Genome Sequences for Six Rhodanobacter Strains, Isolated from Soils and the Terrestrial Subsurface, with Variable Denitrification Capabilities

Kostka, Joel E.; Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Katz, Lee S.; Mariño-Ramírez, Leonardo; Jordan, I. King; Munk, Christine; Ivanova, Natalia; Mikhailova, Natalia; Watson, David B.; Brown, Steven D.; Palumbo, Anthony V.; Brooks, Scott C.

doi:10.1128/jb.00871-12

Cited by 64 publications

(39 citation statements)

References 17 publications

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“…In contrast, when nitrite was used as the first electron acceptor, nirS sequences similar to those found in Gammaproteobacteria, in particular Rhodanobacter sp., were the most abundant. A recent analysis of complete genome sequences of six Rhodanobacter strains isolated from soils have revealed that at least three of them lack the ability to reduce nitrate [50]. Similarly to what has been observed with the nirS gene, bacteria enriched when nitrite was used suggest the exclusive use of nitrite as electron acceptor.…”

Section: Discussionmentioning

confidence: 80%

Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

et al. 2013

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The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m−3 NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m−3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.

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Section: Discussionmentioning

confidence: 80%

Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

et al. 2013

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“…Even though our protocol was validated to detect nitrifiers (Fig. S4), we also found no nitrifiers in the commercial inoculum, which was dominated by Rhodanobacter, a known denitrifying genus [11].…”

Section: Narrativementioning

confidence: 81%

Negative plant-microbiome feedback limits productivity in aquaponics

Day

Otwell

Diener

et al. 2019

Preprint

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“…Some nitrate-reducing organisms carry out only the first step, the dissimilatory reduction of nitrate to nitrite, while others reduce nitrate to ammonium by a process called nitrate ammonification (11). On the other hand, some microorganisms cannot reduce nitrate but contain later steps of the denitrification pathway (12).…”

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confidence: 99%

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

Thorgersen

Lancaster

Vaccaro

et al. 2015

Appl Environ Microbiol

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The concentrations of molybdenum (Mo) and 25 other metals were measured in groundwater samples from 80 wells on the Oak Ridge Reservation (ORR) (Oak Ridge, TN), many of which are contaminated with nitrate, as well as uranium and various other metals. The concentrations of nitrate and uranium were in the ranges of 0.1 M to 230 mM and <0.2 nM to 580 M, respectively. Almost all metals examined had significantly greater median concentrations in a subset of wells that were highly contaminated with uranium (>126 nM). They included cadmium, manganese, and cobalt, which were 1,300-to 2,700-fold higher. A notable exception, however, was Mo, which had a lower median concentration in the uranium-contaminated wells. This is significant, because Mo is essential in the dissimilatory nitrate reduction branch of the global nitrogen cycle. It is required at the catalytic site of nitrate reductase, the enzyme that reduces nitrate to nitrite. Moreover, more than 85% of the groundwater samples contained less than 10 nM Mo, whereas concentrations of 10 to 100 nM Mo were required for efficient growth by nitrate reduction for two Pseudomonas strains isolated from ORR wells and by a model denitrifier, Pseudomonas stutzeri RCH2. Higher concentrations of Mo tended to inhibit the growth of these strains due to the accumulation of toxic concentrations of nitrite, and this effect was exacerbated at high nitrate concentrations. The relevance of these results to a Mo-based nitrate removal strategy and the potential community-driving role that Mo plays in contaminated environments are discussed.

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Genome Sequences for Six Rhodanobacter Strains, Isolated from Soils and the Terrestrial Subsurface, with Variable Denitrification Capabilities

Cited by 64 publications

References 17 publications

Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

Denitrifying Bacterial Communities Affect Current Production and Nitrous Oxide Accumulation in a Microbial Fuel Cell

Negative plant-microbiome feedback limits productivity in aquaponics

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

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