Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete a...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.956860/full |
| _version_ | 1811261094067437568 |
|---|---|
| author | Xueqin Yang Xiaoli Yu Qiang He Ting Deng Xiaotong Guan Yingli Lian Kui Xu Longfei Shu Cheng Wang Qingyun Yan Yuchun Yang Bo Wu Zhili He Zhili He |
| author_facet | Xueqin Yang Xiaoli Yu Qiang He Ting Deng Xiaotong Guan Yingli Lian Kui Xu Longfei Shu Cheng Wang Qingyun Yan Yuchun Yang Bo Wu Zhili He Zhili He |
| author_sort | Xueqin Yang |
| collection | DOAJ |
| description | Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers. |
| first_indexed | 2024-04-12T18:57:22Z |
| format | Article |
| id | doaj.art-1c1b60c2a97c49a0b06787be40135373 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-12T18:57:22Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-1c1b60c2a97c49a0b06787be401353732022-12-22T03:20:16ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-09-011310.3389/fmicb.2022.956860956860Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiersXueqin Yang0Xiaoli Yu1Qiang He2Ting Deng3Xiaotong Guan4Yingli Lian5Kui Xu6Longfei Shu7Cheng Wang8Qingyun Yan9Yuchun Yang10Bo Wu11Zhili He12Zhili He13Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaDepartment of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United StatesEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaState Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha, ChinaDue to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.https://www.frontiersin.org/articles/10.3389/fmicb.2022.956860/fullsynthetic nitrifying communityniche differentiationinteractionammonia affinityspecific growth ratesubstrate tolerance |
| spellingShingle | Xueqin Yang Xiaoli Yu Qiang He Ting Deng Xiaotong Guan Yingli Lian Kui Xu Longfei Shu Cheng Wang Qingyun Yan Yuchun Yang Bo Wu Zhili He Zhili He Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers Frontiers in Microbiology synthetic nitrifying community niche differentiation interaction ammonia affinity specific growth rate substrate tolerance |
| title | Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers |
| title_full | Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers |
| title_fullStr | Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers |
| title_full_unstemmed | Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers |
| title_short | Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers |
| title_sort | niche differentiation among comammox nitrospira inopinata and other metabolically distinct nitrifiers |
| topic | synthetic nitrifying community niche differentiation interaction ammonia affinity specific growth rate substrate tolerance |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.956860/full |
| work_keys_str_mv | AT xueqinyang nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT xiaoliyu nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT qianghe nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT tingdeng nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT xiaotongguan nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT yinglilian nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT kuixu nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT longfeishu nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT chengwang nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT qingyunyan nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT yuchunyang nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT bowu nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT zhilihe nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers AT zhilihe nichedifferentiationamongcomammoxnitrospirainopinataandothermetabolicallydistinctnitrifiers |