Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Song, Bongkeun; Ward, Bess B.

doi:10.1111/j.1574-6941.2003.tb01075.x

Cited by 62 publications

(29 citation statements)

References 28 publications

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“…This cluster also included 10 clones from a number of different environments, including sediments from the River Colne estuary, Puget Sound, and Washington continental margin, as well as water column depths within the Baltic Sea and the coastal Arabian Sea oxygen minimum zone. The only cultivated member of this cluster is Azoarcus tolulyticus , a nitrogen-fixing betaproteobacterium that can degrade toluene under denitrifying conditions (Zhou et al, 1995; Song and Ward, 2002). This cluster is thus not only widely distributed geographically, but also among several different kinds of estuarine and marine environments.…”

Section: Resultsmentioning

confidence: 99%

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

Francis¹,

O’Mullan²,

Cornwell³

et al. 2013

Front. Microbiol.

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Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96–123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.

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Section: Resultsmentioning

confidence: 99%

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

Francis¹,

O’Mullan²,

Cornwell³

et al. 2013

Front. Microbiol.

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“…In addition to supplying biosurfactants, the addition of different nitrate compounds may have stimulated the growth of denitrifying Achromobacter spp. and P. stutzeri (Song and Ward, 2003) in the bio-stimulated community, whereas depletion of nitrate may have favoured the presence of the nitrogen-fixing Azospirillum species in the non-stimulated community. In addition to denitrification, P. stutzeri is well known as naphthalene degrader, which has been isolated in such hydrocarbon enrichments from a wide range of environmental samples (Rosselló-Mora et al , 1994), and was already an important component of the original Nbs soil.…”

Section: Resultsmentioning

confidence: 99%

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

et al. 2012

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Microbial metabolism in aromatic-contaminated environments has important ecological implications, and obtaining a complete understanding of this process remains a relevant goal. To understand the roles of biodiversity and aromatic-mediated genetic and metabolic rearrangements, we conducted ‘OMIC’ investigations in an anthropogenically influenced and polyaromatic hydrocarbon (PAH)-contaminated soil with (Nbs) or without (N) bio-stimulation with calcium ammonia nitrate, NH4NO3 and KH2PO4 and the commercial surfactant Iveysol, plus two naphthalene-enriched communities derived from both soils (CN2 and CN1, respectively). Using a metagenomic approach, a total of 52, 53, 14 and 12 distinct species (according to operational phylogenetic units (OPU) in our work equivalent to taxonomic species) were identified in the N, Nbs, CN1 and CN2 communities, respectively. Approximately 10 out of 95 distinct species and 238 out of 3293 clusters of orthologous groups (COGs) protein families identified were clearly stimulated under the assayed conditions, whereas only two species and 1465 COGs conformed to the common set in all of the mesocosms. Results indicated distinct biodegradation capabilities for the utilisation of potential growth-supporting aromatics, which results in bio-stimulated communities being extremely fit to naphthalene utilisation and non-stimulated communities exhibiting a greater metabolic window than previously predicted. On the basis of comparing protein expression profiles and metagenome data sets, inter-alia interactions among members were hypothesised. The utilisation of curated databases is discussed and used for first time to reconstruct ‘presumptive’ degradation networks for complex microbial communities.

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“…The other six sequenced nirK clones were in the fourth cluster (Cluster 4) and had 69% to 77% similar to the nirK gene of Mesorhizobium sp. (α-Proteobacteria) [21] .…”

Section: Sequences Data and Phylogenetic Analysis Of Nirk And Nosz CLmentioning

confidence: 99%

The diversity of denitrifying bacteria in the alpine meadow soil of Sanjiangyuan natural reserve in Tibet Plateau

Zhang

Wang

et al. 2006

CHINESE SCI BULL

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This is the first time to describe the diversity of denitrifying bacteria in Sanjiangyuan natural reserve in Tibet Plateau by investigating the molecular diversity and phylogenetic analysis of nirK and nosZ genes using PCR-RFLP and sequencing. Four soil samples were collected from alpine meadow communities from over an altitude of 4600 m which had different physicochemical properties by principal component analysis (PCA). For the genes fragment of nirK and nosZ, the diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequenced. A total of 253 nirK clones and 283 nosZ clones were received in four samples, and 78 operational taxonomic units (OTUs) of nirK and 120 OTUs of nosZ by the restriction enzymes MspI and RsaI digested. The analysis of environmental factors showed that altitude and C/N ratio in soil may be the key factors to the denitrifying bacteria community. 36 nirK clones and 17 nosZ clones were sequenced, and their levels of nucleotide identity were from 69% to 98% and 57% to 97%, respectively. The phylogenetic tree was constructed using the Clustal W and Mega softwares, and all the sequenced clones could be subdivided into 4 groups. Some of clone sequences were related to the nirK and nosZ genes belonging to three phylogenetic subdivisions (α-, β-and γ subclasses of the Proteobacteria), while most of the clones were closely related to the genes of the uncultured bacteria. The sequence distributions were not clear relating to the sample sites in the tree.

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Nitrite reductase genes in halobenzoate degrading denitrifying bacteria

Cited by 62 publications

References 28 publications

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation

The diversity of denitrifying bacteria in the alpine meadow soil of Sanjiangyuan natural reserve in Tibet Plateau

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