Illumina MiSeq sequencing reveals the community composition of NirS-Type and NirK-Type denitrifiers in Zhoucun reservoir – a large shallow eutrophic reservoir in northern China

Zhou, Shilei; Huang, Tinglin; Zhang, Chunhua; Fang, Kai; Xia, Chao; Bai, Shiyuan; Zeng, Mingzheng; Qiu, Xiaopeng

doi:10.1039/c6ra18017e

Cited by 34 publications

(17 citation statements)

References 47 publications

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“…Some unknown microorganisms maybe not are captured by the primers used in this study. In addition to nirS-type denitrifers, nirK-type denitrifer was observed in estuarine systems [12,38,39,40]. Although we have done some investigation about nirK gene in the PRE, the primers for nirK gene need to be optimized.…”

Section: Discussionmentioning

confidence: 99%

“…On the contrary, functional genes encoding nitrite reductase are characterized with more sequence changes, which can not only analyze the microbial community structure, but also identify the microbial communities' ecological functions. The functional genes of nirS and nirK have been proven to be credible molecular markers to reveal the community composition and structure of denitrifying microbes [12], which have been widely used to investigated the diversity of denitrifers in various environments, such as the aquatic ecosystems, sediments and also the wastewater treatment plant (WWTP) [13][14][15]. Previous studies showed that nirS-type denitrifers make up more than 70% of known denitrifiers [16].…”

Section: Introductionmentioning

confidence: 99%

“…In recent years, high-throughput sequencing technology has been widely used to investigate microbial diversity. For example, Zhou et al [12] investigated the diversity and community structure of denitrifiers containing nirS gene in Zhoucun, and Fan et al [18] analyzed the ecological distribution of denitrifers in Lake Taihu reservoir using Illumina Miseq sequencing technology. However, a suitable reference taxonomic database of nirS gene has not yet to be constructed and the similarity threshold of nirS gene for OTU (operational taxonomic unit) clustering has also not yet been determined.…”

Section: Introductionmentioning

confidence: 99%

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Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary

et al. 2020

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Denitrification, an important process in microbial mediated nitrogen cycle, plays important roles in nitrogen loss in estuarine sediments. However, the function of denitrifiers in the estuarine subsurface sediments remained poorly understood. In this study, we analyzed the potential activity, abundance and community structure of nirS-type denitrifiers using 15 N-labeled incubation quantitative-PCR and high throughput sequencing techniques in sediment cores from Pearl River Estuary (PRE). Results showed that subsurface sediments had nearly same level denitrification potential activity compare to surface sediments, although the abundance of nirS gene decreased sharply from surface to bottom in sediment cores. Meanwhile, nirS gene abundance exhibit significant temporal variations, which is consistent with denitrification potential activity. Moreover, the community structure and diversity of nirS-type denitrifiers in sediment cores exhibited remarkable temporal shift pattern. For spatial variation, no significant difference was observed of denitrifiers community structure in each sediment core from the surface to the subsurface, while there were significant different diversity characteristic among different cores. Redundancy analysis (RDA) showed that multiple environmental factors including salinity, pH, oxidation-reduction potential, nutrient content and organic substances synergistically shaped the diversity and distribution of nirS-type denitrifers in PRE sediments. Our results showed that nirS-type denitrifers played important roles in the nitrogen removal in subsurface sediments of PRE.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary

et al. 2020

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“…Redundancy analysis (RDA) was used to evaluate the relationship between the bacterial community structure and water environmental parameters with variance inflation factor analysis (VIF < 10) [ 29 , 30 ]. The mantel test was performed to investigate the relationships between water microbial/functional communities and environmental parameters [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Linking Shifts in Bacterial Community Composition and Function with Changes in the Dissolved Organic Matter Pool in Ice-Covered Baiyangdian Lake, Northern China

Zhou

Sun

et al. 2020

Microorganisms

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The relationship between CDOM (Chromophoric dissolved organic matter) and the bacterial community was investigated in ice-covered Baiyangdian Lake. The results showed that environmental parameters significantly differed in Baiyangdian Lake, whereas a-diversity was not significantly different. Moreover, the microbial and functional communities exhibited significant differences, and T (Temperature), pH, ORP (Oxidation-reduction potential), DO (Dissolved oxygen), NO3−-N, NH4+-N, and Mn (Manganese) were the main environmental factors of these differences, based on redundancy analysis and the Mantel test. Biomarkers of the microbial and functional communities were investigated through linear discriminant analysis effect size and STAMP analysis. The number of biomarkers in the natural area was highest among the typical zones, and most top functions were related to carbohydrate metabolism. Two protein-like components (C1 and C2) and one humic-like component (C3) were identified by parallel factor analysis, and C1 was positively related to C2 (R = 0.99, p < 0.001), indicating the same sources. Moreover, CDOM significantly differed among the typical zones (p < 0.001). The high biological index, fluorescence index, β:α, and low humification index indicated a strong autochthonous component and aquatic bacterial origin, which was consistent with the results of UV-vis absorption spectroscopy. Network analysis revealed non-random co-occurrence patterns. The bacterial and functional communities interacted closely with CDOM. The dominant genera were CL500-29_marine_group, Flavobacterium, Limnohabitans, and Candidatus_Aquirestis. Random forest analysis showed that C1, C2, and C3 are important predictors of α- and β-diversity in the water bacterial community and its functional composition. This study provides insight into the interaction between bacterial communities and DOM (Dissolved organic matter) in ice-covered Baiyangdian Lake.

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“…Likewise, the patterns of nirK diversity across soil groups were mirrored by the patterns of nos : nir, suggesting that changes in the size of the nirK community had a dominant influence on the overall ratio of complete and incomplete denitrifiers in soil groups. Independent shifts in nirS and nirK community structures in response to common physicochemical characteristics were recently observed in a eutrophic reservoir (Zhou et al, 2016). In contrast, the structure of nosZ communities did not correspond to any physicochemical property measured.…”

Section: Discussionmentioning

confidence: 99%

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

et al. 2017

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Abstract. Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N 2 O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N 2 O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N 2 O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N 2 O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N 2 O emissions through denitrification across a wide range of soil types.

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Illumina MiSeq sequencing reveals the community composition of NirS-Type and NirK-Type denitrifiers in Zhoucun reservoir – a large shallow eutrophic reservoir in northern China

Abstract: Denitrification is a major biological process that reduces nitrate to nitrogen gas (N2 or N2O).

Cited by 34 publications

References 47 publications

Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary

Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary

Linking Shifts in Bacterial Community Composition and Function with Changes in the Dissolved Organic Matter Pool in Ice-Covered Baiyangdian Lake, Northern China

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

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