Draft Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodopseudomonas palustris XCP

Denitrification is a form of anaerobic respiration wherein nitrate is sequentially reduced via nitrite, nitric oxide, and nitrous oxide to dinitrogen gas. The pathway has mostly been characterized in bacteria that have the complete denitrification pathway. However, each individual step can serve as a form of anaerobic respiration and many bacteria only have partial denitrification pathways. The conditions under which these partial denitrification pathways are activated have received comparatively little attention. Here we report the activity of partial denitrification pathways in two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA009 and Rhodobacter capsulatus SB1003. These bacteria can use one or more denitrification steps as an electron sink during phototrophic growth or to transform energy during anaerobic respiration in the dark. In each case, nitrous oxide reduction required supplementation with a non-catalyzable denitrification intermediate. Thus, bacteria that maintain partial denitrification pathways are still subject to regulation by denitrification intermediates that they cannot use.ImportanceDenitrification is a form of microbial respiration wherein nitrate is converted into dinitrogen gas, a major component of Earth’s atmosphere, via several nitrogen oxide intermediates. Unfortunately, denitrification of nitrate in agricultural fertilizers is often incomplete, resulting in the emission of the potent greenhouse gas, nitrous oxide. Some bacteria do not have all the steps for denitrification, but many can still reduce nitrous oxide into harmless dinitrogen gas. These partial denitrifying bacteria have received little attention. Here we characterized two partial denitrifying bacteria that are capable of nitrous oxide reduction. Surprisingly, nitrous oxide reduction was induced by denitrification intermediates that the bacteria could not respire, suggesting that regulation of nitrous oxide reduction was subject to the same cues as in complete denitrifiers. This work thus informs on how partial denitrifying bacteria can contribute to, and potentially combat, greenhouse gas emissions.

show abstract

“…1B). The spectrum of denitrification activities and gene content also varies for different R. palustris strains (21-23) (Fig. 6).…”

Section: Discussionmentioning

confidence: 99%

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

LaSarre

Morlen

Neumann

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Furthermore, members of this species have been proposed, based on their As detoxification mechanisms, for bioremediation of arsenic contaminated areas surrounding mines as have been shown to be able to oxidize As(III) to As (V) . Members of this species can grow with or without light or oxygen, fix nitrogen, and degrade a wide range of organic compounds, with different strains shown to harbor strain specific genes and exhibit distinctive physiological characteristics with respect to anaerobic fermentation, expanded biodegradation, or expanded light-harvesting capabilities , leading to the proposal that they should be reclassified into different species . Hence, differences in copy number of these strains due to plant and manure induced changes in redox potential, pH and available carbon sources is of considerable interest in the context of arsenic in rice grain.…”

Section: Discussionmentioning

confidence: 99%

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum

Afroz

Carey

et al. 2019

Environ. Sci. Technol.

View full text Add to dashboard Cite

The interplay between rice roots and manuring with respect to arsenic speciation, subsequent assimilation into roots, and translocation to shoots in paddy soil was investigated, alongside bacterial diversity characterization. Planting increased soil Eh and decreased soil solution arsenic species: inorganic arsenic (iAs), monomethylarsonic acid (MMA), trimethylarsenic oxide (TMAO) and dimethylarsinic acid (DMA). Presence of plant roots increased copy number of Clostridium and Tumebacillus 16S rRNA as well as Streptomyces arsenic methylating gene (arsM), but decreased Acidobacteria_GP1 16S rRNA and R. palustris BisB5 arsM. Sum of arsenic species decreased under root influence due to the interplay of inorganic arsenic mobilization in bulk soil under anaerobic and immobilization under oxygenated rhizospheric conditions. Manuring increased all soil solution arsenic species (>90%), shoot total arsenic (60%), copy number of Geobacter 16S rRNA and R. palustris TIE-1 arsM, indicative of a shift towards microbes with iron reduction and oxidation as well as arsenic methylation capabilities.

show abstract

“…Several nominal Rhodopseudomonas strains have been sequenced since 2004 ( 6 – 9 ). When we performed a JSpecies comparison ( 10 ) of the average percentage nucleotide identity between R. rutila R1 and published Rhodopseudomonas genome sequences, the following species/strains showed the highest identities: CG009, 97.4%; TIE, 97.4%; ELI1980, 97.2%; YSC3, 92.5%; PS3, 92.4%; 420L, 88.5%; DX1, 88.3%; pentothenatexigens, 88.3%; thermotolerans, 88.2%; XCP, 88.1%; AAP120, 82.1%; HA2, 81.8%; B29, 81.2%; and B5, 81.2%.…”

Section: Announcementmentioning

confidence: 99%

“…As we recently noted with the Rhodopseudomonas sp. XCP genome ( 9 ), the low average nucleotide identity (ANI) between the various Rhodopseudomonas strains suggests that there is a need to revise and restructure the taxonomy. Based on our current analysis, strains R1, CG009, TIE, and ELI1980 all belong to R. rutila , while only strains 2.1.6 and B5 remain within the confines of the R. palustris species.…”

Section: Announcementmentioning

confidence: 99%

Draft Whole-Genome Sequence of the Purple Nonsulfur Photosynthetic Bacterium Rhodopseudomonas rutila R1

Robertson

Rayyan

Meyer

et al. 2018

Microbiol Resour Announc

Self Cite

View full text Add to dashboard Cite

show abstract

Draft Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodopseudomonas palustris XCP

Cited by 7 publications

References 22 publications

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

Inhibition of Microbial Methylation via arsM in the Rhizosphere: Arsenic Speciation in the Soil to Plant Continuum

Draft Whole-Genome Sequence of the Purple Nonsulfur Photosynthetic Bacterium Rhodopseudomonas rutila R1

Contact Info

Product

Resources

About