470015902.a0001415.pub2

Cited by 30 publications

(21 citation statements)

References 10 publications

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“…There is additional evidence for such syntrophic relationships, with other simple compounds produced from these processes being used by other microbial groups. For example, mixed acid fermentation, where glucose is fermented into either acetate, ethanol, lactate, succinate, or formate (Müller ), was the only fermentation‐related process enriched in the NO 3 − treatment, and may have been facilitated by the production of these simple carbon compounds formed as a result of complex carbohydrate decomposition (Fig. k).…”

Section: Discussionmentioning

confidence: 99%

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

Bulseco

Vineis

Murphy

et al. 2019

Limnology & Oceanography

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High-throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis-driven research. We performed flow-through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems.

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Section: Discussionmentioning

confidence: 99%

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

Bulseco

Vineis

Murphy

et al. 2019

Limnology & Oceanography

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“…In anaerobic environments, microbes often grow on substrates that allow for the synthesis of only 1–4 mol of ATP [59], and in addition, the concentration of membrane‐permeable organic acids such as acetate or succinate will counteract proton‐based energetics, due to uncoupling effects [60,61]. It has long been known that anaerobic members of the third domain of life, the Archaea , such as the methanogens, couple metabolic activities to the generation of primary, transmembrane electrochemical Na + gradients [13,62,63], but Na + ‐driven ATP synthesis could not be demonstrated unequivocally using whole cells [64].…”

Section: Discussionmentioning

confidence: 99%

A sodium ion‐dependent A₁A_O ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus

et al. 2007

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Membrane-bound, multisubunit, ion-translocating ATP synthases ⁄ ATPases are present in every domain of life. They arose from a common ancestor, but evolved into three distinct classes of ATP synthases ⁄ ATPases: the F 1 F O ATP synthase present in bacteria, mitochondria and chloroplasts, the A 1 A O ATP synthase present in archae, and the V 1 V O ATPase associated with cytoplasmic organelles such as vacuoles in eukaryotes [1][2][3][4]. A common feature of ATP synthases ⁄ ATPases is their organization into two domains, a hydrophilic and a membrane-bound domain, that are connected by (at least) two stalks, one central and one to two peripheral [5][6][7][8][9][10][11][12]. The hydrophilic domain catalyzes ATP hydrolysis [13][14][15][16], and the membranebound domain translocates ions from one side of the membrane to the other against their electrochemical gradient [17][18][19][20].ATP synthases ⁄ ATPases are rotary machines that work as a pair of coupled motors: a chemically driven motor (F 1 ⁄ A 1 ⁄ V 1 ) that is attached to the membrane, and an ion gradient-driven membrane-embedded motor (The membrane-embedded motor is composed of a stator and a rotor. The rotor is composed of multiple copies of subunit c that form an oligomeric ring of noncovalently linked subunits, and rotation of the c ring is obligatorily coupled to ion flow across the membrane [28][29][30][31] The rotor subunit c of the A 1 A O ATP synthase of the hyperthermophilic archaeon Pyrococcus furiosus contains a conserved Na + -binding motif, indicating that Na + is a coupling ion. To experimentally address the nature of the coupling ion, we isolated the enzyme by detergent solubilization from native membranes followed by chromatographic separation techniques. The entire membrane-embedded motor domain was present in the preparation. The rotor subunit c was found to form an SDS-resistant oligomer. Under the conditions tested, the enzyme had maximal activity at 100°C, had a rather broad pH optimum between pH 5.5 and 8.0, and was inhibited by diethystilbestrol and derivatives thereof. ATP hydrolysis was strictly dependent on Na + , with a K m of 0.6 mm. Li + , but not K + , could substitute for Na + . The Na + dependence was less pronounced at higher proton concentrations, indicating competition between Na + and H + for a common binding site. Moreover, inhibition of the ATPase by N¢,N¢-dicyclohexylcarbodiimide could be relieved by Na + . Taken together, these data demonstrate the use of Na + as coupling ion for the A 1 A O ATP synthase of Pyrococcus furiosus, the first Na + A 1 A O ATP synthase described.Abbreviation DES, diethylstilbestrol.

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“…Diverse genera belonging to the family Enterobacteriaceae ferment substrates by either mixed-acid or butanediol fermentations (52,56). The Enterobacteriaceae-affiliated phylotype E was associated mainly with Enterobacter-and Klebsiella-related species and displayed a high relative abundance in the arabinose-supplemented treatment (Table 2).…”

Section: Aeromonadaceae Aeromonas-affiliated Phylotype a [Lt838791]mentioning

confidence: 99%

Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris

Meier

Hunger

Drake

2018

Appl Environ Microbiol

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The earthworm gut is an anoxic, saccharide-rich microzone in aerated soils. The apparent degradation of diverse saccharides in the alimentary canal of the model earthworm is concomitant with the production of diverse organic acids, indicating that fermentation is an ongoing process in the earthworm gut. However, little is known about how different gut-associated saccharides are fermented. The hypothesis of this investigation was that different gut-associated saccharides differentially stimulate fermentative microorganisms in gut contents of This hypothesis was addressed by (i) assessing the fermentation profiles of anoxic gut content microcosms that were supplemented with gut-associated saccharides and (ii) the concomitant phylogenic analysis of 16S rRNA sequences. Galactose, glucose, maltose, mannose, arabinose, fucose, rhamnose, and xylose stimulated the production of fermentation products, including H, CO, acetate, lactate, propionate, formate, succinate, and ethanol. Fermentation profiles were dependent on the supplemental saccharide (e.g., glucose yielded large amounts of H and ethanol, whereas fucose did not, and maltose yielded large amounts of lactate, whereas mannose did not). Approximately 1,750,000 16S rRNA sequences were affiliated with 37 families, and phylogenic analyses indicated that a respective saccharide stimulated a subset of the diverse phylotypes. An -related phylotype displayed a high relative abundance in all treatments, whereas key-affiliated phylotypes were stimulated by some but not all saccharides. Collectively, these results reinforce the likelihood that (i) different saccharides stimulate different fermentations in gut contents of the earthworm and (ii) facultative aerobes related to and can be important drivers of these fermentations. The feeding habits of earthworms influence the turnover of elements in the terrestrial biosphere. The alimentary tract of the earthworm constitutes an anoxic saccharide-rich microzone in aerated soils that offers ingested microbes a unique opportunity for anaerobic growth. The fermentative activity of microbes in the alimentary tract are responsible for the production of (i) organic compounds that can be assimilated by the earthworm and (ii) H that is subject to emission by the earthworm and can be trophically linked to secondary microbial events in soils. To gain insight on how fermentative members of the gut microbiome might respond to the saccharide-rich alimentary canal, this study examines the impact of diverse gut-associated saccharides on the differential activation of fermentative microbes in gut contents of the model earthworm.

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Bacterial Fermentation

Cited by 30 publications

References 10 publications

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

A sodium ion‐dependent A₁A_O ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus

Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris

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Bacterial Fermentation

Cited by 30 publications

References 10 publications

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments

A sodium ion‐dependent A1AO ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus

Differential Engagement of Fermentative Taxa in Gut Contents of the Earthworm Lumbricus terrestris

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A sodium ion‐dependent A₁A_O ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus