Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection

Joana, Sousa; Silveira, Célia M.; Fontes, Pedro Mendes; Roma‐Rodrigues, Catarina; Fernandes, Alexandra R.; Driessche, Gonzalez Van; Devreese, Bart; Moura, Isabel; Moura, José J. G.; Almeida, M. Gabriela

doi:10.1016/j.bbapap.2017.07.021

Cited by 9 publications

(3 citation statements)

References 83 publications

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“…Only proteins soluble in a low ionic strength buffer were analysed, so inevitably there are major differences between the proteomic and our RNAseq data. However, increased accumulation of Nap proteins in response to nitrate was confirmed 64 .…”

Section: Discussionmentioning

confidence: 90%

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

Cadby

Faulkner

Chèneby

et al. 2017

Sci Rep

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The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.

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Section: Discussionmentioning

confidence: 90%

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

Cadby

Faulkner

Chèneby

et al. 2017

Sci Rep

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“…This indicates that the akaganeite coating on the pumice may have led to the enrichment of a diverse distribution of Fe(III)-reducers capable of oxidizing both lactate and acetate in anoxic conditions. As for the deployed uncoated pumice slurries, lactate metabolism was observed in the absence of an electron acceptor (Fe(III); Figure 4B), suggesting the presence of other electron acceptors, such as insoluble manganese or sulfate minerals (Sousa et al, 2017;Novotnik et al, 2019), sorbed or precipitated from the spring water. Alternatively, fermentation of lactate could also occur in the absence of an electron acceptor (Oude-Elferink et al, 2001;Tao et al, 2016).…”

Section: Geochemical Changes During the Incubation Of The Deployed "Mmentioning

confidence: 93%

A Novel “Microbial Bait” Technique for Capturing Fe(III)-Reducing Bacteria

et al. 2020

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Microbial reduction of Fe(III) is a key geochemical process in anoxic environments, controlling the degradation of organics and the mobility of metals and radionuclides. To further understand these processes, it is vital to develop a reliable means of capturing Fe(III)-reducing microorganisms from the field for analysis and lab-based investigations. In this study, a novel method of capturing Fe(III)-reducing bacteria using Fe(III)-coated pumice "microbe-baits" was demonstrated. The methodology involved the coating of pumice (approximately diameter 4 to 6 mm) with a bioavailable Fe(III) mineral (akaganeite), and was verified by deployment into a freshwater spring for 2 months. On retrieval, the coated pumice baits were incubated in a series of lab-based microcosms, amended with and without electron donors (lactate and acetate), and incubated at 20 • C for 8 weeks. 16S rRNA gene sequencing using the Illumina MiSeq platform showed that the Fe(III)-coated pumice baits, when incubated in the presence of lactate and acetate, enriched for Deltaproteobacteria (relative abundance of 52% of the sequences detected corresponded to Geobacter species and 24% to Desulfovibrio species). In the absence of added electron donors, Betaproteobacteria were the most abundant class detected, most heavily represented by a close relative to Rhodoferax ferrireducens (15% of species detected), that most likely used organic matter sequestered from the spring waters to support Fe(III) reduction. In addition, TEM-EDS analysis of the Fe(III)-coated pumice slurries amended with electron donors revealed that a biogenic Fe(II) mineral, magnetite, was formed at the end of the incubation period. These results demonstrate that Fe(III)-coated pumice "microbe baits" can potentially help target metal-reducing bacteria for culture-dependent studies, to further our understanding of the nano-scale microbe-mineral interactions in aquifers.

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“…It might be that SRB activity continued despite nitrate addition, because although the preferential use of nitrate by SRB is possible in many systems since nitrate reduction is thermodynamically more favourable, some species of SRB such as Desulfovibrio desulfuricans use sulphate over nitrate when both of the electron acceptors are present in excess ( Dalsgaard and Bak, 1994;Marietou, 2009). For this metabolic preference, Sousa et al (2017) proposed that D. desulfuricans activates additional pathways involving amino acid and/or protein biosynthesis to adapt to nitrate medium, whereas in the presence of sulphate the bacterium expresses predominantly the proteins required for its constitutive energy metabolism. For the current study, we speculate that the addition of nitrate did not kill SRB, but rather induced interspecies competition and after the majority of the sulphate was consumed, it enhanced the oxidation of produced H2S as alternative electron donor.…”

Section: Frequent Nitrate Addition Could Decrease Accumulated H2s In the Pond As A Curative Solutionmentioning

confidence: 99%

Nitrate amendment to control sulphide accumulation in shrimp ponds

Torun

Hostins²,

Teske³

et al. 2020

Aquaculture

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The production of shrimp is often performed in earthen outdoor ponds in which the input of feed and faeces on the bottom results in deterioration of the water quality that results in a negative impact on the aquatic animals and the environment.Nitrate application in shrimp ponds could improve pond water and sediment quality by oxidizing anaerobic zones of the sediment. This study was conducted to evaluate the possible benefits of nitrate treatment in combination with probiotics application to decrease sulphide formation in shrimp ponds, which is a crucial problem during the growth phase of shrimp. A batch system including shrimp feed and faeces, representing the bottom waste produced during 90 days of shrimp culture, was used to test the effect of nitrate addition under anaerobic conditions that mimic the dead zones in shrimp pond bottoms where high amounts of organic matter accumulate. Nitrate addition acted as a curative solution for hydrogen sulphide (H2S) accumulation, rather than preventive. Nitrate amended treatments (12.5 mg/L.day NO3) decreased the accumulated H2S in the headspace of incubation bottles by 93±3% compared to the controls. Nitrate addition increased pH and decreased organic acids accumulation to trace amounts. The use of a denitrifying strain did not improve the beneficial effect of nitrate, indicating that intrinsic capacity for anoxic conversion of waste by the present community was sufficient. In conclusion, nitrate treatment showed a curative potential to control H2S accumulation in the shrimp ponds that is a critical problem during the growth of shrimp.

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Understanding the response of Desulfovibrio desulfuricans ATCC 27774 to the electron acceptors nitrate and sulfate - biosynthetic costs modulate substrate selection

Cited by 9 publications

References 83 publications

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

A Novel “Microbial Bait” Technique for Capturing Fe(III)-Reducing Bacteria

Nitrate amendment to control sulphide accumulation in shrimp ponds

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