Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses

Xinghua Ding; Wenshen Lan; Jiapeng Wu; Yiguo Hong; Yiliang Li; Qingya Ge; Clara Urzì; Yoko Katayama; Ji Dong Gu

doi:10.1007/s00253-020-10886-4

Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses

Xinghua Ding, Wenshen Lan, Jiapeng Wu, Yiguo Hong, Yiliang Li, Qingya Ge, Clara Urzì, Yoko Katayama, Ji Dong Gu^*

^*Corresponding author for this work

Environmental Science and Engineering

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

23 Scopus citations

Abstract

Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called “sediments” here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple. Key Points • Microbiota on Preah Viher temple was analyzed using NGS. • Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected. • N-15 isotope analysis confirmed the active denitrifcation, but not Anammox. • Accumulation of nitrate is a result of less active removal by denitrification.

Original language	English
Pages (from-to)	9823-9837
Number of pages	15
Journal	Applied Microbiology and Biotechnology
Volume	104
Issue number	22
DOIs	https://doi.org/10.1007/s00253-020-10886-4
State	Published - 1 Nov 2020

Keywords

Angkor monuments
Biodeterioration
Comammox
DNRA
Microbiome
Nitrate accumulation
Preah Vihear temple
Sandstone culture heritage

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10.1007/s00253-020-10886-4

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@article{279072b4e1834cd6b6cee359e55a7010,

title = "Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses",

abstract = "Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called “sediments” here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple. Key Points • Microbiota on Preah Viher temple was analyzed using NGS. • Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected. • N-15 isotope analysis confirmed the active denitrifcation, but not Anammox. • Accumulation of nitrate is a result of less active removal by denitrification.",

keywords = "Angkor monuments, Biodeterioration, Comammox, DNRA, Microbiome, Nitrate accumulation, Preah Vihear temple, Sandstone culture heritage",

author = "Xinghua Ding and Wenshen Lan and Jiapeng Wu and Yiguo Hong and Yiliang Li and Qingya Ge and Clara Urz{\`i} and Yoko Katayama and Gu, {Ji Dong}",

year = "2020",

month = nov,

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doi = "10.1007/s00253-020-10886-4",

language = "英语",

volume = "104",

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journal = "Applied Microbiology and Biotechnology",

issn = "0175-7598",

publisher = "Springer Verlag",

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TY - JOUR

T1 - Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses

AU - Ding, Xinghua

AU - Lan, Wenshen

AU - Wu, Jiapeng

AU - Hong, Yiguo

AU - Li, Yiliang

AU - Ge, Qingya

AU - Urzì, Clara

AU - Katayama, Yoko

AU - Gu, Ji Dong

PY - 2020/11/1

Y1 - 2020/11/1

N2 - Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called “sediments” here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple. Key Points • Microbiota on Preah Viher temple was analyzed using NGS. • Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected. • N-15 isotope analysis confirmed the active denitrifcation, but not Anammox. • Accumulation of nitrate is a result of less active removal by denitrification.

AB - Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called “sediments” here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple. Key Points • Microbiota on Preah Viher temple was analyzed using NGS. • Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected. • N-15 isotope analysis confirmed the active denitrifcation, but not Anammox. • Accumulation of nitrate is a result of less active removal by denitrification.

KW - Angkor monuments

KW - Biodeterioration

KW - Comammox

KW - DNRA

KW - Microbiome

KW - Nitrate accumulation

KW - Preah Vihear temple

KW - Sandstone culture heritage

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U2 - 10.1007/s00253-020-10886-4

DO - 10.1007/s00253-020-10886-4

M3 - 文章

C2 - 32949277

AN - SCOPUS:85091176737

SN - 0175-7598

VL - 104

SP - 9823

EP - 9837

JO - Applied Microbiology and Biotechnology

JF - Applied Microbiology and Biotechnology

IS - 22

ER -

Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses

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Keywords

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