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Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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Liu H, Jing H, Wang F. Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches. Front Microbiol 2023; 14:1268790. [PMID: 37840747 PMCID: PMC10568479 DOI: 10.3389/fmicb.2023.1268790] [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: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while NH 4 + concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.
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Affiliation(s)
- Hao Liu
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China
| | - Fangzhou Wang
- CAS Key Lab for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
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Liang D, Bowatte S. Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone. Front Microbiol 2022; 13:1036897. [PMID: 36523826 PMCID: PMC9744808 DOI: 10.3389/fmicb.2022.1036897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/06/2023] Open
Abstract
Background Ammonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question. Methods Metabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil. Results and discussion We found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed. Conclusion These results suggest seed vectored AOB may play a critical role in N cycle.
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Affiliation(s)
- Danni Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Saman Bowatte
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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4
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. FRONTIERS IN PLANT SCIENCE 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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5
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Hoang HG, Thuy BTP, Lin C, Vo DVN, Tran HT, Bahari MB, Le VG, Vu CT. The nitrogen cycle and mitigation strategies for nitrogen loss during organic waste composting: A review. CHEMOSPHERE 2022; 300:134514. [PMID: 35398076 DOI: 10.1016/j.chemosphere.2022.134514] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Composting is a promising technology to decompose organic waste into humus-like high-quality compost, which can be used as organic fertilizer. However, greenhouse gases (N2O, CO2, CH4) and odorous emissions (H2S, NH3) are major concerns as secondary pollutants, which may pose adverse environmental and health effects. During the composting process, nitrogen cycle plays an important role to the compost quality. This review aimed to (1) summarizes the nitrogen cycle of the composting, (2) examine the operational parameters, microbial activities, functions of enzymes and genes affecting the nitrogen cycle, and (3) discuss mitigation strategies for nitrogen loss. Operational parameters such as moisture, oxygen content, temperature, C/N ratio and pH play an essential role in the nitrogen cycle, and adjusting them is the most straightforward method to reduce nitrogen loss. Also, nitrification and denitrification are the most crucial processes of the nitrogen cycle, which strongly affect microbial community dynamics. The ammonia-oxidizing bacteria or archaea (AOB/AOA) and the nitrite-oxidizing bacteria (NOB), and heterotrophic and autotrophic denitrifiers play a vital role in nitrification and denitrification with the involvement of ammonia monooxygenase (amoA) gene, nitrate reductase genes (narG), and nitrous oxide reductase (nosZ). Furthermore, adding additives such as struvite salts (MgNH4PO4·6H2O), biochar, and zeolites (clinoptilolite), and microbial inoculation, namely Bacillus cereus (ammonium strain), Pseudomonas donghuensis (nitrite strain), and Bacillus licheniformis (nitrogen fixer) can help control nitrogen loss. This review summarized critical issues of the nitrogen cycle and nitrogen loss in order to help future composting research with regard to compost quality and air pollution/odor control.
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Affiliation(s)
- Hong Giang Hoang
- Faculty of Health Sciences and Finance - Accounting, Dong Nai Technology University, Bien Hoa, Dong Nai, 76100, Viet Nam
| | - Bui Thi Phuong Thuy
- Faculty of Basic Sciences, Van Lang University, 68/69 Dang Thuy Tram Street, Ward 13, Binh Thanh District, Ho Chi Minh City, 700000, Viet Nam
| | - Chitsan Lin
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, 81157, Taiwan
| | - Dai-Viet N Vo
- Center of Excellence for Green Energy and Environmental Nanomaterials (CE@GrEEN), Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Viet Nam; School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, 14300, Nibong Tebal, Penang, Malaysia
| | - Huu Tuan Tran
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, 81157, Taiwan.
| | - Mahadi B Bahari
- Faculty of Science, Universiti Technoloki Malaysia, 81310, UTM Johor Bahru, Johor, Malaysia
| | - Van Giang Le
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chi Thanh Vu
- Civil and Environmental Engineering Department, University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
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6
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Chen S, Gao R, Xiang X, Yang H, Ma H, Zheng T, Xiao Y, Zhang X, Li H, Fan G, Yu Y. Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China. AMB Express 2021; 11:52. [PMID: 33825988 PMCID: PMC8026789 DOI: 10.1186/s13568-021-01211-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Microbe-mediated ammonia oxidation is a key process in soil nitrogen cycle. However, the effect of maize straw mulching on the ammonia oxidizers in the alkaline purple soil remains largely unknown. A three-year positioning experiment was designed as follows: straw mulching measures as the main-plot treatment and three kinds of nitrogen application as the sub-plot treatment. We found the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK), available nitrogen (AN), available phosphorus (AP), and NH4+-N were increased after straw mulching and nitrogen application in alkaline purple soil, so did the amoA genes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that Thaumarchaeote (448-bp T-RF) was dominated the AOA communities, whereas Nitrosospira sp (111-bp T-RF) dominated the AOB communities. The community compositions of both AOA and AOB were altered by straw mulching and nitrogen application in alkaline purple soil, however, the AOB communities was more responsive than AOA communities to the straw mulching and nitrogen application. Further analysis indicated that SOC and AP were the main factors affecting the abundance and community compositions of AOA and AOB in alkaline purple soil. The present study reported that straw mulching and nitrogen strategies differently shape the soil ammonia oxidizers community structure and abundance, which should be considered when evaluating agricultural management strategies regarding their sustainability and soil quality.
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7
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Wei D, Zeng S, Hou D, Zhou R, Xing C, Deng X, Yu L, Wang H, Deng Z, Weng S, Huang Z, He J. Community diversity and abundance of ammonia-oxidizing archaea and bacteria in shrimp pond sediment at different culture stages. J Appl Microbiol 2020; 130:1442-1455. [PMID: 33021028 DOI: 10.1111/jam.14846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023]
Abstract
AIMS Ammonia oxidation is a significant process of nitrogen cycles in a lot of ecosystems sediments while there are few studies in shrimp culture pond (SCP) sediments. This paper attempted to explore the community diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in SCP sediments at different culture stages. METHODS AND RESULTS We collected SCP sediments and analysed the community diversity and abundance of AOA and bacteria in shrimp pond sediment at different culture stages using the ammonia monooxygenase (amoA) gene with quantitative PCR (qPCR) and 16S rRNA gene sequencing. The AOB-amoA gene abundance was showed higher than AOA-amoA gene abundance in SCP sediments on Day 50 and Day 60 after shrimp larvae introducing into the pond, and the diversity of AOA in SCP sediments was higher than that of AOB. The phylogenetic tree revealed that the most of AOA were the member of Nitrosopumilus and Nitrososphaera, and the majority of AOB sequences were clustered into Nitrosospira, Nitrosomonas clusters 6a and 7. The AOA community has close relationship with total organic carbon (TOC), pH, total phosphorus (TP), nitrate reductase, urease, acid phosphatase and β-glucosidase. The AOB community was related to TOC, C/N and nitrate reductase. CONCLUSIONS AOA and AOB play the different ecological roles in SCP sediments at different culture stages. SIGNIFICANCE AND IMPACT OF THE STUDY Our results suggested that the different community diversity and abundance of AOA and AOB in SCP sediments, which may improve our ecological cognition of shrimp culture stages in SCP ecosystems.
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Affiliation(s)
- D Wei
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - S Zeng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - D Hou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - R Zhou
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - C Xing
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - X Deng
- Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - L Yu
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - H Wang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Z Deng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - S Weng
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - Z Huang
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
| | - J He
- State Key Laboratory of Biocontrol/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences/School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China.,Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, PR China
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He H, Zhen Y, Mi T, Fu L, Yu Z. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China. Front Microbiol 2018; 9:116. [PMID: 29456526 PMCID: PMC5801408 DOI: 10.3389/fmicb.2018.00116] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/18/2018] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.
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Affiliation(s)
- Hui He
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Lulu Fu
- College of Marine Life Science, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, China
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9
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Jenkins SN, Murphy DV, Waite IS, Rushton SP, O'Donnell AG. Ancient landscapes and the relationship with microbial nitrification. Sci Rep 2016; 6:30733. [PMID: 27480661 PMCID: PMC4969748 DOI: 10.1038/srep30733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/06/2016] [Indexed: 11/09/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) drive nitrification and their population dynamics impact directly on the global nitrogen cycle. AOA predominate in the majority of soils but an increasing number of studies have found that nitrification is largely attributed to AOB. The reasons for this remain poorly understood. Here, amoA gene abundance was used to study the distribution of AOA and AOB in agricultural soils on different parent materials and in contrasting geologic landscapes across Australia (n = 135 sites). AOA and AOB abundances separated according to the geologic age of the parent rock with AOB higher in the more weathered, semi-arid soils of Western Australia. AOA dominated the younger, higher pH soils of Eastern Australia, independent of any effect of land management and fertilization. This differentiation reflects the age of the underlying parent material and has implications for our understanding of global patterns of nitrification and soil microbial diversity. Western Australian soils are derived from weathered archaean laterite and are acidic and copper deficient. Copper is a co-factor in the oxidation of ammonia by AOA but not AOB. Thus, copper deficiency could explain the unexpectedly low populations of AOA in Western Australian soils.
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Affiliation(s)
- Sasha N Jenkins
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Daniel V Murphy
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Ian S Waite
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Steven P Rushton
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK
| | - Anthony G O'Donnell
- Soil Biology and Molecular Ecology Group, School of Earth and Environment and the Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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Saijai S, Ando A, Inukai R, Shinohara M, Ogawa J. Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics. Biosci Biotechnol Biochem 2016; 80:2247-2254. [PMID: 27351990 DOI: 10.1080/09168451.2016.1200459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ( ) and nitrite ions ( ) into nitrate ions ( ). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during and oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.
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Affiliation(s)
- Sakuntala Saijai
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Akinori Ando
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan.,b Research Unit for the Physiological Chemistry , Kyoto University , Kyoto , Japan
| | - Ryuya Inukai
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Makoto Shinohara
- c National Institute of Vegetable and Tea Science, National Agriculture Research Organization , Tsu , Japan
| | - Jun Ogawa
- a Division of Applied Life Sciences , Graduate School of Agriculture, Kyoto University , Kyoto , Japan.,b Research Unit for the Physiological Chemistry , Kyoto University , Kyoto , Japan
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Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:3762159. [PMID: 27006640 PMCID: PMC4783532 DOI: 10.1155/2016/3762159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/14/2015] [Accepted: 01/10/2016] [Indexed: 12/28/2022]
Abstract
This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.
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de Gannes V, Eudoxie G, Bekele I, Hickey WJ. Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad. Front Microbiol 2015; 6:1045. [PMID: 26483772 PMCID: PMC4588118 DOI: 10.3389/fmicb.2015.01045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/14/2015] [Indexed: 11/15/2022] Open
Abstract
Understanding how community structure of Bacteria, Archaea, and Fungi varies as a function of edaphic characteristics is key to elucidating associations between soil ecosystem function and the microbiome that sustains it. In this study, non-managed tropical soils were examined that represented a range of edaphic characteristics, and a comprehensive soil microbiome analysis was done by Illumina sequencing of amplicon libraries that targeted Bacteria (universal prokaryotic 16S rRNA gene primers), Archaea (primers selective for archaeal 16S rRNA genes), or Fungi (internal transcribed spacer region). Microbiome diversity decreased in the order: Bacteria > Archaea > Fungi. Bacterial community composition had a strong relationship to edaphic factors while that of Archaea and Fungi was comparatively weak. Bacterial communities were 70–80% alike, while communities of Fungi and Archaea had 40–50% similarity. While each of the three component communities differed in species turnover patterns, soils having relatively similar bacterial communities also housed similar archaeal communities. In contrast, the composition of fungal communities had no correlation to bacterial or archaeal communities. Bacterial and archaeal diversity had significant (negative) correlations to pH, whereas fungal diversity was not correlated to pH. Edaphic characteristics that best explained variation between soils in bacterial community structure were: total carbon, sodium, magnesium, and zinc. For fungi, the best variables were: sodium, magnesium, phosphorus, boron, and C/N. Archaeal communities had two sets of edaphic factors of equal strength, one contained sulfur, sodium, and ammonium-N and the other was composed of clay, potassium, ammonium-N, and nitrate-N. Collectively, the data indicate that Bacteria, Archaea, and Fungi did not closely parallel one another in community structure development, and thus microbiomes in each soil acquired unique identities. This divergence could in part reflect the finding that unknown factor(s) were stronger than edaphic characteristics in shaping fungal and archaeal communities.
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Affiliation(s)
- Vidya de Gannes
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Gaius Eudoxie
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Isaac Bekele
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison Madison, WI, USA
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