High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

Qian Qian Hu; Zhi Chao Zhou; Yi Fan Liu; Lei Zhou; Serge Maurice Mbadinga; Jin Feng Liu; Shi Zhong Yang; Ji Dong Gu; Bo Zhong Mu

doi:10.1016/j.ibiod.2019.05.025

High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

Qian Qian Hu, Zhi Chao Zhou, Yi Fan Liu, Lei Zhou, Serge Maurice Mbadinga, Jin Feng Liu, Shi Zhong Yang, Ji Dong Gu, Bo Zhong Mu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel) nitric oxide dismutase-encoding gene PCR products could confer the diversity of nitric oxide dismutase in additional microbial groups other than the two known lineages, but the distribution pattern of nod gene is unclear in different environments including oil reservoirs. Here, we surveyed the distribution and diversity of nod genes by clone library sequencing together with the inference of 16S rRNA gene-based taxonomy by amplicon sequencing in diverse samples including wastewater treatment plants (WWTP), wetland, hydrocarbon-contaminated soil, and oil reservoirs. A total of 730 phylogenetically diverse nod-related sequences recovered from these samples were clustered into 42 operational taxonomic units (OTUs) showing a considerably high diversity of nod gene in these different ecosystems. The abundance of nod gene in five environmental samples were ∼1.80 × 10⁷–2.62 × 10⁸ copies g⁻¹ soil (sludge) and ∼9.67 × 10⁶ copies l⁻¹ water. The dominant microorganisms were Bacteroidetes, Firmicutes, Actinobacteria, and Chloroflexi. Our results expanded significantly the diversity of microbial groups potentially involved in nitric oxide dismutation, suggesting the ubiquity of microbial members in the different ecosystems carrying out NO dismutation reaction. Further studies on the functional capacity of this new microbial group will advance a better understanding of the microbially-driven nitrogen cycling and provide thorough information on N-removal processes and potential applications.

Original language	English
Article number	104708
Journal	International Biodeterioration and Biodegradation
Volume	143
DOIs	https://doi.org/10.1016/j.ibiod.2019.05.025
State	Published - Sep 2019
Externally published	Yes

Keywords

Distribution
Environmental samples
N-removal
Nitric oxide dismutase

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10.1016/j.ibiod.2019.05.025

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title = "High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene",

abstract = "Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel) nitric oxide dismutase-encoding gene PCR products could confer the diversity of nitric oxide dismutase in additional microbial groups other than the two known lineages, but the distribution pattern of nod gene is unclear in different environments including oil reservoirs. Here, we surveyed the distribution and diversity of nod genes by clone library sequencing together with the inference of 16S rRNA gene-based taxonomy by amplicon sequencing in diverse samples including wastewater treatment plants (WWTP), wetland, hydrocarbon-contaminated soil, and oil reservoirs. A total of 730 phylogenetically diverse nod-related sequences recovered from these samples were clustered into 42 operational taxonomic units (OTUs) showing a considerably high diversity of nod gene in these different ecosystems. The abundance of nod gene in five environmental samples were ∼1.80 × 107–2.62 × 108 copies g−1 soil (sludge) and ∼9.67 × 106 copies l−1 water. The dominant microorganisms were Bacteroidetes, Firmicutes, Actinobacteria, and Chloroflexi. Our results expanded significantly the diversity of microbial groups potentially involved in nitric oxide dismutation, suggesting the ubiquity of microbial members in the different ecosystems carrying out NO dismutation reaction. Further studies on the functional capacity of this new microbial group will advance a better understanding of the microbially-driven nitrogen cycling and provide thorough information on N-removal processes and potential applications.",

keywords = "Distribution, Environmental samples, N-removal, Nitric oxide dismutase",

author = "Hu, {Qian Qian} and Zhou, {Zhi Chao} and Liu, {Yi Fan} and Lei Zhou and Mbadinga, {Serge Maurice} and Liu, {Jin Feng} and Yang, {Shi Zhong} and Gu, {Ji Dong} and Mu, {Bo Zhong}",

note = "Publisher Copyright: {\textcopyright} 2019 The Authors",

year = "2019",

month = sep,

doi = "10.1016/j.ibiod.2019.05.025",

language = "英语",

volume = "143",

journal = "International Biodeterioration and Biodegradation",

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T1 - High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

AU - Hu, Qian Qian

AU - Zhou, Zhi Chao

AU - Liu, Yi Fan

AU - Zhou, Lei

AU - Mbadinga, Serge Maurice

AU - Liu, Jin Feng

AU - Yang, Shi Zhong

AU - Gu, Ji Dong

AU - Mu, Bo Zhong

PY - 2019/9

Y1 - 2019/9

N2 - Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel) nitric oxide dismutase-encoding gene PCR products could confer the diversity of nitric oxide dismutase in additional microbial groups other than the two known lineages, but the distribution pattern of nod gene is unclear in different environments including oil reservoirs. Here, we surveyed the distribution and diversity of nod genes by clone library sequencing together with the inference of 16S rRNA gene-based taxonomy by amplicon sequencing in diverse samples including wastewater treatment plants (WWTP), wetland, hydrocarbon-contaminated soil, and oil reservoirs. A total of 730 phylogenetically diverse nod-related sequences recovered from these samples were clustered into 42 operational taxonomic units (OTUs) showing a considerably high diversity of nod gene in these different ecosystems. The abundance of nod gene in five environmental samples were ∼1.80 × 107–2.62 × 108 copies g−1 soil (sludge) and ∼9.67 × 106 copies l−1 water. The dominant microorganisms were Bacteroidetes, Firmicutes, Actinobacteria, and Chloroflexi. Our results expanded significantly the diversity of microbial groups potentially involved in nitric oxide dismutation, suggesting the ubiquity of microbial members in the different ecosystems carrying out NO dismutation reaction. Further studies on the functional capacity of this new microbial group will advance a better understanding of the microbially-driven nitrogen cycling and provide thorough information on N-removal processes and potential applications.

AB - Microbial nitric oxide dismutation reaction (NOD), involved in the biogeochemical nitrogen cycle on Earth, has been implemented to N removal in laboratory-scale wastewater treatment systems, but microorganisms from relatively a few lineages have been implicated to be associated with this biochemical process. Detection of abundant putative (or novel) nitric oxide dismutase-encoding gene PCR products could confer the diversity of nitric oxide dismutase in additional microbial groups other than the two known lineages, but the distribution pattern of nod gene is unclear in different environments including oil reservoirs. Here, we surveyed the distribution and diversity of nod genes by clone library sequencing together with the inference of 16S rRNA gene-based taxonomy by amplicon sequencing in diverse samples including wastewater treatment plants (WWTP), wetland, hydrocarbon-contaminated soil, and oil reservoirs. A total of 730 phylogenetically diverse nod-related sequences recovered from these samples were clustered into 42 operational taxonomic units (OTUs) showing a considerably high diversity of nod gene in these different ecosystems. The abundance of nod gene in five environmental samples were ∼1.80 × 107–2.62 × 108 copies g−1 soil (sludge) and ∼9.67 × 106 copies l−1 water. The dominant microorganisms were Bacteroidetes, Firmicutes, Actinobacteria, and Chloroflexi. Our results expanded significantly the diversity of microbial groups potentially involved in nitric oxide dismutation, suggesting the ubiquity of microbial members in the different ecosystems carrying out NO dismutation reaction. Further studies on the functional capacity of this new microbial group will advance a better understanding of the microbially-driven nitrogen cycling and provide thorough information on N-removal processes and potential applications.

KW - Distribution

KW - Environmental samples

KW - N-removal

KW - Nitric oxide dismutase

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DO - 10.1016/j.ibiod.2019.05.025

M3 - 文章

AN - SCOPUS:85066839236

SN - 0964-8305

VL - 143

JO - International Biodeterioration and Biodegradation

JF - International Biodeterioration and Biodegradation

M1 - 104708

ER -

High microbial diversity of the nitric oxide dismutation reaction revealed by PCR amplification and analysis of the nod gene

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Keywords

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