Comparison of microbial taxonomic and functional shift pattern along contamination gradient
Identifieur interne : 000045 ( Main/Exploration ); précédent : 000044; suivant : 000046Comparison of microbial taxonomic and functional shift pattern along contamination gradient
Auteurs : Youhua Ren [République populaire de Chine] ; Jiaojiao Niu [République populaire de Chine] ; Wenkun Huang [République populaire de Chine] ; Deliang Peng [République populaire de Chine] ; Yunhua Xiao [République populaire de Chine] ; Xian Zhang [République populaire de Chine] ; Yili Liang [République populaire de Chine] ; Xueduan Liu [République populaire de Chine] ; Huaqun Yin [République populaire de Chine]Source :
- BMC Microbiology [ 1471-2180 ] ; 2016.
Abstract
The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial.
By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of
Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.
The online version of this article (doi:10.1186/s12866-016-0731-6) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12866-016-0731-6
PubMed: 27301322
PubMed Central: 4908767
Affiliations:
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Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">College of Food Science and Technology, Hunan Agricultural University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Food Science and Technology, Hunan Agricultural University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Niu, Jiaojiao" sort="Niu, Jiaojiao" uniqKey="Niu J" first="Jiaojiao" last="Niu">Jiaojiao Niu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Wenkun" sort="Huang, Wenkun" uniqKey="Huang W" first="Wenkun" last="Huang">Wenkun Huang</name><affiliation wicri:level="3"><nlm:aff id="Aff4">State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Peng, Deliang" sort="Peng, Deliang" uniqKey="Peng D" first="Deliang" last="Peng">Deliang Peng</name><affiliation wicri:level="3"><nlm:aff id="Aff4">State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xiao, Yunhua" sort="Xiao, Yunhua" uniqKey="Xiao Y" first="Yunhua" last="Xiao">Yunhua Xiao</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Xian" sort="Zhang, Xian" uniqKey="Zhang X" first="Xian" last="Zhang">Xian Zhang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Liang, Yili" sort="Liang, Yili" uniqKey="Liang Y" first="Yili" last="Liang">Yili Liang</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Xueduan" sort="Liu, Xueduan" uniqKey="Liu X" first="Xueduan" last="Liu">Xueduan Liu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author><author><name sortKey="Yin, Huaqun" sort="Yin, Huaqun" uniqKey="Yin H" first="Huaqun" last="Yin">Huaqun Yin</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Minerals Processing and Bioengineering, Central South University, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2">Key laboratory of Biometallurgy, Ministry of Education, Changsha, 410083 China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key laboratory of Biometallurgy, Ministry of Education, Changsha</wicri:regionArea><wicri:noRegion>Changsha</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Microbiology</title><idno type="eISSN">1471-2180</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial.</p></sec><sec><title>Results</title><p>By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of <italic>Geobacter</italic> and <italic>Fusibacter</italic> decreased along contamination gradient (from high to low), while <italic>Janthinobacterium</italic> and <italic>Arthrobacter</italic> increased their abundances. Most genes involved in heavy metal resistance (e.g., <italic>metc</italic>, <italic>aoxb</italic> and <italic>mer</italic>) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from <italic>Geobacter</italic>, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test.</p></sec><sec><title>Conclusions</title><p>Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12866-016-0731-6) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kim, O S" uniqKey="Kim O">O-S Kim</name></author><author><name sortKey="Cho, Y J" uniqKey="Cho Y">Y-J Cho</name></author><author><name sortKey="Lee, K" uniqKey="Lee K">K Lee</name></author><author><name sortKey="Yoon, S H" uniqKey="Yoon S">S-H Yoon</name></author><author><name sortKey="Kim, M" uniqKey="Kim M">M Kim</name></author><author><name sortKey="Na, H" uniqKey="Na H">H 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Stams</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ren, Youhua" sort="Ren, Youhua" uniqKey="Ren Y" first="Youhua" last="Ren">Youhua Ren</name></noRegion><name sortKey="Huang, Wenkun" sort="Huang, Wenkun" uniqKey="Huang W" first="Wenkun" last="Huang">Wenkun Huang</name><name sortKey="Liang, Yili" sort="Liang, Yili" uniqKey="Liang Y" first="Yili" last="Liang">Yili Liang</name><name sortKey="Liang, Yili" sort="Liang, Yili" uniqKey="Liang Y" first="Yili" last="Liang">Yili Liang</name><name sortKey="Liu, Xueduan" sort="Liu, Xueduan" uniqKey="Liu X" first="Xueduan" last="Liu">Xueduan Liu</name><name sortKey="Liu, Xueduan" sort="Liu, Xueduan" uniqKey="Liu X" first="Xueduan" last="Liu">Xueduan Liu</name><name sortKey="Niu, Jiaojiao" sort="Niu, Jiaojiao" uniqKey="Niu J" first="Jiaojiao" last="Niu">Jiaojiao Niu</name><name sortKey="Niu, Jiaojiao" sort="Niu, Jiaojiao" uniqKey="Niu J" first="Jiaojiao" last="Niu">Jiaojiao Niu</name><name sortKey="Peng, Deliang" sort="Peng, Deliang" uniqKey="Peng D" first="Deliang" last="Peng">Deliang Peng</name><name sortKey="Ren, Youhua" sort="Ren, Youhua" uniqKey="Ren Y" first="Youhua" last="Ren">Youhua Ren</name><name sortKey="Ren, Youhua" sort="Ren, Youhua" uniqKey="Ren Y" first="Youhua" last="Ren">Youhua Ren</name><name sortKey="Xiao, Yunhua" sort="Xiao, Yunhua" uniqKey="Xiao Y" first="Yunhua" last="Xiao">Yunhua Xiao</name><name sortKey="Xiao, Yunhua" sort="Xiao, Yunhua" uniqKey="Xiao Y" first="Yunhua" last="Xiao">Yunhua Xiao</name><name sortKey="Yin, Huaqun" sort="Yin, Huaqun" uniqKey="Yin H" first="Huaqun" last="Yin">Huaqun Yin</name><name sortKey="Yin, Huaqun" sort="Yin, Huaqun" uniqKey="Yin H" first="Huaqun" last="Yin">Huaqun Yin</name><name sortKey="Zhang, Xian" sort="Zhang, Xian" uniqKey="Zhang X" first="Xian" 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