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Jiang C, Wu J, Ye J, Hong Y. High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay. MARINE POLLUTION BULLETIN 2024; 200:116046. [PMID: 38246016 DOI: 10.1016/j.marpolbul.2024.116046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.
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Affiliation(s)
- Cuihong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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Ma M, Zhao Y, Jiang X, Guan D, Yuan M, Cao F, Li L, Zhou J, Ding J, Li J. Fertilization altered co-occurrence patterns and microbial assembly process of ammonia-oxidizing microorganisms. Sci Rep 2023; 13:8234. [PMID: 37217543 DOI: 10.1038/s41598-022-26293-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/13/2022] [Indexed: 05/24/2023] Open
Abstract
Ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) are important intermediate links in the nitrogen cycle. Apart from the AOA and AOB communities in soil, we further investigated co-occurrence patterns and microbial assembly processes subjected to inorganic and organic fertilizer treatments for over 35 years. The amoA copy numbers and AOA and AOB communities were found to be similar for the CK and organic fertilizer treatments. Inorganic fertilizers decreased the AOA gene copy numbers by 0.75-0.93-fold and increased the AOB gene copy numbers by 1.89-3.32-fold compared to those of the CK treatment. The inorganic fertilizer increased Nitrososphaera and Nitrosospira. The predominant bacteria in organic fertilizer was Nitrosomonadales. Furthermore, the inorganic fertilizer increased the complexity of the co-occurrence pattern of AOA and decreased the complexity pattern of AOB comparing with organic fertilizer. Different fertilizer had an insignificant effect on the microbial assembly process of AOA. However, great difference exists in the AOB community assembly process: deterministic process dominated in organic fertilizer treatment and stochastic processes dominated in inorganic fertilizer treatment, respectively. Redundancy analysis indicated that the soil pH, NO3-N, and available phosphorus contents were the main factors affecting the changes in the AOA and AOB communities. Overall, this findings expanded our knowledge concerning AOA and AOB, and ammonia-oxidizing microorganisms were more disturbed by inorganic fertilizers than organic fertilizers.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Yubin Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Ming Yuan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161006, Heilongjiang, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Li Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China
| | - Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, 273165, China
| | - Jianli Ding
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, 100081, China.
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Liu F, Zhang Y, Liang H, Gao D. Resilience of methane cycle and microbial functional genes to drought and flood in an alkaline wetland: A metagenomic analysis. CHEMOSPHERE 2021; 265:129034. [PMID: 33239237 DOI: 10.1016/j.chemosphere.2020.129034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/11/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Alkaline wetlands distributed in arid or semi-arid areas are hotspots of methane (CH4) emissions. Periods of drought and flood, although regular, are stressful events encountered by methanogenic anaerobes in alkaline wetlands. To investigate the response of the CH4 cycle of alkaline wetlands to such stresses, we take Zhalong wetland as an example, then determined the CH4 flux and soil microbiomes in the wetland during wet, dry, and flooded periods. The in-situ CH4 flux in the wet period was 9.55-17.29 mg‧m-2‧h-1, but sharply degraded to 3.37-6.61 mg‧m-2‧h-1 in the dry period. It resumed to 4.51-20.80 mg‧m-2‧h-1 when the wetland was flooded again, which indicated that methanogenesis is quite resilient to drought. Syntrophic acetogenesis, and subsequently aceticlastic methanogenesis, were the dominant methanogenic pathways and resisted drought. Members belonging to Syntrophobacterales were the dominant syntrophic acetogens. They enter a viable but non-culturable (VBNC) state to resist drought. The dominant Methanosarcinales have the ability to repair reactive oxygen species damage during dry periods. The community of CH4 sink was governed by anaerobic methanotrophs, which entered a VBNC state or used repair systems to survive dry periods. This study revealed the responses of the CH4 cycle and microbial functional genes to drought and flood in alkaline wetlands.
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Affiliation(s)
- Fengqin Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yupeng Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hong Liang
- Centre for Urban Environmental Remedeation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; Centre for Urban Environmental Remedeation, Beijing University of Civil Engineering and Architecture, Beijing, 100044, China.
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Ding J, Ma M, Jiang X, Liu Y, Zhang J, Suo L, Wang L, Wei D, Li J. Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field. Microbiologyopen 2020; 9:e00942. [PMID: 31568679 PMCID: PMC6957403 DOI: 10.1002/mbo3.942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 11/21/2022] Open
Abstract
In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.
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Affiliation(s)
- Jianli Ding
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Xin Jiang
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Yao Liu
- National Center for Science and Technology EvaluationMOSTBeijingChina
| | - Junzheng Zhang
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbinChina
| | - Linna Suo
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Lei Wang
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Dan Wei
- Institute of Plant Nutrition and ResourcesBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jun Li
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
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Liu F, Zhang Y, Liang H, Gao D. Specific quorum sensing molecules of ammonia oxidizers and their role during ammonium metabolism in Zhalong wetland, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:1106-1113. [PMID: 30970476 DOI: 10.1016/j.scitotenv.2019.02.261] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
The primary challenge of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) surviving in wetlands are the rapid and unpredictable environmental changes. To adapt to a fluctuant environment, ammonia oxidizers have to communicate with each other via acyl-homoserine lactones (AHLs). In this study, AOA and AOB in the soil samples taken from Zhalong wetland were incubated. Dynamics of AHLs during the incubation of ammonia oxidizers were measured. Then, the specific AHLs of AOA and AOB were identified, respectively. The results showed that AOA secreted N-butyryl-dl-homoserine lactone (C4-HSL) and N-octanoyl-l-homoserine lactone (C8-HSL) to cope with nitrite accumulation, while they secreted N-(3-oxododecanoyl)-dl-homoserine lactone (OXOC12-HSL) to regulate their ammonium metabolism activity. AOB secreted N-hexanoyl-dl-homoserine lactone (C6-HSL), N-dodecanoyl-l-homoserine lactone (C12-HSL), N-tetradecanoyl-dl-homoserine lactone (C14-HSL) and N-(3-oxododecanoyl)-tetradecanoyl-dl-homoserine lactone (OXOC14-HSL) only to enhance the metabolism activity. The dominant AOA belonged to the Nitrososphaera lineage, while the dominant AOB grouped into the Nitrosomonas lineage. The AHLs receptor homologs were identified in both AOA and AOB, which confirmed that AOA and AOB had the QS system. The present work was the first study that elucidated the QS system of AOA and AOB in multidimensional, and confirmed the role of QS system in ammonia oxidizers' metabolism.
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Affiliation(s)
- Fengqin Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Yupeng Zhang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hong Liang
- School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China; School of Environment, Harbin Institute of Technology, Harbin, China.
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