Denitrifying organisms are essential in removing fixed nitrogen pollutants from ecosystems (e.g. sewage sludge). They can be detrimental (e.g. for agricultural soil) and can also produce the greenhouse gas N2O (nitrous oxide). Therefore a more comprehensive understanding of this process has become increasingly important regarding its global environmental impact. Even though bacterial genome sequencing projects may reveal new data, to date the denitrification abilities and features in Gram-positive bacteria are still poorly studied and understood. The present review evaluates current knowledge on the denitrification trait in Gram-positive bacteria and addresses the likely existence of unknown denitrification genes. In addition, current molecular tools to study denitrification gene diversity in pure cultures and environmental samples seem to be highly biased, and additional novel approaches for the detection of denitrifying (Gram-positive) bacteria appear to be crucial in re-assessing the real diversity of denitrifiers.
"PCR-based approaches require the prior sequence data of the specific target gene of interest. Consequently, q-PCR can only be used for targeting of known genes and is inevitably limited to access the 'unknown' genes (Smith and Osborn, 2009; Verbaendert et al., 2011). Because the majority of microorganisms in the environment are highly divergent from those of most cultured organisms, the employment of emerging " omics " approaches along with advanced analytical chemistry provides new opportunities to bridge the knowledge gap across scales and to link microbial functions with biogeochemical cycles (Lin et al., 2014). "
[Show abstract][Hide abstract] ABSTRACT: Various studies have been conducted to investigate effects of dams on river ecosystems, but less information is available regarding damming impacts on downstream denitrification. We measured denitrification enzyme activity (potential denitrification rate) and denitrifier abundances (using nirS, nirK, and nosZ as markers) in dammed headstreams of the Nakdong River in South Korea. Sediments in Phragmites-dominated riparian areas and in-stream areas across streams (dammed vs. reference) with different streambed materials (gravel and sand) were sampled occasionally. We hypothesized that (i) the higher available N and C contents in sediments downstream of dams foster larger denitrifier communities than in the reference system and (ii) differences in potential denitrification rates across the systems correspond with denitrifier abundances. Despite 30 years of different hydrological management with dams and greater inorganic N and DOC contents in sediments downstream of dams, compared to the references, abundances of denitrifier communities and potential denitrification rates within the whole sediment were not significantly different across the systems. However, nirS and nosZ denitrifier abundances and potential denitrification rates were considerably increased in specific sediments downstream of dams (gravelly riparian and sandy in-stream) with regard to flooding events and seasonal temperature variation. nirK was not amplified in all sediments. Canonical correspondence analyses (CCA) revealed that the relationship between abundances of denitrifier communities and nutrient availabilities and potential denitrification rates was a weak one.
Korean Journal of Microbiology 06/2014; 50(2):137-151. DOI:10.7845/kjm.2014.4021
"In-depth studies of only a limited number of organisms lie at the basis of the current knowledge of denitrification (Bergaust et al., 2011), but organism-based research has proven to provide novel insights into all aspects of the process (Green et al., 2010; Jones et al., 2011; Heylen & Keltjens, 2012), and comparison of individual denitrifying strains can provide new insights into denitrifier diversity (Jones et al., 2011). Despite the fact that the denitrification trait has been observed in several Gram-positive strains (Shapleigh, 2006; Jones et al., 2011; Verbaendert et al., 2011a, b), the fundamentals of denitrification within this group, such as biochemistry, majors drivers of end product stoichiometry and denitrification regulatory phenotype (DRP) (Bergaust et al., 2011), are still underexplored . Furthermore, molecular community analyses of denitrifiers in the environment fail to detect this group of organisms because most available PCR primers for nitrite reductase (nir), nitric oxide reductase (nor), and nitrous oxide reductase (nosZ) genes have been designed on genes of Gram-negative Proteobacteria (Braker et al., 1998; Scala & Kerkhof, 1998; Hallin & Lindgren, 1999; Casciotti & Ward, 2001; Kloos et al., 2001; Braker & Tiedje, 2003; "
[Show abstract][Hide abstract] ABSTRACT: Although efforts have been made the past few years, knowledge on genomic and phenotypic diversity and occurrence of the denitrification ability in Gram-positive bacteria is still fragmentary. Many environmental monitoring approaches have used nir, nor and nos genes as marker genes for detection of denitrification or denitrifying bacteria. However, primers used in these methods often fail to detect the genes in specific bacterial taxa, such as Gram-positive denitrifiers. In this study, novel primer sets specifically targeting nirK, qnorB and nosZ genes of the Firmicute genus Geobacillus were developed by genomic mining and tested in parallel with commonly used primers on a set of phylogenetically closely related denitrifying geobacilli. Novel nirK and qnorB sequences were recovered from all strains tested, whereas nosZ was detected in part of the strain set, which was in agreement with phenotypic testing. Inter-species and modest intra-species variations in AFLP (Amplified Fragment Length Polymorphism) patterns were observed, verifying presence of genomic variation within the strain set. Our study shows that closely related Gram-positive denitrifiers may differ in denitrification phenotype and genotype. But foremost, novel primers targeting very divergent nirK, qnorB and nosZ gene sequences of Gram-positive denitrifiers, are now available for cultivation-independent environmental surveys. This article is protected by copyright. All rights reserved.
"The apparent discrepancies are likely explained by the different test systems used. In addition, a proper metabolic analysis of the dissimilatory nitrogen pathways should use defined culture media, and many of these steps are medium dependent and strain rather then species specific  . "
[Show abstract][Hide abstract] ABSTRACT: The phenotypic and genotypic characteristics of fourteen human clinical Achromobacter strains representing four genogroups which were delineated by sequence analysis of nusA, eno, rpoB, gltB, lepA, nuoL and nrdA loci, demonstrated that they represent four novel Achromobacter species. The present study also characterized and provided two additional reference strains for Achromobacter ruhlandii and Achromobacter marplatensis, species for which, thus far, only single strains are publicly available, and further validated the use of 2.1% concatenated nusA, eno, rpoB, gltB, lepA, nuoL and nrdA sequence divergence as a threshold value for species delineation in this genus. Finally, although most Achromobacter species can be distinguished by biochemical characteristics, the present study also highlighted considerable phenotypic intraspecies variability and demonstrated that the type strains may be phenotypically poor representatives of the species. We propose to classify the fourteen human clinical strains as Achromobacter mucicolens sp. nov. (with strain LMG 26685(T) [=CCUG 61961(T)] as the type strain), Achromobacter animicus sp. nov. (with strain LMG 26690(T) [=CCUG 61966(T)] as the type strain), Achromobacter spiritinus sp. nov. (with strain LMG 26692(T) [=CCUG 61968(T)] as the type strain), and Achromobacter pulmonis sp. nov. (with strain LMG 26696(T) [=CCUG 61972(T)] as the type strain).
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