Microbial metabolism | EPFL Graph Search

Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles. Types Primary nutritional groups All microbial metabolisms can be arranged according to three principles:

How the organism obtains carbon for synthesizing cell mass:

autotrophic – carbon is obtained from carbon dioxide ()
heterotrophic – carbon is obtained from organic compounds
mixotrophic – carbon is obtained from both organic compounds and by fixing carbon dioxide

How the organism obtains reducing equivalents (hydrogen atoms or electrons) used either in e

H2-fuelled microbial metabolism in Opalinus Clay

Rizlan Bernier-Latmani, Aislinn Ann Boylan, Niels Burzan, Luca Loreggian, Carla Perez Mon

In Switzerland, the Opalinus Clay formation is considered the most likely host rock for a deep geological repository for nuclear waste. In deep geological repositories, H2 is expected to be the most abundant gas formed from the degradation of waste and from metal corrosion. The microbial community present in Opalinus Clay is capable of utilizing H2 as an electron donor and sulfate as an electron acceptor to produce hydrogen sulfide. This could be problematic due to its potential for increasing the corrosion of metal waste canisters containing radioactive waste, however, the possible impacts of these processes on the clay rock have not been fully investigated. In this study, a series of microcosm experiments were set-up containing Opalinus Clay and porewater from the Mont Terri underground research laboratory (Switzerland) as an inoculum. Uninoculated microcosms were established to investigate abiotic processes. In the presence of clay, a higher aqueous sulfate concentration was detected than in those with only porewater present and this concentration decreased over time in the inoculated experiments. However, there was no evidence of hydrogen sulfide production in the aqueous phase. In all experiments with clay, there was an increase in aqueous Fe2+ concentrations with the highest concentrations found in uninoculated experiments. The sulfur speciation of the Opalinus Clay was analysed and the results of the inoculated sample suggested that hydrogen sulfide reacted with Fe2+, precipitating iron sulfide minerals. After the incubation period, the microbial community was dominated by the sulfate-reducing Desulfobulbaceae family. The study suggests that H2-fuelled, microbially-mediated sulfate reduction can affect the mineral composition within the Opalinus Clay due to the precipitation of iron sulfide minerals. These precipitation reactions may enhance the long-term integrity of the repository by removing corrosive hydrogen sulfide from solution when sufficient Fe2+ is available and so protecting the canisters containing the nuclear waste.

2019

In vivo regulation of organohalide respiration in Desulfitobacterium hafniense DCB-2

Céline Berruex, Julien Maillard, Marie Vingerhoets, Mathilde Stéphanie Willemin

Background Organohalide respiration (OHR) is a bacterial anaerobic respiratory metabolism which takes advantage of halogenated compounds (= organohalides) as terminal electron acceptors. While its environmental interest does not have to be demonstrated anymore, many aspects of this process remain poorly characterized. We have decided to explore the regulatory network of OHR in Desulfitobacterium hafniense strain DCB-2, a typical OHR bacterium showing a versatile energy metabolism which harbours seven distinct reductive dehalogenase (rdh) gene clusters potentially involved in OHR. Methods Strain DCB-2 was cultivated anaerobically with lactate and fumarate (under respiration conditions) or with pyruvate (under fermentation conditions) and exposed to various chlorinated phenol derivatives, after which RNA was extracted from samples collected at different time intervals. A combination of reverse transcription, qPCR and transcriptomic analysis targeting genes belonging to rdh gene clusters will allow a quantitative analysis of the activity of selected RdhK proteins which are involved in transcriptional regulation. Results This study aims at deciphering the role and cross-talk of characterized and uncharacterized RdhK regulatory proteins of strain DCB-2 in vivo. The activation of transcription of rdh gene clusters after addition of selected chlorophenols will be presented and discussed. Conclusions These data will be confronted to results obtained from in vitro experiments describing the tripartite interaction of purified RdhK proteins with the chlorophenols and the targeted DNA promoters (see also the abstract by M. Willemin et al.).

2018

Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism

Neeraj Dhar, Ping Lu, John McKinney, Muhittin Emre Özdemir

Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multidrug-resistant tuberculosis in decades. Though BDQ has shown excellent efficacy in clinical trials, its early bactericidal activity during the first week of chemotherapy is minimal. Here, using microfluidic devices and time-lapse microscopy of Mycobacterium tuberculosis, we confirm the absence of significant bacteriolytic activity during the first 3-4 days of exposure to BDQ. BDQ-induced inhibition of ATP synthesis leads to bacteriostasis within hours after drug addition. Transcriptional and proteomic analyses reveal that M. tuberculosis responds to BDQ by induction of the dormancy regulon and activation of ATP-generating pathways, thereby maintaining bacterial viability during initial drug exposure. BDQ-induced bacterial killing is significantly enhanced when the mycobacteria are grown on non-fermentable energy sources such as lipids (impeding ATP synthesis via glycolysis). Our results show that BDQ exposure triggers a metabolic remodelling in mycobacteria, thereby enabling transient bacterial survival.

Nature Publishing Group2014

H2-fuelled microbial metabolism in Opalinus Clay

Rizlan Bernier-Latmani, Aislinn Ann Boylan, Niels Burzan, Luca Loreggian, Carla Perez Mon

2019