Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462T Improved Environmental Adaptability

Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities

Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.

Incomplete denitrification phenotypes in diverse Thermus species from diverse geothermal spring sediments and adjacent soils in southwest China

A few members of the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite (NO₂⁻) or nitrous oxide (N₂O). However, the denitrification abilities of the genus as a whole remain poorly characterized. Here, we describe diverse denitrification phenotypes and genotypes of a collection of 24 strains representing ten species, all isolated from a variety of geothermal systems in China. Confirmed terminal products of nitrate reduction were nitrite or N₂O, while nitric oxide (NO) was inferred as the terminal product in some strains. Most strains produced N₂O; complete denitrification was not observed. Denitrification phenotypes were largely consistent with the presence of denitrification genes, and strains of the same species often had the same denitrification phenotypes and largely syntenous denitrification gene clusters. Genes for nirS and nirK coexisted in three Thermus brockianus and three Thermus oshimai genomes, which is a unique hallmark of some denitrifying Thermus strains and may be ecologically important. These results show that incomplete denitrification phenotypes are prominent, but variable, within and between Thermus species. The incomplete denitrification phenotypes described here suggest Thermus species may play important roles in consortial denitrification in high-temperature terrestrial biotopes where sufficient supply of oxidized inorganic nitrogen exists.

Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle, and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments. However, neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood. Here, we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains. We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene. Ancestral character state reconstructions and phylogenetic analyses showed that narG, nirS, and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically. In contrast, nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis. This study expands our understanding of the genomic potential for incomplete denitrification in Thermus, revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae, and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.

Treatment of Low C/N Ratio Wastewater by a Carbon Cloth Bipolar Plate Multicompartment Electroenhanced Bioreactor (CBM-EEB)

The traditional biological denitrification process has the problems of low removal rates and lack of a carbon source when treating wastewater with high ammonia nitrogen concentration and a low carbon-nitrogen ratio. Based on a bio-electrochemical system (BES), a novel carbon cloth bipolar plate multicompartment electroenhanced bioreactor (CBM-EEB) system was constructed. In this study, nitrogen removal efficiency and enrichment of functional bacteria using CBM-EEB under different voltage conditions were investigated. The results from next-generation sequencing indicated that the CBM-EEB included heterotrophic nitrification and aerobic denitrification (HNAD) and was dominated by heterotrophic nitrification aerobic denitrifying bacteria (HNADB). The applied voltage was confirmed as having the ability to regulate the microbial community structure and abundance of functional genes, thereby further enhancing the nitrogen removal efficiency of the system. The total nitrogen removal efficiency was 77.70 ± 1.14, 87.10 ± 0.56, 86.40 ± 0.59, and 89.30 ± 0.53% under applied voltages of 0.4, 0.7, 1.0, and 1.3 V, respectively. All values were significantly higher than the control group (62.86 ± 2.06%). HNADB had the highest abundance among the 17 detected genera related to nitrogen metabolism. Facultative denitrifying bacteria, Pseudoxanthomonas, along with key bacteria of HNADB, such as Flavobacterium, constructed a shortcut simultaneous nitrification-denitrification (SND) process. Poisson analysis and redundancy analysis (RDA) showed that the applied voltage improved the denitrification efficiency by changing the microbial community structure, reducing the abundance of heterotrophic bacteria, and increasing the unit abundance of key functional genes so that less organics were required for the denitrification process. The increased nitrogen removal efficiency in the experimental group was mainly related to simultaneous nitrification-denitrification process and cooperation of microbial communities in the anode and the cathode. This study highlighted the feasibility of CBM-EEB to enhance the HNAD reaction and the response of wastewater with a low C/N ratio to enhance the abundance of microbial bacteria and their functional gene abundance.