Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems
Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-01-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00007/full |
| _version_ | 1828771293374185472 |
|---|---|
| author | Juan Ling Xiancheng Lin Xiancheng Lin Yanying Zhang Yanying Zhang Weiguo Zhou Weiguo Zhou Qingsong Yang Qingsong Yang Liyun Lin Liyun Lin Siquan Zeng Siquan Zeng Ying Zhang Ying Zhang Cong Wang Cong Wang Manzoor Ahmad Manzoor Ahmad Lijuan Long Junde Dong Junde Dong |
| author_facet | Juan Ling Xiancheng Lin Xiancheng Lin Yanying Zhang Yanying Zhang Weiguo Zhou Weiguo Zhou Qingsong Yang Qingsong Yang Liyun Lin Liyun Lin Siquan Zeng Siquan Zeng Ying Zhang Ying Zhang Cong Wang Cong Wang Manzoor Ahmad Manzoor Ahmad Lijuan Long Junde Dong Junde Dong |
| author_sort | Juan Ling |
| collection | DOAJ |
| description | Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems. |
| first_indexed | 2024-12-11T14:22:38Z |
| format | Article |
| id | doaj.art-289ce0e3cc304f649098eeb03503ae53 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-11T14:22:38Z |
| publishDate | 2018-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-289ce0e3cc304f649098eeb03503ae532022-12-22T01:02:49ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-01-01910.3389/fmicb.2018.00007269913Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef EcosystemsJuan Ling0Xiancheng Lin1Xiancheng Lin2Yanying Zhang3Yanying Zhang4Weiguo Zhou5Weiguo Zhou6Qingsong Yang7Qingsong Yang8Liyun Lin9Liyun Lin10Siquan Zeng11Siquan Zeng12Ying Zhang13Ying Zhang14Cong Wang15Cong Wang16Manzoor Ahmad17Manzoor Ahmad18Lijuan Long19Junde Dong20Junde Dong21CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaTropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaCAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaTropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, ChinaSeagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00007/fullseagrassammonia-oxidizing archaea and bacteriaammonia monooxygenase subunit A (amoA)cDNAcommunity structurecoral reef ecosystems |
| spellingShingle | Juan Ling Xiancheng Lin Xiancheng Lin Yanying Zhang Yanying Zhang Weiguo Zhou Weiguo Zhou Qingsong Yang Qingsong Yang Liyun Lin Liyun Lin Siquan Zeng Siquan Zeng Ying Zhang Ying Zhang Cong Wang Cong Wang Manzoor Ahmad Manzoor Ahmad Lijuan Long Junde Dong Junde Dong Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems Frontiers in Microbiology seagrass ammonia-oxidizing archaea and bacteria ammonia monooxygenase subunit A (amoA) cDNA community structure coral reef ecosystems |
| title | Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems |
| title_full | Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems |
| title_fullStr | Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems |
| title_full_unstemmed | Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems |
| title_short | Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems |
| title_sort | community composition and transcriptional activity of ammonia oxidizing prokaryotes of seagrass thalassia hemprichii in coral reef ecosystems |
| topic | seagrass ammonia-oxidizing archaea and bacteria ammonia monooxygenase subunit A (amoA) cDNA community structure coral reef ecosystems |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00007/full |
| work_keys_str_mv | AT juanling communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT xianchenglin communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT xianchenglin communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT yanyingzhang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT yanyingzhang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT weiguozhou communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT weiguozhou communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT qingsongyang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT qingsongyang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT liyunlin communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT liyunlin communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT siquanzeng communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT siquanzeng communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT yingzhang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT yingzhang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT congwang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT congwang communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT manzoorahmad communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT manzoorahmad communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT lijuanlong communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT jundedong communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems AT jundedong communitycompositionandtranscriptionalactivityofammoniaoxidizingprokaryotesofseagrassthalassiahemprichiiincoralreefecosystems |