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Zhou X, Liu X, Liu M, Liu W, Xu J, Li Y. Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management. Front Microbiol 2024; 15:1424795. [PMID: 39077744 PMCID: PMC11284604 DOI: 10.3389/fmicb.2024.1424795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/01/2024] [Indexed: 07/31/2024] Open
Abstract
Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.
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Affiliation(s)
- Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Xiaoyin Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Meiyu Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Weixuan Liu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
- The National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, China
| | - Yawei Li
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
- Jiangsu Province Engineering Research Center for Agricultural Soil-Water Efficient Utilization, Carbon Sequestration and Emission Reduction, Hohai University, Nanjing, China
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Liu X, Sun D, Huang H, Zhang J, Zheng H, Jia Q, Zhao M. Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171642. [PMID: 38479518 DOI: 10.1016/j.scitotenv.2024.171642] [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: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/16/2024]
Abstract
Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg-1 as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.
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Affiliation(s)
- Xing Liu
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Daolin Sun
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Huaqiao Huang
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jiaen Zhang
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China.
| | - Hongjun Zheng
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qi Jia
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Min Zhao
- Guangdong Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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3
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Qiang R, Wang M, Li Q, Li Y, Li C, Zhang J, Liu H. The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China. Front Microbiol 2024; 15:1374618. [PMID: 38774509 PMCID: PMC11106429 DOI: 10.3389/fmicb.2024.1374618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/05/2024] [Indexed: 05/24/2024] Open
Abstract
Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.
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Affiliation(s)
- Ruowen Qiang
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Meng Wang
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qian Li
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yingjie Li
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Cuilan Li
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Jinjing Zhang
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
| | - Hang Liu
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, China
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Hu Z, Delgado-Baquerizo M, Fanin N, Chen X, Zhou Y, Du G, Hu F, Jiang L, Hu S, Liu M. Nutrient-induced acidification modulates soil biodiversity-function relationships. Nat Commun 2024; 15:2858. [PMID: 38570522 PMCID: PMC10991381 DOI: 10.1038/s41467-024-47323-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Nutrient enrichment is a major global change component that often disrupts the relationship between aboveground biodiversity and ecosystem functions by promoting species dominance, altering trophic interactions, and reducing ecosystem stability. Emerging evidence indicates that nutrient enrichment also reduces soil biodiversity and weakens the relationship between belowground biodiversity and ecosystem functions, but the underlying mechanisms remain largely unclear. Here, we explore the effects of nutrient enrichment on soil properties, soil biodiversity, and multiple ecosystem functions through a 13-year field experiment. We show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon (C) availability, is the primary factor negatively affecting the relationship between soil diversity and ecosystem multifunctionality. Nitrogen and phosphorus additions significantly reduce soil pH, diversity of bacteria, fungi and nematodes, as well as an array of ecosystem functions related to C and nutrient cycling. Effects of nutrient enrichment on microbial diversity also have negative consequences at higher trophic levels on the diversity of microbivorous nematodes. These results indicate that nutrient-induced acidification can cascade up its impacts along the soil food webs and influence ecosystem functioning, providing novel insight into the mechanisms through which nutrient enrichment influences soil community and ecosystem properties.
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Affiliation(s)
- Zhengkun Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
| | - Nicolas Fanin
- INRAE, Bordeaux Sciences Agro, UMR 1391 ISPA, Villenave-d'Ornon, France
| | - Xiaoyun Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Manqiang Liu
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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5
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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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6
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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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Ding F, He T, Qi X, Zhang H, An L, Xu S, Zhang X. Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167653. [PMID: 37806577 DOI: 10.1016/j.scitotenv.2023.167653] [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: 08/03/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.
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Affiliation(s)
- Fan Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Tianjiao He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xing'e Qi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hui Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China; The College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Shijian Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xinfang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China.
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8
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Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
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Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
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9
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Sieradzki ET, Nuccio EE, Pett-Ridge J, Firestone MK. Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development. mSystems 2023; 8:e0031523. [PMID: 37754554 PMCID: PMC10654102 DOI: 10.1128/msystems.00315-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.
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Affiliation(s)
- Ella T. Sieradzki
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
| | - Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, UC Merced, Merced, California, USA
- Innovative Genomics Institute, UC Berkeley, Berkeley, California, USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, USA
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10
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Mason CN, Shahar S, Beals KK, Kelley ST, Lipson DA, Swingley WD, Barber NA. Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiol Ecol 2023; 99:fiad120. [PMID: 37791391 DOI: 10.1093/femsec/fiad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.
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Affiliation(s)
- Cayla N Mason
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Shayla Shahar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Kendall K Beals
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - David A Lipson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Nicholas A Barber
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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11
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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12
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Zhao L, Fu G, Zeng A, Cheng B, Song Z, Hu Z. Effects of different aeration strategies and ammonia-nitrogen loads on nitrification performance and microbial community succession of mangrove constructed wetlands for saline wastewater treatment. CHEMOSPHERE 2023; 339:139685. [PMID: 37532202 DOI: 10.1016/j.chemosphere.2023.139685] [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: 02/18/2023] [Revised: 07/25/2023] [Accepted: 07/29/2023] [Indexed: 08/04/2023]
Abstract
In highly salinized environments, nitrification is the process that limits the rate of nitrogen transformation and removal. Therefore, this study concentrated on the impacts of different aeration strategies and NH4+-N loads on the nitrification performance of mangrove constructed wetlands (CWs), as well as investigating the succession mechanism of ammonia-oxidizing microorganisms (AOMs). The results showed that both the CW with continuous aeration (CA-CW) and intermittent aeration (IA-CW) achieved a nitrification efficiency of more than 98% under an NH4+-N loading of 1.25-4.7 g/(m2·d). However, the total nitrogen removal rates of IA-CW under low and high ammonia-nitrogen loads (LAL, 20.09 ± 4.4% and HAL, 8.77 ± 1.35%, respectively) were higher than those of CA-CW (16.11 ± 4.7% and 3.32 ± 2.3%, respectively), especially under HAL (p < 0.05). Pearson correlation analysis showed that under different operating conditions, the differential secretion of Kandelia candel rhizosphere organic matter had a certain regulatory effect on nitrification and denitrification groups such as Candidatus Nitrocosmicus, Nitrancea, Truepera, Pontibacter, Halomonas, and Sulfurovum in the wetland root layer. The quantitative polymerase chain reaction revealed that the NH4+-N load rate was the primary factor driving the succession of the AOMs, with different aeration strategies exacerbating this process. Overall, this study revealed that the dominant AOMs in mangrove CWs could be significantly altered by regulating the aeration modes and pollution loads to adjust the rhizosphere organic matter in situ, thereby resulting in more efficient nitrification.
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Affiliation(s)
- Lin Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China; Anhui Province Key Laboratory of Environmental Hormone and Reproduction, College of Biology and Food engineering, Fuyang Normal University, Fuyang, 236037, China.
| | - Guiping Fu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Anzu Zeng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Bingzhen Cheng
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zihao Song
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China.
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13
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Ni G, Leung PM, Daebeler A, Guo J, Hu S, Cook P, Nicol GW, Daims H, Greening C. Nitrification in acidic and alkaline environments. Essays Biochem 2023; 67:753-768. [PMID: 37449414 PMCID: PMC10427799 DOI: 10.1042/ebc20220194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.
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Affiliation(s)
- Gaofeng Ni
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Queensland, Australia
| | - Perran Cook
- School of Chemistry, Monash University, Melbourne, Victoria, Australia
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134 Ecully, France
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Securing Antarctica's Environmental Future, Monash University, Melbourne, Victoria, Australia
- Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia
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14
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Mougi A. Eco-evolutionary dynamics in microbial interactions. Sci Rep 2023; 13:9042. [PMID: 37270654 DOI: 10.1038/s41598-023-36221-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/31/2023] [Indexed: 06/05/2023] Open
Abstract
Microbes play an important role in ecosystem functioning and human health. A key feature of microbial interactions is a feedback system in which they modify the physical environment and react to it. Recently, it has been shown that the ecological consequences of microbial interactions driven by the modification of their surrounding pH environment can be predicted from the effects of their metabolic properties on pH. The optimum environmental pH for a given species can adaptively change in response to the changes in environmental pH that are induced by them. However, the mechanisms underlying the effect of these adaptive changes in pH niche on microbial coexistence are yet to be explored. In this study, I theoretically demonstrate that ecological theory can only accurately predict the qualitative ecological consequences if the growth and pH change rates are the same for each species, which suggests that adaptive pH niche changes can generally make ecological consequence predictions based on ecological theory difficult.
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Affiliation(s)
- Akihiko Mougi
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu-Cho, Matsue, 690-8504, Japan.
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15
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Zheng P, Zhang Q, Zou J, Han Q, Han J, Wang Q, Yao L, Yu G, Liang Y. A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162385. [PMID: 36842598 DOI: 10.1016/j.scitotenv.2023.162385] [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: 12/26/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C6-HSL, C8-HSL, C10-HSL, C14-HSL and 3-oxo-C14-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C8-HSL of 400 nmol/L and C10-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.
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Affiliation(s)
- Peihan Zheng
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiaxing Zou
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qi Han
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiarong Han
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Qixin Wang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Liting Yao
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Guangwei Yu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuhai Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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16
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Liu N, Hu H, Ma W, Deng Y, Dimitrov D, Wang Q, Shrestha N, Su X, Feng K, Liu Y, Hao B, Zhang X, Feng X, Wang Z. Relationships Between Soil Microbial Diversities Across an Aridity Gradient in Temperate Grasslands : Soil Microbial Diversity Relationships. MICROBIAL ECOLOGY 2023; 85:1013-1027. [PMID: 35364696 DOI: 10.1007/s00248-022-01997-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/11/2022] [Indexed: 05/04/2023]
Abstract
Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Here we assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea and explored how environmental factors influence these relationships. We sampled soil along a 1500-km-long aridity gradient in temperate grasslands of Inner Mongolia (China) and sequenced the 16S rRNA gene of bacteria and archaea and the ITS2 gene of fungi. The diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between different microbial functional groups were evaluated using α-diversity and co-occurrence networks based on microbial abundance. Our results indicate insignificant correlations among the diversity patterns of bacterial, fungal, and archaeal domains using α-diversity but mostly positive correlations among diversity patterns of microbial functional groups based on α-diversity and co-occurrence networks along the aridity gradient. These results suggest that studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights on patterns that cannot be accessed using only overall microbial α-diversity. Increase in aridity weakens the diversity correlations between bacteria and fungi and between bacterial and archaeal functional groups, but strengthens the positive diversity correlations between bacterial functional groups and between fungal functional groups and the negative diversity correlations between bacterial and fungal functional groups. These variations of the diversity correlations are associated with the different responses of microbes to environmental factors, especially aridity. Our findings demonstrate the complex responses of microbial community structure to environmental conditions (especially aridity) and suggest that understanding diversity correlations and co-occurrence patterns between soil microbial groups is essential for predicting changes in microbial communities under future climate change in arid regions.
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Affiliation(s)
- Nana Liu
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huifeng Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenhong Ma
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Qinggang Wang
- Department of Ecology and Ecological Engineering, College of Resources and Environmental Sciences, and Key Laboratory of Biodiversity and Organic Farming of Beijing City, China Agricultural University, Beijing, 100193, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiangyan Su
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuqing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Baihui Hao
- College of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, China
| | - Xinying Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaojuan Feng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhiheng Wang
- Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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17
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Jiang L, Yu J, Wang S, Wang X, Schwark L, Zhu G. Complete ammonia oxidization in agricultural soils: High ammonia fertilizer loss but low N 2 O production. GLOBAL CHANGE BIOLOGY 2023; 29:1984-1997. [PMID: 36607170 DOI: 10.1111/gcb.16586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/22/2022] [Indexed: 05/28/2023]
Abstract
The contribution of agriculture to the sustainable development goals requires climate-smart and profitable farm innovations. Increasing the ammonia fertilizer applications to meet the global food demands results in high agricultural costs, environmental quality deterioration, and global warming, without a significant increase in crop yield. Here, we reported that a third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is contributing to a significant ammonia fertilizer loss (41.9 ± 4.8%) at the rate of 3.53 ± 0.55 mg N kg-1 day-1 in agricultural soils around the world. The contribution of comammox to ammonia fertilizer loss, occurring mainly in surface agricultural soil profiles (0-0.2 m), was equivalent to that of bacterial ammonia oxidation (48.6 ± 4.5%); both processes were significantly more important than archaeal ammonia oxidation (9.5 ± 3.6%). In contrast, comammox produced less N2 O (0.98 ± 0.44 μg N kg-1 day-1 , 11.7 ± 3.1%), comparable to that produced by archaeal ammonia oxidation (16.4 ± 4.4%) but significantly lower than that of bacterial ammonia oxidation (72.0 ± 5.1%). The efficiency of ammonia conversion to N2 O by comammox (0.02 ± 0.01%) was evidently lower than that of bacterial (0.24 ± 0.06%) and archaeal (0.16 ± 0.04%) ammonia oxidation. The comammox rate increased with increasing soil pH values, which is the only physicochemical characteristic that significantly influenced both comammox bacterial abundance and rates. Ammonia fertilizer loss, dominated by comammox and bacterial ammonia oxidation, was more intense in soils with pH >6.5 than in soils with pH <6.5. Our results revealed that comammox plays a vital role in ammonia fertilizer loss and sustainable development in agroecosystems that have been previously overlooked for a long term.
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Affiliation(s)
- Liping Jiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Yu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lorenz Schwark
- Organic Geochemistry Unit, Kiel University, Kiel, Germany
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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18
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Jiang Z, Tang S, Liao Y, Li S, Wang S, Zhu X, Ji G. Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands. CHEMOSPHERE 2023; 313:137585. [PMID: 36529166 DOI: 10.1016/j.chemosphere.2022.137585] [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: 07/15/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N2O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N2O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N2O through lab-scale subsurface CWs. The N2O emission flux of CW at 8 °C was 1.23 mg m-2·h-1, significantly lower than that at 25 °C (1.92 mg m-2·h-1). The contribution of ammonia oxidation to N2O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N2O production from AOA increased from 1.91 ng N·g-1 at 25 °C to 4.11 ng N·g-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N2O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N2O at low temperature.
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Affiliation(s)
- Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shuangyu Tang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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19
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Ren BJ, Shen LD, Liu X, Jin JH, Huang HC, Tian MH, Yang YL, Yang WT, Liu JQ, Geng CY, Wu HS, Hu ZH. Effect of gradual increase of atmospheric CO 2 concentration on nitrification potential and communities of ammonia oxidizers in paddy fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116597. [PMID: 36308785 DOI: 10.1016/j.jenvman.2022.116597] [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: 08/17/2022] [Revised: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Currently, the influence of elevated atmospheric CO2 concentration (eCO2) on ammonia oxidation to nitrite, the rate-limiting step of nitrification in paddy soil, is poorly known. Previous studies that simulate the effect of eCO2 on nitrification are primarily based on an abrupt increase of atmospheric CO2 concentration. However, paddy ecosystems are experiencing a gradual increase of CO2 concentration. To better understand how the nitrification potential, abundance and communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) respond to eCO2 in paddy ecosystems, a field experiment was conducted using the following two treatments: a gradual increase of CO2 (EC, increase of 40 ppm per year until 200 ppm above ambient) and ambient CO2 (CK). The results demonstrated that the EC treatment significantly (P < 0.05) stimulated the soil potential nitrification rate (PNR) at the jointing and milky stages, which increased by 127.83% and 27.35%, respectively, compared with CK. Furthermore, the EC treatment significantly (P < 0.05) stimulated the AOA and AOB abundance by 56.60% and 133.84%, respectively, at the jointing stage. Correlation analysis showed that the PNR correlated well with the abundance of AOB (R2 = 0.7389, P < 0.001). In addition, the EC treatment significantly (P < 0.05) altered the community structure of AOB, while it had little effect on that of AOA. A significant difference in the proportion of Nitrosospira was observed between CO2 treatments. In conclusion, the gradual increase of CO2 positively influenced the PNR and abundance of ammonia oxidizers, and AOB could be more important than AOA in nitrification under eCO2.
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Affiliation(s)
- Bing-Jie Ren
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jing-Hao Jin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - He-Chen Huang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Cai-Yu Geng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hong-Sheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Zheng-Hua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters (CIC-FEMD), Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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20
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Zhao J, Rodriguez J, Martens-Habbena W. Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils. Front Microbiol 2023; 14:1140487. [PMID: 36910167 PMCID: PMC9995467 DOI: 10.3389/fmicb.2023.1140487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Jonathan Rodriguez
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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21
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Zou Y, Yang Y, Wu S, Chen F, Zhu R. Effect of steel slag on ammonia removal and ammonia-oxidizing microorganisms in zeolite-based tidal flow constructed wetlands. CHEMOSPHERE 2022; 309:136727. [PMID: 36209854 DOI: 10.1016/j.chemosphere.2022.136727] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/07/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
The ammonia removal performance of tidal flow constructed wetlands (TFCWs) requires to be improved under high hydraulic loading rates (HLRs). The pH decrease caused by nitrification may adversely affect the NH4+-N removal and ammonia-oxidizing microorganisms (AOMs) of TFCWs. Herein, TFCWs with zeolite (TFCW_Z) and a mixture of zeolite and steel slag (TFCW_S) were built to investigate the influence of steel slag on NH4+-N removal and AOMs. Both TFCWs were operated under short flooding/drying (F/D) cycles and high HLRs (3.13 and 4.69 m3/(m2 d)). The results revealed that a neutral effluent pH (6.98-7.82) was achieved in TFCW_S owing to the CaO dissolution of steel slag. The NH4+-N removal efficiencies in TFCW_S (91.2 ± 5.1%) were much higher than those in TFCW_Z (73.2 ± 7.1%). Total nitrogen (TN) removal was poor in both TFCWs mainly due to the low influent COD/TN. Phosphorus removal in TFCW_S was unsatisfactory because of the short hydraulic retention time. The addition of steel slag stimulated the flourishing AOMs, including Nitrosomonas (ammonia-oxidizing bacteria, AOB), Candidatus_Nitrocosmicus (ammonia-oxidizing archaea, AOA), and comammox Nitrospira, which may be responsible for the better ammonia removal performance in TFCW_S. PICRUSt2 showed that steel slag also enriched the relative abundance of functional genes involved in nitrification (amoCAB, hao, and nxrAB) but inhibited genes related to denitrification (nirK, norB, and nosZ). Quantitative polymerase chain reaction (qPCR) revealed that complete AOB (CAOB) and AOB contributed more to the amoA genes in TFCW_S and TFCW_Z, respectively. Therefore, this study revealed that the dominant AOMs could be significantly changed in zeolite-based TFCW by adding steel slag to regulate the pH in situ, resulting in a more efficient NH4+-N removal performance.
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Affiliation(s)
- Yuhuan Zou
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yongqiang Yang
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China.
| | - Shijun Wu
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
| | - Fanrong Chen
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
| | - Runliang Zhu
- CAS Key Laboratory of Mineralogy and Metallogeny & Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, 511 Kehua Street, Guangzhou, 510640, China
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22
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The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N 2O emission in alkaline and neutral purple soils. Sci Rep 2022; 12:19928. [PMID: 36402873 PMCID: PMC9675842 DOI: 10.1038/s41598-022-23084-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Nitrification is believed to be one of the primary processes of N2O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH4+ availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N2O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N2O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N2O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH4+) observably stimulated the production of both AOA and AOB-related N2O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N2O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N2O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N2O production in purple soils. We speculate that both NH4+ content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N2O yield led to the different N2O emission characteristics in purple soils. These results may help inform the development of N2O reduction strategies in the future.
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Zhang X, Shan X, Fu H, Sun Z. Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 2022; 10:e14088. [PMID: 36213504 PMCID: PMC9536323 DOI: 10.7717/peerj.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 01/20/2023] Open
Abstract
Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4 + content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4 +, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
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Sun X, Zhao J, Zhang L, Zhou X, Xia W, Zhao Y, Jia Z. Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155568. [PMID: 35490817 DOI: 10.1016/j.scitotenv.2022.155568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.
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Affiliation(s)
- Xiangxin Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhao
- Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie 33314, FL, USA
| | - Liyan Zhang
- College of Environment, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Weiwei Xia
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, Jiangsu Province, China
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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Monteiro GGTN, Barros DJ, Gabriel GVM, Venturini AM, Veloso TGR, Vazquez GH, Oliveira LC, Neu V, Bodelier PLE, Mansano CFM, Tsai SM, Navarrete AA. Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities. Front Microbiol 2022; 13:913453. [PMID: 35979497 PMCID: PMC9376453 DOI: 10.3389/fmicb.2022.913453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 -), which can be further oxidized to nitrate (NO3 -). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 - and NO3 -, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 +) and NO3 --and NO2 --dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.
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Affiliation(s)
| | - Dayane J. Barros
- Graduate Program in Biodiversity and Biotechnology (BIONORTE), Federal University of Tocantins (UFT), Palmas, Brazil
| | - Gabriele V. M. Gabriel
- Graduate Program in Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Andressa M. Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, United States
| | - Tomás G. R. Veloso
- Graduate Program in Agricultural Microbiology, Federal University of Viçosa, Viçosa, Brazil
| | - Gisele H. Vazquez
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
| | - Luciana C. Oliveira
- Department of Physics, Chemistry, and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Vania Neu
- Federal Rural University of Amazonia (UFRA), Belém, Brazil
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | - Acacio A. Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo (USP), Piracicaba, Brazil
- Graduate Program in Environmental Sciences, University Brazil, Fernandópolis, Brazil
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26
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Bai X, Hu X, Liu J, Gu H, Jin J, Liu X, Wang G. Evaluation of four primer sets for analysis of comammox communities in black soils. Front Microbiol 2022; 13:944373. [PMID: 35958136 PMCID: PMC9362984 DOI: 10.3389/fmicb.2022.944373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3–-N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.
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Affiliation(s)
- Xin Bai
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haidong Gu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaobing Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- *Correspondence: Guanghua Wang,
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27
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Wu J, Hong Y, He X, Liu X, Ye J, Jiao L, Li Y, Wang Y, Ye F, Yang Y, Du J. Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea. iScience 2022; 25:104333. [PMID: 35602962 PMCID: PMC9118673 DOI: 10.1016/j.isci.2022.104333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022] Open
Abstract
The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.
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Affiliation(s)
- 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
| | - 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
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Xiang He
- 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
| | - Xiaohan Liu
- 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
| | - Lijing Jiao
- 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
| | - Yiben Li
- 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
| | - Yu Wang
- 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
| | - Fei 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
| | - Yunhua Yang
- 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
| | - Juan Du
- 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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Zheng J, Tao L, Dini-Andreote F, Luan L, Kong P, Xue J, Zhu G, Xu Q, Jiang Y. Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency. Front Microbiol 2022; 13:911799. [PMID: 35633707 PMCID: PMC9135446 DOI: 10.3389/fmicb.2022.911799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.
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Affiliation(s)
- Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Tao
- Guangdong Key Laboratory of Integrated Agroenvironmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peijun Kong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingrong Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qinsong Xu
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Yuji Jiang,
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29
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Fisk LM, Barton L, Maccarone LD, Jenkins SN, Murphy DV. Seasonal dynamics of ammonia-oxidizing bacteria but not archaea influence soil nitrogen cycling in a semi-arid agricultural soil. Sci Rep 2022; 12:7299. [PMID: 35508560 PMCID: PMC9068766 DOI: 10.1038/s41598-022-10711-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow.
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Affiliation(s)
- L M Fisk
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - L Barton
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - L D Maccarone
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - S N Jenkins
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - D V Murphy
- SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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30
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Li S, Peng L, Yang C, Song S, Xu Y. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114336. [PMID: 34953231 DOI: 10.1016/j.jenvman.2021.114336] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/27/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.
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Affiliation(s)
- Shengjun Li
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Lai Peng
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
| | - Chenguang Yang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya Hainan, 572000, China
| | - Shaoxian Song
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China
| | - Yifeng Xu
- Hubei Key Laboratory of Mineral Resources Processing and Environment, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China; School of Resources and Environmental Engineering, Wuhan University of Technology, Luoshi Road 122, Wuhan, Hubei, 430070, China.
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31
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Zhao J, Wang B, Zhou X, Alam MS, Fan J, Guo Z, Zhang H, Gubry-Rangin C, Zhongjun J. Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories. MICROBIAL ECOLOGY 2022; 83:424-435. [PMID: 33970312 PMCID: PMC8891100 DOI: 10.1007/s00248-021-01763-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/21/2021] [Indexed: 06/01/2023]
Abstract
Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems.
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Affiliation(s)
- Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, China
| | - Mohammad Saiful Alam
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Department of Soil Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhiying Guo
- Soil Subcenter of Chinese Ecological Research Network, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Huimin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Cécile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen, AB24 3UU, UK.
| | - Jia Zhongjun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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32
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Sun X, Zhao J, Zhou X, Bei Q, Xia W, Zhao B, Zhang J, Jia Z. Salt tolerance-based niche differentiation of soil ammonia oxidizers. THE ISME JOURNAL 2022; 16:412-422. [PMID: 34389794 PMCID: PMC8776802 DOI: 10.1038/s41396-021-01079-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 02/03/2023]
Abstract
Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined 13C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmolc exchangeable Na+ kg-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na+ extrusion/H+ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na+ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.
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Affiliation(s)
- Xiangxin Sun
- grid.9227.e0000000119573309State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Jun Zhao
- grid.15276.370000 0004 1936 8091Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL USA
| | - Xue Zhou
- grid.257065.30000 0004 1760 3465College of Agricultural Science and Engineering, Hohai University, Nanjing, Jiangsu Province China
| | - Qicheng Bei
- grid.419554.80000 0004 0491 8361Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Weiwei Xia
- grid.260478.f0000 0000 9249 2313College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, Jiangsu Province China
| | - Bingzi Zhao
- grid.9227.e0000000119573309State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Jiabao Zhang
- grid.9227.e0000000119573309State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Zhongjun Jia
- grid.9227.e0000000119573309State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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33
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Huang L, Luo J, Li L, Jiang H, Sun X, Yang J, She W, Liu W, Li L, Davis AP. Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns. WATER RESEARCH 2022; 209:117895. [PMID: 34864344 DOI: 10.1016/j.watres.2021.117895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.
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Affiliation(s)
- Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China
| | - Junyue Luo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Linxin Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Liqing Li
- School of Environmental Science, China University of Geosciences, Wuhan 430074, China.
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
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34
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Lin YP, Ansari A, Wunderlich RF, Lur HS, Ngoc-Dan Cao T, Mukhtar H. Assessing the influence of environmental niche segregation in ammonia oxidizers on N 2O fluxes from soil and sediments. CHEMOSPHERE 2022; 289:133049. [PMID: 34838835 DOI: 10.1016/j.chemosphere.2021.133049] [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: 07/21/2021] [Revised: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N2O) production is essential for predicting N2O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N2O fluxes over pH (4.0-9.0) and temperature (10-45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N2O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N2O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N2O fluxes decreased with increasing pH. Consequently, net N2O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R2 = 0.45, p < 0.01) between PAO and N2O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N2O fluxes, highlighting the potential for mitigating N2O emissions via pH manipulation.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taiwan
| | - Thanh Ngoc-Dan Cao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taiwan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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35
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Herrera-Alsina L, Mynard P, Sudiana IM, Juliandi B, Travis JMJ, Gubry-Rangin C. Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylogenies. Methods Mol Biol 2022; 2569:305-326. [PMID: 36083455 DOI: 10.1007/978-1-0716-2691-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The relative contribution of speciation and extinction into current diversity is certainly unknown, but mathematical frameworks that use genetic information have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e., rates). Nevertheless, diversification models show poor fit when assuming that single rate of speciation/extinction is constant over time and across lineages: species exhibit such a great variation in features that it is unlikely they give birth and die at the same pace. The state-dependent diversification framework (SSE) reconciles the species phenotypic variation with heterogeneous rates of diversification observed in a clade. This family of models allows testing contrasting hypotheses on mode of speciation, trait evolution, and its influence on speciation/extinction regimes. Although microbial species richness outnumbers diversity in plants and animals, diversification models are underused in microbiology. Here, we introduce microbiologists to models that estimate diversification rates and provide a detailed description of SSE models. Besides theoretical principles underlying the method, we also show how SSE analysis should be set up in R. We use pH evolution in Thaumarchaeota to explain its evolutionary dynamic in the light of SSE model. We hope this chapter spurs the study of trait evolution and evolutionary outcomes in microorganisms.
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Affiliation(s)
| | - Poppy Mynard
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - I Made Sudiana
- Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Berry Juliandi
- Department of Biology, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, Indonesia
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36
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Saghaï A, Banjeree S, Degrune F, Edlinger A, García-Palacios P, Garland G, van der Heijden MGA, Herzog C, Maestre FT, Pescador DS, Philippot L, Rillig MC, Romdhane S, Hallin S. Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol 2021; 24:341-356. [PMID: 34796612 DOI: 10.1111/1462-2920.15830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/28/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Anna Edlinger
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gina Garland
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Soil Quality and Use Group, Agroscope, Zurich, Switzerland.,Department of Environmental System Sciences, Soil Resources Group, ETH Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain.,Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - David S Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Móstoles, Spain
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Sana Romdhane
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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Shen LD, Yang YL, Liu JQ, Hu ZH, Liu X, Tian MH, Yang WT, Jin JH, Wang HY, Wang YY, Wu HS. Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO 2 concentration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117558. [PMID: 34119867 DOI: 10.1016/j.envpol.2021.117558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/30/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0-5 cm) and subsurface (5-10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Zheng-Hua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jing-Hao Jin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hao-Yu Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuan-Yuan Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hong-Sheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
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Fan C, Zhang W, Chen X, Li N, Li W, Wang Q, Duan P, Chen M. Residual effects of four-year amendments of organic material on N 2O production driven by ammonia-oxidizing archaea and bacteria in a tropical vegetable soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146746. [PMID: 33798878 DOI: 10.1016/j.scitotenv.2021.146746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Organic material (OM) applied to cropland not only enhances soil fertility but also profoundly affects soil nitrogen cycling. However, little is known about the relative contributions of soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrous oxide (N2O) production during ammonia oxidation in response to the additions of diverse types of OMs in the tropical soil for vegetable production. Herein, the soils were sampled from a tropical vegetable field subjected to 4-year consecutive amendments of straw or manure. All the soils were amended with ammonium sulfate ((NH4)2SO4, applied at a dose of 150 mg N kg-1) and incubated aerobically for four weeks under 50% water holding capacity. 1-octyne or acetylene inhibition technique was used to differentiate the relative contributions of AOA and AOB to N2O production. Results showed that AOA dominated N2O production in soil managements of unfertilized control (CK), chemical fertilization (NPK), and NPK with straw (NPKS), whereas AOB contributed more in soil under NPK with manure (NPKM). Straw addition stimulated AOA-dependent N2O production by 94.8% despite the decreased AOA-amoA abundance. Moreover, manure incorporation triggered both AOA- and AOB-dependent N2O production by 147.2% and 233.7%, respectively, accompanied with increased AOA and AOB abundances. Those stimulating effects were stronger for AOB, owing to its sensitivity to the alleviated soil acidification and decreased soil C/N ratio. Our findings highlight the stimulated N2O emissions during ammonia oxidation by historical OM amendments in tropical vegetable soil, with the magnitude of those priming effects dependent on the types of OM, and appropriate measures need to be taken to counter this challenge in tropical agriculture ecosystems.
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Affiliation(s)
- Changhua Fan
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China
| | - Wen Zhang
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China
| | - Xin Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China
| | - Ning Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China
| | - Wei Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China
| | - Qing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Pengpeng Duan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China.
| | - Miao Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571737, China; National Agricultural Experimental Station for Agricultural Environment, Danzhou 571737, China; College of Ecology and Environment, Hainan University, Haikou 570228, China.
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Hu J, Zhao Y, Yao X, Wang J, Zheng P, Xi C, Hu B. Dominance of comammox Nitrospira in soil nitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146558. [PMID: 33765470 DOI: 10.1016/j.scitotenv.2021.146558] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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Wang L, Huang D. Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements. Sci Rep 2021; 11:14563. [PMID: 34267287 PMCID: PMC8282617 DOI: 10.1038/s41598-021-93898-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/30/2021] [Indexed: 11/09/2022] Open
Abstract
Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO2- –N g-1 d.w.day-1) was found in T2 (optimal irrigation and fertilization)—treated soils, whereas the lowest PAO (0.004 μg NO2- –N g-1 d.w.day-1) in T0 (traditional irrigation)- treated soils. Compared with the T0—treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2—treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2—treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.
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Affiliation(s)
- Limin Wang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350012, People's Republic of China.,Fujian Key Laboratory of Agro - Products Quality and Safety, Fujian Academy of Agricultural Sciences, Fuzhou, 350000, People's Republic of China
| | - Dongfeng Huang
- Soil and Fertilizer Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350012, People's Republic of China. .,Fujian Key Laboratory of Agro - Products Quality and Safety, Fujian Academy of Agricultural Sciences, Fuzhou, 350000, People's Republic of China.
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Rodriguez J, Chakrabarti S, Choi E, Shehadeh N, Sierra-Martinez S, Zhao J, Martens-Habbena W. Nutrient-Limited Enrichments of Nitrifiers From Soil Yield Consortia of Nitrosocosmicus-Affiliated AOA and Nitrospira-Affiliated NOB. Front Microbiol 2021; 12:671480. [PMID: 34322099 PMCID: PMC8312096 DOI: 10.3389/fmicb.2021.671480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/22/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing (comammox) bacteria widespread in terrestrial ecosystems indicates an important role of these organisms in terrestrial nitrification. Recent evidence indicated a higher ammonia affinity of comammox bacteria than of terrestrial AOA and ammonia-oxidizing bacteria (AOB), suggesting that comammox bacteria could potentially represent the most low-nutrient adapted nitrifiers in terrestrial systems. We hypothesized that a nutrient-limited enrichment strategy could exploit the differences in cellular kinetic properties and yield enrichments dominated by high affinity and high yield comammox bacteria. Using soil with a mixed community of AOA, AOB, and comammox Nitrospira, we compared performance of nutrient-limited chemostat enrichment with or without batch culture pre-enrichment in two different growth media without inhibitors or antibiotics. Monitoring of microbial community composition via 16S rRNA and amoA gene sequencing showed that batch enrichments were dominated by AOB, accompanied by low numbers of AOA and comammox Nitrospira. In contrast, nutrient-limited enrichment directly from soil, and nutrient-limited sub-cultivation of batch enrichments consistently yielded high enrichments of Nitrosocosmicus-affiliated AOA associated with multiple canonical nitrite-oxidizing Nitrospira strains, whereas AOB numbers dropped below 0.1% and comammox Nitrospira were lost completely. Our results reveal competitiveness of Nitrosocosmicus sp. under nutrient limitation, and a likely more complex or demanding ecological niche of soil comammox Nitrospira than simulated in our nutrient-limited chemostat experiments.
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Affiliation(s)
| | | | | | | | | | | | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, United States
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Kitamura R, Kozaki T, Ishii K, Iigo M, Kurokura T, Yamane K, Maeda I, Iwabuchi K, Saito T. Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization. Microbes Environ 2021; 36. [PMID: 33907062 PMCID: PMC8209447 DOI: 10.1264/jsme2.me20148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.
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Affiliation(s)
- Rika Kitamura
- Center for Bioscience Research and Education, Utsunomiya University
| | - Toshinori Kozaki
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology
| | | | - Masayuki Iigo
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Takeshi Kurokura
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Kenji Yamane
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Isamu Maeda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Kazunori Iwabuchi
- Department of Bioresource and Environmental Engineering, Faculty of Agriculture, Hokkaido University
| | - Takahiro Saito
- Department of Environmental Engineering, Faculty of Agriculture, Utsunomiya University
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Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China. World J Microbiol Biotechnol 2021; 37:126. [PMID: 34180026 DOI: 10.1007/s11274-021-03087-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO3-) was significantly higher in secondary broad-leaved forests, while ammonium (NH4+) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.
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Jia X, Gao Y, Li X, Zhao Y, Wang L, Zhang C. Effects of cadmium on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings under elevated atmospheric CO 2 scenarios. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145023. [PMID: 33581544 DOI: 10.1016/j.scitotenv.2021.145023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/02/2021] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
The individual impacts of elevated CO2 and heavy metals on soil nitrification have been widely reported. However, studies on the combined effects of elevated CO2 and heavy metals on soil nitrification are still limited. Here, a 135-day growth chamber experiment was conducted to investigate the impacts of elevated CO2 and cadmium (Cd) levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. Elevated CO2 combined with Cd pollution generally stimulated ammonia monooxygenase (AMO), hydroxylamine oxidase (HAO), and nitrite oxidoreductase (NXR) activities. Compared to the control, the abundance of ammonia-oxidizing bacteria (AOB) at day 135 and ammonia-oxidizing archaea (AOA) increased significantly (p < 0.05) and the abundance of AOB at days 45 and 90 and that of the nitrite-oxidizing bacteria (NOB) decreased under elevated CO2 + Cd. Elevated CO2 mostly led to a significant (p < 0.05) decrease in soil nitrification intensity in the rhizosphere of R. pseudoacacia exposed to Cd. The effects of Cd, CO2, and their interaction on HAO and NXR activities were significant (p < 0.01). Soil pH, the C/N ratio, water-soluble organic carbon, water-soluble organic nitrogen (WSON), and total carbon were the dominant factors (p < 0.05) affecting nitrifying enzyme activities and nitrification intensity in rhizosphere soils. Elevated CO2 clearly affected AOA, AOB, and NOB community structures and dominant genera by shaping C/N ratio, pH, and Cd and WSON contents in rhizosphere soils under Cd exposure. Overall, the responses of pH, C/N ratio, WSON, and Cd to elevated CO2 led to changes in rhizosphere soil nitrification under the combination of elevated CO2 and Cd pollution.
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Affiliation(s)
- Xia Jia
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China.
| | - Yunfeng Gao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Xiaodi Li
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Yonghua Zhao
- Shaanxi Key Laboratory of Land Consolidation, School of Land Engineering, Chang'an University, Xi'an 710054, PR China
| | - Lu Wang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
| | - Chunyan Zhang
- Key laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Land and Resources, Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of Ministry of Education, Shaanxi Key Laboratory of Land Consolidation, School of Water and Environment, Chang'an University, Xi'an 710054, PR China
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Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/aem.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
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Mueller RC, Peach JT, Skorupa DJ, Copié V, Bothner B, Peyton BM. An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol Ecol 2021; 97:6021323. [PMID: 33501490 DOI: 10.1093/femsec/fiaa246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.
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Affiliation(s)
- Rebecca C Mueller
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA
| | - Dana J Skorupa
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
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Shi Y, Zhang X, Wang Z, Xu Z, He C, Sheng L, Liu H, Wang Z. Shift in nitrogen transformation in peatland soil by nitrogen inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142924. [PMID: 33127151 DOI: 10.1016/j.scitotenv.2020.142924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/17/2020] [Accepted: 10/03/2020] [Indexed: 06/11/2023]
Abstract
Inputs of nitrogen (N) to peatlands in the form of fertilizers have rapidly increased due to the intensification of agricultural systems, impacting ecological processes, and the carbon storage function of peatland. However, detailed information on the impacts of long-term N inputs on the individual steps of N transformation processes in peatland soils still needs to be fully understood. We investigated N mineralization and nitrification rates as well as nitrite dependent anaerobic methane oxidation (n-damo), anaerobic ammonium oxidation (anammox), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) in a peatland affected by N inputs for >50 years, using isotope tracing technique and quantitative PCR. Based on the results, N inputs increased N mineralization and nitrification rates by 77 and 43%, respectively. Notably, the contributions of n-damo and anammox to N2 production were enhanced by 242 and 170%, accounting for 30 and 12%, respectively. The contributions of denitrification and DNRA to N2 production decreased by 27 and 52%, accounting for 48 and 10% of N2 production, respectively. Nitrifier abundance increased significantly, with AOA being the dominant prokaryote (from 696 to 1090 copies g-1), but AOB responded more strongly to N inputs (from 5 to 68 copies g-1). The N inputs also promoted the growth of n-damo and anammox bacteria, whose abundances increased by 3.7% (from 565 to 586 copies g-1) and 85.7% (from 305 to 567 copies g-1), respectively, while denitrifier abundance was significantly reduced, with nirK and nirS abundances decreasing by 58% (from 738 to 308 copies g-1) and 50% (from 218 to 109 copies g-1), respectively. Soil pH was the key environmental factor influencing N transformations. We show that n-damo plays important roles in N cycling in peatland subjected to N inputs, providing a scientific basis for improved peatland management.
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Affiliation(s)
- Yao Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinyu Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zucheng Wang
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China
| | - Zhiwei Xu
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China
| | - Chunguang He
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China
| | - Lianxi Sheng
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China
| | - Hanyu Liu
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China
| | - Zhongqiang Wang
- Key Laboratory of Geographical Processes and Ecological Security of Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China; State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, Changchun 130117, China.
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Aigle A, Gubry-Rangin C, Thion C, Estera-Molina KY, Richmond H, Pett-Ridge J, Firestone MK, Nicol GW, Prosser JI. Experimental testing of hypotheses for temperature- and pH-based niche specialization of ammonia oxidizing archaea and bacteria. Environ Microbiol 2021; 22:4032-4045. [PMID: 32783333 DOI: 10.1111/1462-2920.15192] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022]
Abstract
Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.
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Affiliation(s)
- A Aigle
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - C Thion
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - K Y Estera-Molina
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - H Richmond
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
| | - J Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA, 94551, USA
| | - M K Firestone
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, 94720, USA
| | - G W Nicol
- Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, 69134, France
| | - J I Prosser
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, UK
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Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
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