1
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He BH, Wang HX, Jin RF, Tian T, Zhou JT. Enhanced-nitrogen removal through Fe(III)-triggered partial dissimilatory nitrate reduction to ammonium coupling with anammox in anammox bioreactor. BIORESOURCE TECHNOLOGY 2024; 408:131195. [PMID: 39098358 DOI: 10.1016/j.biortech.2024.131195] [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: 03/11/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 08/06/2024]
Abstract
Anammox is recognized as a prospective alternative for future biological nitrogen removal technologies. However, the nitrate by-products produced by anammox bacteria limit its overall nitrogen removal efficiency below 88 %. This study introduced Fe(III) into the anammox bioreactor to enhance the nitrogen removal efficiency to approximately 95 %, surpassing the biochemical limit of 88 % imposed by anammox stoichiometry. Anammox sludge was demonstrated to utilize extracellular polymeric substances to reduce Fe(III) into Fe(II), and this process promoted the dominance of Ca. Brocadia. The iron addition improved the abundance of narGHI genes and facilitated the partial dissimilatory nitrate reduction to ammonium, with nitrite as the end product. The accumulated nitrite was then eliminated through the anammox pathway, along with the excess ammonium (30 mg/L) in the influent. Overall, this study deepens our understanding of the enhanced nitrogen removal triggered by Fe(III) in anammox sludge and offers an effective approach to boost anammox process.
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Affiliation(s)
- Bang-Hui He
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Hui-Xuan Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ruo-Fei Jin
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Tian Tian
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Ji-Ti Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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2
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Li F, Yuan Q, Li M, Zhou J, Gao H, Hu N. Nitrogen retention and emissions during membrane-covered aerobic composting for kitchen waste disposal. ENVIRONMENTAL TECHNOLOGY 2024; 45:4397-4407. [PMID: 37615415 DOI: 10.1080/09593330.2023.2252162] [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: 04/28/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
The composting performance and nitrogen transformation during membrane-covered aerobic composting of kitchen waste were investigated. The aerobic composting products of the kitchen waste had a high seed germination index of ∼180%. The application of the membrane increased the mean temperature in the early cooling stage of composting by 4.5℃, resulted in a lower moisture content, and reduced the emissions of NH3 and N2O by 48.5% and 44.1%, respectively, thereby retaining 7.9% more nitrogen in the compost. The adsorption of the condensed water layer under inner-membrane was the reason for reducing NH3 emissions, and finite element modeling revealed that the condensed water layer was present throughout the composting process with a maximum thickness of ∼2 mm in the thermophilic stage. The reduction of N2O emissions was related to the micro-positive pressure in the reactor, which promoted the distribution of oxygen, thus weakening denitrification. In addition, the membrane cover decreased the diversity of the bacterial community and increased the diversity of ammonia-oxidizing strains. This study confirmed that membrane-covered composting was suitable for kitchen waste management and could be used as a strategy to mitigate NH3 and N2O emissions.
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Affiliation(s)
- Fei Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qingbin Yuan
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Meng Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Haofeng Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Nan Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
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3
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Liu Y, Du Y, Li Y, Li C, Zhong S, Xu Z, Wang C, Du D. Does Bidens pilosa L. Affect Carbon and Nitrogen Contents, Enzymatic Activities, and Bacterial Communities in Soil Treated with Different Forms of Nitrogen Deposition? Microorganisms 2024; 12:1624. [PMID: 39203466 PMCID: PMC11356382 DOI: 10.3390/microorganisms12081624] [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: 07/13/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The deposition of nitrogen in soil may be influenced by the presence of different nitrogen components, which may affect the accessibility of soil nitrogen and invasive plant-soil microbe interactions. This, in turn, may alter the success of invasive plants. This study aimed to clarify the influences of the invasive plant Bidens pilosa L. on the physicochemical properties, carbon and nitrogen contents, enzymatic activities, and bacterial communities in soil in comparison to the native plant Pterocypsela laciniata (Houtt.) Shih treated with simulated nitrogen deposition at 5 g nitrogen m-2 yr-1 in four forms (nitrate, ammonium, urea, and mixed nitrogen). Monocultural B. pilosa resulted in a notable increase in soil pH but a substantial decrease in the moisture, electrical conductivity, ammonium content, and the activities of polyphenol oxidase, β-xylosidase, FDA hydrolase, and sucrase in soil in comparison to the control. Co-cultivating B. pilosa and P. laciniata resulted in a notable increase in total soil organic carbon content in comparison to the control. Monocultural B. pilosa resulted in a notable decrease in soil bacterial alpha diversity in comparison to monocultural P. laciniata. Soil FDA hydrolase activity and soil bacterial alpha diversity, especially the indices of Shannon's diversity, Simpson's dominance, and Pielou's evenness, exhibited a notable decline under co-cultivated B. pilosa and P. laciniata treated with nitrate in comparison to those treated with ammonium, urea, and mixed nitrogen.
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Affiliation(s)
- Yingsheng Liu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
| | - Yizhuo Du
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
| | - Yue Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
| | - Chuang Li
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
| | - Shanshan Zhong
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
| | - Zhelun Xu
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Congyan Wang
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; (Y.L.); (Y.D.); (Y.L.); (C.L.); (S.Z.); (Z.X.)
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Daolin Du
- Jingjiang College, Jiangsu University, Zhenjiang 212013, China
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4
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Hird K, Campeciño JO, Lehnert N, Hegg EL. Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway. J Inorg Biochem 2024; 256:112542. [PMID: 38631103 DOI: 10.1016/j.jinorgbio.2024.112542] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/19/2024]
Abstract
Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.
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Affiliation(s)
- Krystina Hird
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Julius O Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
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5
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Chisholm C, Di H, Cameron K, Podolyan A, Shen J, Zhang L, Sirisena K, Godsoe W. Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171627. [PMID: 38471592 DOI: 10.1016/j.scitotenv.2024.171627] [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: 10/18/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.
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Affiliation(s)
- C Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - H Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand.
| | - K Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - A Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - J Shen
- Fujian Normal University, China
| | - L Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - K Sirisena
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - W Godsoe
- Department of Pest Management and Conservation, Lincoln University, New Zealand
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6
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von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
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Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
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7
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Xin W, Zhang J, Yu Y, Tian Y, Li H, Chen X, Li W, Liu Y, Lu T, He B, Xiong Y, Yang Z, Xu T, Tang W. Root microbiota of tea plants regulate nitrogen homeostasis and theanine synthesis to influence tea quality. Curr Biol 2024; 34:868-880.e6. [PMID: 38366595 DOI: 10.1016/j.cub.2024.01.044] [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: 07/25/2023] [Revised: 11/26/2023] [Accepted: 01/16/2024] [Indexed: 02/18/2024]
Abstract
The flavor profile of tea is influenced not only by different tea varieties but also by the surrounding soil environment. Recent studies have indicated the regulatory role of soil microbes residing in plant roots in nutrient uptake and metabolism. However, the impact of this regulatory mechanism on tea quality remains unclear. In this study, we showed that a consortium of microbes isolated from tea roots enhanced ammonia uptake and facilitated the synthesis of theanine, a key determinant of tea taste. Variations were observed in the composition of microbial populations colonizing tea roots and the rhizosphere across different seasons and tea varieties. By comparing the root microorganisms of the high-theanine tea variety Rougui with the low-theanine variety Maoxie, we identified a specific group of microbes that potentially modulate nitrogen metabolism, subsequently influencing the theanine levels in tea. Furthermore, we constructed a synthetic microbial community (SynCom) mirroring the microbe population composition found in Rougui roots. Remarkably, applying SynCom resulted in a significant increase in the theanine content of tea plants and imparted greater tolerance to nitrogen deficiency in Arabidopsis. Our study provides compelling evidence supporting the use of root microorganisms as functional microbial fertilizers to enhance tea quality.
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Affiliation(s)
- Wei Xin
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; College of Ecology and Resources Engineering, Wuyi University, Wuyishan 354300, Fujian, China
| | - Jianming Zhang
- College of Ecology and Resources Engineering, Wuyi University, Wuyishan 354300, Fujian, China
| | - Yongdong Yu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yunhe Tian
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hao Li
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaolu Chen
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Wei Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanlin Liu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Ting Lu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Biyun He
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yan Xiong
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhenbiao Yang
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong 518055, P.R. China; Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P.R. China.
| | - Tongda Xu
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
| | - Wenxin Tang
- College of Horticulture, School of Future Technology, and Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
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8
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Mao Y, Wu J, Yang R, Ma Y, Ye J, Zhong J, Deng N, He X, Hong Y. Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106342. [PMID: 38185001 DOI: 10.1016/j.marenvres.2024.106342] [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: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.
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Affiliation(s)
- Yixiang Mao
- 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.
| | - Ruotong 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
| | - Yuexi Ma
- 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
| | - Jiarui Zhong
- 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
| | - Nanling Deng
- 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
| | - 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
| | - 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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9
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Yang Y, Liu H, Zhang Y, Fang X, Zhong X, Lv J. Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments. Sci Rep 2023; 13:20722. [PMID: 38007550 PMCID: PMC10676402 DOI: 10.1038/s41598-023-44147-x] [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: 02/21/2023] [Accepted: 10/04/2023] [Indexed: 11/27/2023] Open
Abstract
The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Yang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianhui Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianbao Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China.
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10
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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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11
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Zhang M, Jiao T, Chen S, Zhou W. A review of microbial nitrogen transformations and microbiome engineering for biological nitrogen removal under salinity stress. CHEMOSPHERE 2023; 341:139949. [PMID: 37648161 DOI: 10.1016/j.chemosphere.2023.139949] [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: 04/30/2023] [Revised: 07/30/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
The osmotic stress caused by salinity exerts severe inhibition on the process of biological nitrogen removal (BNR), leading to the deterioration of biosystems and the discharge of nitrogen with saline wastewater. Feasible strategies to solve the bottleneck in saline wastewater treatment have attracted great attention, but relevant studies to improve nitrogen transformations and enhance the salt-tolerance of biosystems in terms of microbiome engineering have not been systematically reviewed and discussed. This work attempted to provide a more comprehensive explanation of both BNR and microbiome engineering approaches for saline wastewater treatment. The effect of salinity on conventional BNR pathways, nitrification-denitrification and anammox, was summarized at cellular and metabolic levels, including the nitrogen metabolic pathways, the functional microorganisms, and the inhibition threshold of salinity. Promising nitrogen transformations, such as heterotrophic nitrification-aerobic denitrification, ammonium assimilation and the coupling of conventional pathways, were introduced and compared based on advantages and challenges in detail. Strategies to improve the salt tolerance of biosystems were proposed and evaluated from the perspective of microbiome engineering. Finally, prospects of future investigation and applications on halophilic microbiomes in saline wastewater treatment were discussed.
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Affiliation(s)
- Mengru Zhang
- School of Civil Engineering, Shandong University, 250061 Jinan, China; Laboratory of Water-Sediment Regulation and Eco-decontamination, 250061, Jinan, China
| | - Tong Jiao
- School of Civil Engineering, Shandong University, 250061 Jinan, China; Laboratory of Water-Sediment Regulation and Eco-decontamination, 250061, Jinan, China
| | - Shigeng Chen
- Shandong Nongda Fertilizer Sci.&Tech. Co., Ltd., Taian, Shandong, PR China
| | - Weizhi Zhou
- School of Civil Engineering, Shandong University, 250061 Jinan, China; Laboratory of Water-Sediment Regulation and Eco-decontamination, 250061, Jinan, China.
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12
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Gusmão ACB, Peres FV, Paula FS, Pellizari VH, Kolm HE, Signori CN. Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. Int Microbiol 2023; 26:1041-1051. [PMID: 37093322 DOI: 10.1007/s10123-023-00358-w] [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: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
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Affiliation(s)
- Ana Carolina Bercini Gusmão
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil.
| | - Francielli Vilela Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Hedda Elisabeth Kolm
- Department of Oceanography, Center for Marine Studies, Federal University of Paraná, Pontal do Paraná, Brazil
| | - Camila Negrão Signori
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
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13
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Liu ZD, Song YY, Ma XY, Yuan JB, Lou YJ, Yang C, Tang HR, Song CC. Deep soil microbial carbon metabolic function is important but often neglected: a study on the Songnen Plain reed wetland, Northeast China. FUNDAMENTAL RESEARCH 2023; 3:833-843. [PMID: 38933016 PMCID: PMC11197545 DOI: 10.1016/j.fmre.2022.06.013] [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: 04/29/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022] Open
Abstract
Soil microbial carbon metabolism is critical in wetland soil carbon cycling, and is also a research hotspot at present. However, most studies focus on the surface soil layer in the wetlands and the microorganisms associated with this layer. In this study, 0-75 cm soil profiles were collected from five widely separated reed wetlands in the Songnen Plain, which has a large number of middle-high latitude inland saline-sodic wetlands. The Biolog-ECO method was used to determine the carbon metabolic activity and functional diversity of soil microorganisms. The results showed that soil carbon metabolic activity decreased with increasing soil depth. The carbon metabolic activity of soil microorganisms in the 60-75 cm layer was approximately 57.41%-74.60% of that in the 0-15 cm layer. The soil microbial Shannon index and utilization rate of amines decreased with an increase in soil depth, while the Evenness index and utilization rate of polymers tended to increase with soil depth. Dissolved organic carbon (DOC) is the most important factor affecting microbial carbon source utilization preference, because microorganisms mainly obtain the carbon source from DOC. The result of the correlation analysis showed that the soil microbial carbon metabolic activity, Shannon index, and Evenness index significantly correlated with soil total carbon (TC), microbial biomass carbon (MBC), DOC, total nitrogen (TN), ammonium nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N) contents, and electrical conductivity (EC). This study emphasized the important role of microbial carbon metabolic function in deep soil.
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Affiliation(s)
- Zhen-Di Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Yu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xiu-Yan Ma
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jia-Bao Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan-Jing Lou
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chen Yang
- Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hao-Ran Tang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang-Chun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- School of Hydraulic Engineering, Dalian University of Technology, Dalian 116024, China
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14
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Xie Y, Tian X, Liu Y, Zhao K, Li Y, Luo K, Wang B, Dong S. Nitrogen removal capability and mechanism of a novel heterotrophic nitrifying-aerobic denitrifying strain H1 as a potential candidate in mariculture wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106366-106377. [PMID: 37728674 DOI: 10.1007/s11356-023-29666-4] [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: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
The nitrogen removal performance and mechanisms of Bacillus subtilis H1 isolated from a mariculture environment were investigated. Strain H1 efficiently removed NH4+-N, NO2--N, and NO3--N in simulated wastewater with removal efficiencies of 85.61%, 90.58%, and 57.82%, respectively. Strain H1 also efficiently degraded mixed nitrogen (NH4+-N mixed with NO2--N and/or NO3--N) and had removal efficiencies ranging from 82.39 to 89.54%. Nitrogen balance analysis revealed that inorganic nitrogen was degraded by heterotrophic nitrification-aerobic denitrification (HN-AD) and assimilation. 15N isotope tracing indicated that N2O was the product of the HN-AD process, while N2 as the final product was only detected during the reduction of 15NO2--N. The nitrogen assimilation and dissimilation pathways by strain H1 were further clarified using complete genome sequencing, nitrification inhibitor addition, and enzymatic activity measurement, and the ammonium oxidation process was speculated as NH4+ → NH2OH → NO → N2O. These results showed the application prospect of B. subtilis H1 in treating mariculture wastewater.
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Affiliation(s)
- Yumeng Xie
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China.
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kun Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Yongmei Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Bo Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Shuanglin Dong
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China
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15
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [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: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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16
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Gao J, Zhi Y, Huang Y, Shi S, Tan Q, Wang C, Han L, Yao J. Effects of benthic bioturbation on anammox in nitrogen removal at the sediment-water interface in eutrophic surface waters. WATER RESEARCH 2023; 243:120287. [PMID: 37451126 DOI: 10.1016/j.watres.2023.120287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
Anaerobic ammonium oxidation (anammox) significantly contributes to nitrogen loss in freshwater ecosystems. The sediment-water interface (SWI), known as a "hot spot" for anammox, also harbors numerous macroinvertebrates. However, the impact of their bioturbation on anammox has generally been overlooked. This study compared the effects of three representative macroinvertebrates (i.e., Propsilocerus akamusi, Branchiura sowerbyi and Radix swinhoei) with different bioturbation modes on anammox and the N-removal processes at the SWI by using a microcosmic system. The results demonstrated that all three benthic macroinvertebrates promoted anammox in addition to denitrification processes. The highest N-removal was achieved in the presence of P. akamusi considered as a gallery-diffuser, where the relative abundance of Planctomycetes (to which the anammox bacteria belong) increased by 70%. P. akamusi increased the abundance of anammox hzsB gene by 2.58-fold and promoted potential anammox rate by 12.79 nmol N g-1 h-1, which in turn facilitated total N-removal mass increased by 2.42-fold. In the presence of B. sowerbyi and R. swinhoei, the potential anammox rates increased by 4.81 and 5.57 nmol N g-1 h-1, respectively. These results underscore the substantial impact of macroinvertebrates on anammox and N-removal processes, highlighting their crucial role in N pollution control, and sustaining the overall health and stability of eutrophic water bodies.
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Affiliation(s)
- Jie Gao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yue Zhi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yuyue Huang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Sijie Shi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Qiujun Tan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Chengcheng Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Le Han
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Jingmei Yao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China.
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17
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Huang L, Levintal E, Erikson CB, Coyotl A, Horwath WR, Dahlke HE, Mazza Rodrigues JL. Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37467434 PMCID: PMC10399200 DOI: 10.1021/acs.est.3c01356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.
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Affiliation(s)
- Laibin Huang
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Elad Levintal
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Christian Bernard Erikson
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Adolfo Coyotl
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - William R Horwath
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Helen E Dahlke
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
| | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California, Davis, Davis, California 95616, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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18
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Harland JB, Samanta S, Lehnert N. Bacterial nitric oxide reductase (NorBC) models employing click chemistry. J Inorg Biochem 2023; 246:112280. [PMID: 37352656 DOI: 10.1016/j.jinorgbio.2023.112280] [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: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/30/2023] [Indexed: 06/25/2023]
Abstract
Bacterial NO Reductase (NorBC or cNOR) is a membrane-bound enzyme found in denitrifying bacteria that catalyzes the two-electron reduction of NO to N2O and water. The mechanism by which NorBC operates is highly debated, due to the fact that this enzyme is difficult to work with, and no intermediates of the NO reduction reaction could have been identified so far. The unique active site of NorBC consists of a heme b3/non-heme FeB diiron center. Synthetic model complexes provide the opportunity to obtain insight into possible mechanistic alternatives for this enzyme. In this paper, we present three new synthetic model systems for NorBC, consisting of a tetraphenylporphyrin-derivative clicked to modified BMPA-based ligands (BMPA = bis(methylpyridyl)amine) that model the non-heme site in the enzyme. These complexes have been characterized by EPR, IR and UV-Vis spectroscopy. The reactivity with NO was then investigated, and it was found that the complex with the BMPA-carboxylate ligand as the non-heme component has a very low affinity for NO at the non-heme iron site. If the carboxylate functional group is replaced with a phenolate or pyridine group, reactivity is restored and formation of a diiron dinitrosyl complex was observed. Upon one-electron reduction of the nitrosylated complexes, following the semireduced pathway for NO reduction, formation of dinitrosyl iron complexes (DNICs) was observed in all three cases, but no N2O could be detected.
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Affiliation(s)
- Jill B Harland
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Subhra Samanta
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Nicolai Lehnert
- Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, United States.
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19
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Li S, Jiang H, Guo W, Zhang W, Zhang Q. From Soil to River: Revealing the Mechanisms Underlying the High Riverine Nitrate Levels in a Forest Dominated Catchment. WATER RESEARCH 2023; 241:120155. [PMID: 37270954 DOI: 10.1016/j.watres.2023.120155] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Elevated riverine nitrate (NO3-) levels have led to increased eutrophication and other ecological implications. While high riverine NO3- levels were generally ascribed to anthropogenic activities, high NO3- levels in some pristine or minimally disturbed rivers were reported. The drivers of these unexpectedly high NO3- levels remain unclear. This study combined natural abundance isotopes, 15N-labeling techniques, and molecular techniques to reveal the processes driving the high NO3- levels in a sparsely populated forest river. The natural abundance isotopes revealed that the NO3- was mainly from soil sources and that NO3- removal processes were insignificant. The 15N-labeling experiments also quantitatively showed that the biological NO3- removal processes, i.e., denitrification, dissimilatory NO3- reduction to ammonium (DNRA), and anaerobic ammonia oxidation (anammox), in the soils and sediments were weak relative to nitrification in summer. While nitrification was minor in winter, the NO3- removal was insignificant relative to the large NO3- stock in the catchment. Stepwise multiple regression analyses and structural equation models revealed that in summer, nitrification in the soils was regulated by the amoA-AOB gene abundances and NH4+-N contents. Low temperature constrained nitrification in winter. Denitrification was largely controlled by moisture content in both seasons, and anammox and DNRA could be explained by the competition with nitrification and denitrification on their substrate (nitrite-NO2-). We also revealed the strong hydrological control on the transport of soil NO3- to the river. This study effectively revealed the mechanisms underlying the high NO3- levels in a nearly pristine river, which has implications for the understanding of riverine NO3- levels worldwide.
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Affiliation(s)
- Shen Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China.
| | - Wenjing Guo
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Wenshi Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China
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20
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Yao S, Jin T, Zhang L, Zhang Y, Chen R, Wang Q, Lv M, Hu C, Ma T, Xia W. N/S element transformation modulating lithospheric microbial communities by single-species manipulation. MICROBIOME 2023; 11:107. [PMID: 37194043 DOI: 10.1186/s40168-023-01553-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation. RESULTS Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil. CONCLUSIONS The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.
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Affiliation(s)
- Shun Yao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Tianzhi Jin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Lu Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Yong Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Qian Wang
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Mingjie Lv
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Chuxiao Hu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China.
| | - Wenjie Xia
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China.
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Guo W, Zhang D, Zhang W, Li S, Pan K, Jiang H, Zhang Q. Anthropogenic impacts on the nitrate pollution in an urban river: Insights from a combination of natural-abundance and paired isotopes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 333:117458. [PMID: 36758410 DOI: 10.1016/j.jenvman.2023.117458] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Urban rivers are often characterized by high nitrate (NO3-) loadings. High NO3- loadings cause water quality and ecological damages, which undermines the sustainable development of cities. To date, the drivers of these high NO3- loadings remain unclear. This study, for the first time, integrated natural-abundance isotopes (δ15 N/δ18O-NO3- and δD/δ18O-H2O) and 15N-pairing techniques to comprehensively reveal the anthropogenic impacts on the NO3- pollution in an urban river. Natural-abundance isotopes suggested that in both the wet and dry seasons, the NO3- was predominantly from the conservative mixing of different sources, and biological NO3- removal was minor. The 15N-pairing experiments supported the natural-abundance isotope data, quantitatively showing that in-soil nitrification was prevailing, while NO3- removal processes (denitrification, anammox, and dissimilatory NO3- reduction to ammonium) were weak. A Bayesian isotope-mixing model showed that soil sources (soil organic nitrogen and chemical fertilizer) dominated the NO3- in the upper reaches, while in the lower reaches, the impermeable riparian zone short-circuited the access of soils to the river. Here, the wastewater treatment plants became a significant source of NO3-. This study quantitatively revealed the drivers of high NO3- loadings in an urban river, and generated important clues for effective NO3- pollution control and remediation in urban rivers.
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Affiliation(s)
- Wenjing Guo
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Dong Zhang
- School of Resource and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Wenshi Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shen Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China.
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan, 430074, China
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22
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Ren J, Qi X, Zhang J, Niu D, Shen Y, Yu C, Zhi J, Wang C, Jiang X, Zhang W, Li C. Biodegradation efficiency and mechanism of erythromycin degradation by Paracoccus versutus W7. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117372. [PMID: 36731410 DOI: 10.1016/j.jenvman.2023.117372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Continuous and excessive usage of erythromycin results in serious environmental pollution and presents a health risk to humans. Biological treatment is considered as an efficient and economical method to remove it from the environment. In this study, a novel erythromycin-degrading bacterial strain, W7, isolated from sewage sludge was identified as Paracoccus versutus. Strain W7 degraded 58.5% of 50 mg/L erythromycin in 72 h under the optimal conditions of 35 °C, pH 7.0, and 0.1% sodium citrate with yeast powder in mineral salt medium. It completely eliminated erythromycin from erythromycin fermentation residue at concentrations of 100 and 300 mg/L within 36 and 60 h, respectively. Erythromycin esterase (EreA) was found to be involved in erythromycin metabolism in this strain and was expressed successfully. EreA could hydrolyze erythromycin, and its maximum activity occurred at pH 8.5 and 35 °C. Finally, six intermediates of erythromycin degraded by strain W7 were detected by high performance liquid chromatography mass spectrometry. Based on the novel intermediates and enzymes, we determined two possible pathways of erythromycin degradation by strain W7. This study broadened our understanding of the erythromycin catabolic processes of P. versutus and developed a feasible microbial strategy for removing erythromycin from erythromycin fermentation residue, wastewater, and other erythromycin-contaminated environments.
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Affiliation(s)
- Jianjun Ren
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Xiancheng Qi
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; School of Pharmacy & School of Biological and Food Engineering, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Jian Zhang
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Dongze Niu
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Yunpeng Shen
- Yili Chuanning Biotechnology Co., Ltd. No. 156 Alamutuya Country, Yining District, Yili 835000, China
| | - Changyong Yu
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Junqiang Zhi
- Beijing General Station of Animal Husbandry, No. 21 Chaoqian Road, Changping District, Beijing, 100101, China
| | - Chongqing Wang
- Beijing General Station of Animal Husbandry, No. 21 Chaoqian Road, Changping District, Beijing, 100101, China
| | - Xingmei Jiang
- Bijie Institute of Animal Husbandry and Veterinary Sciences, Degoumajiayuan Road, Qixingguan District, Bijie 551700, China
| | - Wenfan Zhang
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China
| | - Chunyu Li
- Institute of Urban and Rural Mining, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China; National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, No.21 Gehu Road, Wujin District, Changzhou 213164, China.
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Geochemical properties of blue carbon sediments through an elevation gradient: study of an anthropogenically impacted coastal lagoon. BIOGEOCHEMISTRY 2023; 162:381-408. [PMID: 36873378 PMCID: PMC9971090 DOI: 10.1007/s10533-022-00974-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Global research is showing that coastal blue carbon ecosystems are vulnerable to climate change driven threats including accelerated sea-level rise and prolonged periods of drought. Furthermore, direct anthropogenic impacts present immediate threats through deterioration of coastal water quality, land reclamation, long-term impact to sediment biogeochemical cycling. These threats will invariably alter the future efficacy of carbon (C) sequestration processes and it is imperative that currently existing blue carbon habitats be protected. Knowledge of underlying biogeochemical, physical and hydrological interactions occurring in functioning blue carbon habitats is essential for developing strategies to mitigate threats, and promote conditions to optimise C sequestration/storage. In this current work, we investigated how sediment geochemistry (0-10 cm depth) responds to elevation, an edaphic factor driven by long-term hydrological regimes consequently exerting control over particle sedimentation rates and vegetation succession. This study was performed in an anthropogenically impacted blue carbon habitat along a coastal ecotone encompassing an elevation gradient transect from intertidal sediments (un-vegetated and covered daily by tidal water), through vegetated salt marsh sediments (periodically covered by spring tides and flooding events), on Bull Island, Dublin Bay. We determined the quantity and distributions of bulk geochemical characteristics in sediments through the elevation gradient, including total organic carbon (TOC), total nitrogen (TN), total metals, silt, clay, and also, 16 individual polyaromatic hydrocarbon's (PAH's) as an indication of anthropogenic input. Elevation measurements for sample sites were determined on this gradient using a LiDAR scanner accompanied by an IGI inertial measurement unit (IMU) on board a light aircraft. Considering the gradient from the Tidal mud zone (T), through the low-mid marsh (M) to the most elevated upper marsh (H), there were significant differences between all zones for many measured environmental variables. The results of significance testing using Kruskal-Wallis analysis revealed, that %C, %N, PAH (µg/g), Mn (mg/kg), TOC:NH4 + and pH are significantly different between all zones on the elevation gradient. The highest values for all these variables exists (excluding pH which followed a reverse trend) in zone H, decreasing in zone M and lowest in the un-vegetated zone T. TC content is 16 fold higher overall in vegetated (3.43 -21.84%) than uninhabited (0.21-0.56%) sediments. TN was over 50 times higher (0.24-1.76%), more specifically increasing in % mass on approach to the upper salt marsh with distance from the tidal flats sediments zone T (0.002-0.05%). Clay and silt distributions were greatest in vegetated sediments, increasing in % content towards upper marsh zones The retention of water, metals, PAHs, mud, chloride ions, NH4 +, PO4 3- and SO4 2- increased with elevated C concentrations, concurrently where pH significantly decreased. Sediments were categorized with respect to PAH contamination where all SM samples were placed in the high polluted category. The results highlight the ability of Blue C sediments to immobilise increasing levels of C, N, and metals, and PAH with over time and with both lateral and vertical expansion. This study provides a valuable data set for an anthropogenically impacted blue carbon habitat predicted to suffer from sea-level rise and exponential urban development. GRAPHICAL ABSTRACT Summarized results from this study demonstrating the geochemical changes through an elevation gradient, with a transect encompassing intertidal sediments through supratidal salt marsh sediments within Bull Island's blue carbon lagoon zones. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-00974-0.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, N. Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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25
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Coupling of Anammox Activity and PAH Biodegradation: Current Insights and Future Directions. Processes (Basel) 2023. [DOI: 10.3390/pr11020458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal.
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26
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Chisholm C, Di HJ, Cameron K, Podolyan A, Shah A, Hsu L, Shen J. Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159961. [PMID: 36343813 DOI: 10.1016/j.scitotenv.2022.159961] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The objectives of this study were to investigate the abundance and community composition of comammox Nitrospira under: (i) pasture-based dairy farms from different regions, and (ii) different land uses from the same region and soil type. The results clearly showed that comammox Nitrospira were most abundant (3.0 × 106 copies) under the west coast dairy farm conditions, where they were also significantly more abundant than canonical ammonia oxidisers. This was also true in the Canterbury dairy farm. The six land uses investigated were pine monoculture, a long term no input ecological trial, sheep + beef and Dairy, both irrigated and non-irrigated. It was concluded that comammox Nitrospira was most abundant under the irrigated dairy farm (2.7 × 106 copies). Contrary to the current industry opinion, the relatively high abundance of comammox Nitrospira under fertile irrigated dairy land suggests that comammox Nitrospira found in terrestrial ecosystems may be copiotrophic. it was also determined that comammox Nitrospira was more abundant under irrigated land use than their non-irrigated counterparts, suggesting that soil moisture is a key environmental parameter influencing comammox abundance. Comammox abundance was also positively correlated with annual rainfall, further supporting this theory. Phylogenetic analysis of the comammox Nitrospira detected determined that 17 % of the comammox community belonged to a newly distinguished subclade, clade B.2. The remaining 83 % belonged to clade B.1. No sequences from clade A were found.
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Affiliation(s)
- Chris Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand.
| | - Keith Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Anish Shah
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Lisa Hsu
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
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Tao W, Carter S, Trevino R, Zhang W, Shafaat HS, Zhang S. Reductive NO Coupling at Dicopper Center via a [Cu 2(NO) 2] 2+ Diamond-Core Intermediate. J Am Chem Soc 2022; 144:22633-22640. [PMID: 36469729 DOI: 10.1021/jacs.2c09523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Treatment of a dicopper(I,I) complex with excess amounts of NO leads to the formation of a dicopper dinitrosyl [Cu2(NO)2]2+ complex capable of (i) releasing two equivalents of NO reversibly in 90% yield and (ii) reacting with another equivalent of NO to afford N2O and dicopper nitrosyl oxo species [Cu2(NO)(O)]2+. Resonance Raman characterization of the [Cu2(NO)2]2+ complex shows a 15N-sensitive N═O stretch at 1527.6 cm-1 and two Cu-N stretches at 390.6 and 414.1 cm-1, supporting a symmetric diamond-core structure with bis-μ-NO ligands. The conversion of [Cu2(NO)2]2+ to [Cu2(NO)O]2+ occurs via a rate-limiting reaction with NO and bypasses the dicopper oxo intermediate, a mechanism distinct from that of diFe-mediated NO reduction to N2O.
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Affiliation(s)
- Wenjie Tao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Samantha Carter
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Regina Trevino
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Weiyao Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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28
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Chow C, Padda KP, Puri A, Chanway CP. An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture. Curr Microbiol 2022; 79:322. [PMID: 36125558 DOI: 10.1007/s00284-022-03016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/31/2022] [Indexed: 11/03/2022]
Abstract
Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.
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Affiliation(s)
- Chanelle Chow
- Department of Biology, Faculty of Science, University of British Columbia, Vancouver, Canada
| | - Kiran Preet Padda
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Akshit Puri
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Chris P Chanway
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
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Nie Y, Lau SYL, Tan X, Lu X, Liu S, Tahvanainen T, Isoda R, Ye Q, Hashidoko Y. Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions. FRONTIERS IN PLANT SCIENCE 2022; 13:974251. [PMID: 36160957 PMCID: PMC9490422 DOI: 10.3389/fpls.2022.974251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.
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Affiliation(s)
- Yanxia Nie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sharon Yu Ling Lau
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Sarawak Tropical Peat Research Institute, Kota Samarahan, Malaysia
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiankai Lu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Suping Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Teemu Tahvanainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Reika Isoda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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Wang F, Fang Y, Wang L, Xiang H, Chen G, Chang X, Liu D, He X, Zhong R. Effects of residual monensin in livestock manure on nitrogen transformation and microbial community during "crop straw feeding-substrate fermentation-mushroom cultivation" recycling system. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 149:333-344. [PMID: 35780758 DOI: 10.1016/j.wasman.2022.06.015] [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: 02/05/2022] [Revised: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Although crop-livestock integration recycling systems improve nitrogen (N) utilization in agroecosystems, there are limited studies regarding impacts of residual antibiotics in livestock manure on N transformation in entire recycling system. The objective was to evaluate effects of feeding monensin on N recycling during "straw feeding-substrate fermentation-mushroom cultivation". This experiment contained 3 steps. During straw feeding, beef cattle were allocated into 2 groups and fed diets with or without monensin, respectively. During fermentation, beef cattle manure (with or without monensin) and straw (corn or wheat) and were co-fermented for 35 d to produce substrates. During cultivation, Agaricus bisporus was cultivated on 4 substrates to recycle N in the form of mushrooms. Rates of N retention during fermentation were significant higher for monensin and corn straw treatments and there was an significant interaction between straw and antibiotic on N retention rate during cultivation. However, residual monensin significantly reduced amount of recycled N during entire recycling system, due to changes in N transformation-associated enzyme activity, ammonification and denitrification plus microbial community structure and succession. Specifically, residual monensin inhibited growth of dominant bacterial phylum Bacteroidetes and fungal phylum Neocallimastigomycota, and increased bacterial phylla Actinobacteriota and Firmicutes. These alterations in functional microbes increased N retention rates but reduced mushroom yields in antibiotic treatments during cultivation. In conclusion, monensin decreased the N recycling rate in recycling system, but also reduced N losses during fermentation by inhibiting ammonification and denitrification, so, avoiding antibiotics usage is an effective strategy to improve the efficiency of recycling systems.
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Affiliation(s)
- Fei Wang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Yi Fang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Lixia Wang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Hai Xiang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Guoshuang Chen
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China
| | - Xiao Chang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, PR China
| | - Rongzhen Zhong
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin, PR China.
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Ku Y, Lei Y, Han X, Peng J, Zhu Y, Zhao Z. Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale. Front Microbiol 2022; 13:918134. [PMID: 35814641 PMCID: PMC9263705 DOI: 10.3389/fmicb.2022.918134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.
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Affiliation(s)
- Yongli Ku
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Yuting Lei
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Xiaoting Han
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Jieying Peng
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Ying Zhu
- Key Laboratory of Soil and Water Conservation and Ecological Restoration of State Forestry and Grassland Administration, Shaanxi Academy of Forestry, Xi’an, China
| | - Zhong Zhao
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
- Key Laboratory of Silviculture on the Loess Plateau State Forestry Administration, Northwest A&F University, Yangling, China
- *Correspondence: Zhong Zhao, ;
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A Comparison Study of the Nutrient Fluxes in a Newly Impounded Riverine Lake (Longjing Lake): Model Calculation and Sediment Incubation. WATER 2022. [DOI: 10.3390/w14132015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Diffusion flux is an essential tool to estimate the contribution of internal nitrogen and phosphorus in eutrophic lakes. There are mainly two methods, i.e., model calculation based on in-situ porewater sampling and water quality monitoring in laboratory incubation. The results obtained by the two methods are rarely compared, decreasing the validity of internal contribution and following management strategies. In this study, sediment samples were collected from a lake in China, then the fluxes were estimated by model calculation and laboratory incubation. The results show that there is an order of magnitude difference in the fluxes measured by these two methods. The mean values of ammonia (NH4+-N) and soluble reactive phosphate (SRP) obtained from the model calculations were 24.4 and 1.30, respectively. The mean values of NH4+-N and SRP obtained in the undisturbed group of sediment incubation were 7.84 and 5.47, respectively, and in the disturbed group of sediment incubation were 16.2 and 4.06, respectively. Sediment incubation is a combination of multiple influencing factors to obtain fluxes, while porewater model is based on molecular diffusion as the theoretical basis for obtaining fluxes. According to the different approaches of the two methods, sediment incubation is recommended as a research tool in lake autochthonous release management when the main objective is to remove pollution, while the porewater model is recommended as a research tool when the main objective is to control pollution. When assessing the diffusive flux of nitrogen, it is recommended to choose the stable form of total dissolved nitrogen to discuss the flux results.
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Wei D, Zhang X, Zhang S, Dai J, Du J, He Y, Wen X. Organics alleviate the inhibition of sulfate on ANAMMOX sludge. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 57:510-517. [PMID: 35670526 DOI: 10.1080/10934529.2022.2083901] [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: 10/15/2021] [Revised: 05/05/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic ammonium oxidation (Anammox) was an innovative process for nitrogen removal. In this study, the influence of sulfate in different concentrations (100, 200, 300, and 400 mg L-1) on Anammox process were investigated in nine identical sequential batch reactors, four of which were extra supplied for organics, to study the combined effect. The results indicated the obvious inhibition by sulfate which decreased the total nitrogen removal efficiency (TNRE) to 84.1%, 81.2%, 81.2%, and 72.5%, from the control results as 91.9%. Whereas, the organics addition alleviated the inhibitory effect, through consuming the oxygen in influent, promoting the secretion of protein, and inducing the denitrifying bacteria, for which the sulfate only slightly decreased the TNRE to 89.0%, 83.7%, 83.6%, and 75.7%, respectively. Candidatus Kuenenia and Denitratisoma could coexist in Anammox system and cooperatively contribute to the nitrogen removal, when treating the nitrogenous wastewater contains both sulfate and organics.
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Affiliation(s)
- Denghui Wei
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Xiaojing Zhang
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Shengnan Zhang
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Jiaqian Dai
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Jianghui Du
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Yu He
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
| | - Xiaoyu Wen
- School of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
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Zhong L, Qing J, Liu M, Cai X, Li G, Li FY, Chen G, Xu X, Xue K, Wang Y. Fungi and Archaea Control Soil N 2O Production Potential in Chinese Grasslands Rather Than Bacteria. Front Microbiol 2022; 13:844663. [PMID: 35651488 PMCID: PMC9149426 DOI: 10.3389/fmicb.2022.844663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.
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Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Min Liu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian Cai
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Gaoyuan Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Guanyi Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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35
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36
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Chamkhi I, El Omari N, Balahbib A, El Menyiy N, Benali T, Ghoulam C. Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement? Saudi J Biol Sci 2022; 29:1246-1259. [PMID: 35241967 PMCID: PMC8864493 DOI: 10.1016/j.sjbs.2021.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.
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Key Words
- AMF, Arbuscular Mycorrhizal Fungi
- AOA, Ammonia-Oxidizing Archaea
- BMV, Brome Mosaic Virus
- C, Carbon
- CMV, Cucumber mosaic virus
- LDH, Layered double hydroxides
- MF, Mycorrhizal fungi
- Microorganisms
- P, Phosphorus
- PAL, L-Phenylalanine Ammonia Lyase
- PCA, Phenazine-1-Carboxylic Acid
- PGPR, Plant Growth-Promoting Rhizobacteria
- POX, Peroxidase
- PPO, Polyphenol Oxidase
- Plant growth promoting microbes
- Plant-microbes interactions
- Rhizosphere
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Affiliation(s)
- Imane Chamkhi
- Geo-Biodiversity and Natural Patrimony Laboratory (GeoBio), Geophysics, Natural Patrimony Research Center (GEOPAC), Scientific Institute, Mohammed V University in Rabat, Morocco.,University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Abdelaali Balahbib
- Laboratory of Zoology and General Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Naoual El Menyiy
- Faculty of Science, University Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Safi, Morocco
| | - Cherki Ghoulam
- University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco.,Cadi Ayyad University, Faculty of Sciences and Techniques, PO Box 549, Gueliz, Marrakech,Morocco
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Valiente N, Jirsa F, Hein T, Wanek W, Prommer J, Bonin P, Gómez-Alday JJ. The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150726. [PMID: 34606874 DOI: 10.1016/j.scitotenv.2021.150726] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Nitrate (NO3-) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N2O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO3- pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO3- removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO3- pollution. The revised 15N-isotope pairing technique (15N-IPT) was used to determine NO3- sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N2O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO3- reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N2O emissions to the atmosphere.
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Affiliation(s)
- N Valiente
- Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, Section for Aquatic Biology and Toxicology, University of Oslo, PO Box 1066, Blindern, 0316, Oslo, Norway; Biotechnology and Natural Resources Section, Institute for Regional Development (IDR), University of Castilla-La Mancha (UCLM), Campus Universitario s/n, 02071 Albacete, Spain.
| | - F Jirsa
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria; Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006 Johannesburg, South Africa
| | - T Hein
- Institute of Hydrobiology and Aquatic Ecosystem Management, Department of Water, Atmosphere and Environment, University of Natural Resources and Life Sciences, Gregor-Mendel-Str. 33, 1180 Vienna, Austria; WasserCluster Lunz - Inter-university Center for Aquatic Ecosystem Research, Lunz am See, Dr. Carl Kupelwieser Prom. 5, 3293 Lunz/See, Austria
| | - W Wanek
- Division of Terrestrial Ecosystem Research, Centre of Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - J Prommer
- Division of Terrestrial Ecosystem Research, Centre of Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - P Bonin
- Aix-Marseille Université, CNRS, Université de Toulon, IRD, MIO UMR 110, 13288 Marseille, France
| | - J J Gómez-Alday
- Biotechnology and Natural Resources Section, Institute for Regional Development (IDR), University of Castilla-La Mancha (UCLM), Campus Universitario s/n, 02071 Albacete, Spain
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Hu J, Ke X, Wang B, Mei Y, Xiao N, Wan X, Liu G, Hu M, Zhao J. SSThe coexistence and diversity of Candidatus methylomirabilis oxyfera-like and anammox bacteria in sediments of an urban eutrophic lake. Int Microbiol 2022; 25:457-469. [DOI: 10.1007/s10123-021-00230-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022]
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39
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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Beman JM, Vargas SM, Wilson JM, Perez-Coronel E, Karolewski JS, Vazquez S, Yu A, Cairo AE, White ME, Koester I, Aluwihare LI, Wankel SD. Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones. Nat Commun 2021; 12:7043. [PMID: 34857761 PMCID: PMC8639706 DOI: 10.1038/s41467-021-27381-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/15/2021] [Indexed: 01/04/2023] Open
Abstract
Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 µM. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and 15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 µM. Nitrite oxidation can account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns are consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results demonstrate that nitrite oxidation plays a pivotal role in the maintenance and biogeochemical dynamics of OMZs.
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Affiliation(s)
- J. M. Beman
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - S. M. Vargas
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - J. M. Wilson
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA ,grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - E. Perez-Coronel
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - J. S. Karolewski
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - S. Vazquez
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - A. Yu
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - A. E. Cairo
- grid.266096.d0000 0001 0049 1282Life and Environmental Sciences, University of California, Merced, Merced, CA USA
| | - M. E. White
- grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - I. Koester
- grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - L. I. Aluwihare
- grid.266100.30000 0001 2107 4242Scripps Institution of Oceanography, University of California, San Diego, CA USA
| | - S. D. Wankel
- grid.56466.370000 0004 0504 7510Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA USA
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Rajendran RK, Lin CC. Stability and Microbial Toxicity of Silver Nanoparticles under Denitrifying Conditions. ACS APPLIED MATERIALS & INTERFACES 2021; 13:46233-46246. [PMID: 34547889 DOI: 10.1021/acsami.1c10662] [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] [Indexed: 06/13/2023]
Abstract
While the antibacterial effect of silver nanoparticles (AgNPs) on environmentally beneficial microbes has drawn considerable attention, the stability and microbial toxicity of AgNPs in a system where nitrate reduction is the dominant terminal electron-accepting process remain understudied. Here, we explore the impact of citrate-coated AgNPs (cit-AgNPs) on the growth and metabolism of two metal-sensitive and one nonsensitive bacterial strains under denitrifying conditions. Dose-response analysis revealed that in contrast to the bacteriostatic effect exhibited at 1 ppm, 5 ppm cit-AgNPs were bactericidal to the metal-sensitive strains. It was observed that the growth of the cells initiated Ag(I) formation, and the supplement of chloride (2.7 mM) to the cultures substantially mitigated the bactericidal capacity of cit-AgNPs, indicating that AgNP dissolution to ionic Ag(I) played a key role in AgNP toxicity. Abiotic experiments confirmed that nitrite, not nitrate, had the capacity to oxidize cit-AgNPs. Transcriptomic analysis revealed that (i) the gene encoding for membrane stress was upregulated proportionally to cit-AgNP concentrations; (ii) cit-AgNPs and Ag(I) at higher levels upregulated genes involved in oxidative stress and iron-sulfur clusters, whereas expressions of the genes responsible for electron transport, ATP synthesis, and denitrification were substantially repressed; (iii) the addition of chloride significantly altered the level of transcriptional profiles of all of the genes. These results not only provide evidence of abiotic AgNP oxidation by metabolic intermediate nitrogen species but also suggest that AgNPs and Ag(I) may induce differential toxicity modes to prokaryotes. Our findings reinforce the importance of evaluating the potential ecological toxicity and risks associated with the transformation of nanomaterials.
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Affiliation(s)
- Ranjith Kumar Rajendran
- Institute of Environmental Engineering, National Central University, Taoyuan City 32001, Taiwan
| | - Chu-Ching Lin
- Institute of Environmental Engineering, National Central University, Taoyuan City 32001, Taiwan
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42
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Yu Z, Pei Y, Zhao S, Kakade A, Khan A, Sharma M, Zain H, Feng P, Ji J, Zhou T, Wang H, Wu J, Li X. Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1527-1537. [PMID: 33123966 DOI: 10.1007/s10646-020-02290-5] [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] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.
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Affiliation(s)
- Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Yaxin Pei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Shuai Zhao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Apurva Kakade
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Monika Sharma
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Hajira Zain
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Pengya Feng
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Jing Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Haoyang Wang
- McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Jingyuan Wu
- The First Clinical Medical College, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
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Li J, Hua G, Liu S, Liu X, Huang Y, Shi Y. Effects of crab disturbance on nitrogen migration and transformation in a coastal tidal flat wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:52345-52356. [PMID: 34009575 DOI: 10.1007/s11356-021-14393-5] [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: 12/10/2020] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The influence of crab disturbances on nitrogen migration and the transformations of pore water and overlying water in a coastal tidal flat wetland were investigated at the lab scale, and the nitrogen exchange flux at the sediment-water interface was calculated. The results showed that crabs, combined with tidal effects, had significant effects on the microtopography of the studied crab box. In addition, there was no significant difference in the concentrations of NH4+-N, NO3--N, or TN between two points in the horizontal direction (P > 0.05), and there were significant differences in the concentrations of NH4+-N and TN in the vertical direction (P < 0.05); the NO3--N concentration difference was not obvious (P > 0.05). The NO3--N concentration in the surface pore water of the crab box had a downward trend with time. Furthermore, the NH4+-N and TN contents in the overlying water in the crab box were significantly higher than those of the control box, indicating that crab disturbances also had significant effects on the concentrations of NH4+-N, NO3--N, and TN in the overlying water. The existence of crab caves greatly promoted the nitrogen exchange flux at the sediment-water interface, and the mean exchange fluxes of NH4+-N, NO3--N and TN were 51.40 mmol (m2 day)-1, -13.44 mmol (m2 day)-1 and 39.74 mmol (m2 day)-1, respectively (much higher than those measured in the control box), implying that NH4+-N and TN were released from the sediment to the overlying water, while NO3--N was released from the overlying water to the sediment.
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Affiliation(s)
- Jinli Li
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China
| | - Guofen Hua
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China.
| | - Shangqing Liu
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China
| | - Xiangdong Liu
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China
| | - Yuying Huang
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China
| | - Ying Shi
- College of Water Conservancy and Hydroelectric Power, Hohai University, Nanjing, 210098, People's Republic of China
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44
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Tong N, Xia Z, Xie T, Liu X, Shen J, Zhang Z, Wang X. Photochemistry of Nitrate Ion: Reduction by Formic Acid under UV Irradiation. Photochem Photobiol 2021; 98:404-411. [PMID: 34515997 DOI: 10.1111/php.13518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/05/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Mutual transformations of various nitrogen compounds and their reaction mechanisms have been a subject of great concern to the chemical, ecological and environmental communities. In the paper, the reactions of NO 3 - ion with small organic acids such as formic acid (HCOOH), acetic acid (CH3 COOH) and lactic acid (C3 H6 O3 ) under ultraviolet illumination were investigated systematically. It was found that NO 3 - ion is easily reduced into NO 2 - and NOx and then further into N2 and NH3 (in the form of NH 4 + ) in the process. The carboxyl anion radicals and hydrogen formed by photodecomposition of formic acid are responsible for the rapid photoreduction reaction of nitrate. The initial pH and the nitrate concentration considerably affect the product distribution and nitrate conversion. Based on a preliminary simulation study, we speculated that the photoinduced reaction may effectively proceed in oceans, lakes and rivers because of ever-increasing nitrate and organic emissions. This research is helpful to understand nitrogen cycle mechanism and develop water environmental control technologies.
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Affiliation(s)
- Na Tong
- State Key Laboratory of Photocatalysis on Energy and Environment, Research Institute of Photocatalysis, College of Chemistry, Fuzhou University, Fujian, China.,Patent Examination Cooperation Fujian Center of the Patent Office, SIPO, Fujian, China
| | - Zhonglei Xia
- College of Materials Science and Engineering, Fuzhou University, Fujian, China
| | - Tianzhu Xie
- College of Materials Science and Engineering, Fuzhou University, Fujian, China
| | - Xu Liu
- College of Materials Science and Engineering, Fuzhou University, Fujian, China
| | - Jinni Shen
- State Key Laboratory of Photocatalysis on Energy and Environment, Research Institute of Photocatalysis, College of Chemistry, Fuzhou University, Fujian, China
| | - Zizhong Zhang
- State Key Laboratory of Photocatalysis on Energy and Environment, Research Institute of Photocatalysis, College of Chemistry, Fuzhou University, Fujian, China
| | - Xuxu Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Research Institute of Photocatalysis, College of Chemistry, Fuzhou University, Fujian, China
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45
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Liao H, Qu M, Hou X, Lin X, Li H, Duan CS, Tian Y. Nitrogeniibacter mangrovi gen. nov., sp. nov., a novel anaerobic and aerobic denitrifying betaproteobacterium and reclassification of Azoarcus pumilus as Aromatoleum pumilum comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34369861 DOI: 10.1099/ijsem.0.004946] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Denitrification is a vital link in the global bio-nitrogen cycle. Here, we isolated a strain (M9-3-2T) that is a novel benzo[a]pyrene (BaP)-tolerant, anaerobic and aerobic denitrifying bacterium from a continuous BaP-enrichment cultured mangrove sediment. In silico comparative genomics and taxonomic analysis clearly revealed that strain M9-3-2T (=MCCC 1K03313T=JCM 32045T) represents a novel species of a novel genus named as Nitrogeniibacter mangrovi gen. nov., sp. nov., belonging to family Zoogloeaceae, order Rhodocyclales. In addition, the species Azoarcus pumilus is transferred into genus Aromatoleum and named Aromatoleum pumilum comb. nov. The predominant respiratory quinone of strain M9-3-2T was ubiquinone-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and three unidentified aminophospholipids. In this study, the capacity of strain M9-3-2T to eliminate nitrate was detected under anaerobic and aerobic conditions, and the removal rates of nitrate were 6.1×10-6 µg N/l/h/cell and 3×10-7 µg N/l/h/cell, respectively. Our results suggested that strain M9-3-2T could play an important role in the nitrogen removal regardless of the presence of oxygen in natural or/and man-made ecosystems.
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Affiliation(s)
- Hu Liao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Mingming Qu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xinyue Hou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China
| | - Chen-Song Duan
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, PR China
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46
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Huang L, Chakrabarti S, Cooper J, Perez A, John SM, Daroub SH, Martens-Habbena W. Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil. ISME COMMUNICATIONS 2021; 1:19. [PMID: 37938645 PMCID: PMC9723749 DOI: 10.1038/s43705-021-00020-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/14/2021] [Indexed: 12/21/2022]
Abstract
Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O-N per µg NOx-N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.
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Affiliation(s)
- Laibin Huang
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences, University of Florida, Belle Glade, FL, USA
| | - Ana Perez
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Sophia M John
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences, University of Florida, Belle Glade, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Microbiology and Cell Science, University of Florida, Davie, FL, USA.
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47
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Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
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Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
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48
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Different nutrient levels, rather than seasonal changes, significantly affected the spatiotemporal dynamic changes of ammonia-oxidizing microorganisms in Lake Taihu. World J Microbiol Biotechnol 2021; 37:91. [PMID: 33939019 DOI: 10.1007/s11274-021-03053-y] [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: 05/04/2020] [Accepted: 04/09/2021] [Indexed: 01/23/2023]
Abstract
Ammonia-oxidizing microorganisms (AOM) play crucial roles in the degradation of ammonia nitrogen in freshwater lakes. Hence, it is necessary to reveal the spatiotemporal dynamic changes of AOM in freshwater lakes. Here, we conducted a study on the spatial and temporal dynamic changes of AOM in different lake regions under gradient nutrient levels in Lake Taihu, and found that the abundance of AOM had significant spatial changes, while the seasonal changes had relatively little effect on the abundance of AOM. We also found that ammonia-oxidizing archaea (AOA) were adapted to freshwater habitats with low nutrient levels, while ammonia-oxidizing bacteria (AOB) and anaerobic ammonia-oxidizing bacteria (AAOB) had higher abundance in high nutrient level lake regions. Moreover, the amoA gene abundance of AOB was much higher than that of AOA, indicating that AOB was the dominant aerobic ammonia oxidizer in the water of Lake Taihu. In addition, temperature, pH and dissolved oxygen all had a positive effect on AOM, especially AOB; while C- and N-related physicochemical factors had a significant positive effect on AAOB, but exhibited a significant negative correlation with AOA. The community structure of AOM also had obvious spatial changes and Group I.1a, Nitrosomonas and Candidatus Brocadia fulgida were the dominant cluster of AOA, AOB and AAOB, respectively.
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49
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Hui C, Li Y, Zhang W, Yang G, Wang H, Gao Y, Niu L, Wang L, Zhang H. Coupling Genomics and Hydraulic Information to Predict the Nitrogen Dynamics in a Channel Confluence. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4616-4628. [PMID: 33760605 DOI: 10.1021/acs.est.0c04018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The simulation of nitrogen dynamics in urban channel confluences is essential for the evaluation and improvement of water quality. The omics-based modeling approaches that have been rapidly developed have been increasingly applied to characterize metabolisms of the microbial community and transformation of the associated materials. However, the transport of microorganisms and chemicals within and among different phases, which could be the rate-limiting step for the nitrogen dynamics, are always neglected or oversimplified in omics-based models. Therefore, this study proposes a novel simulation system coupling genomic and hydraulic information to simulate transport and transformation processes and provide predictions of nitrogen dynamics in a confluence. The proposed model was able to capture multiphase mass transport, microbial population dynamics, and nitrogen transformation and accurately predict gene abundances and nitrogen concentrations in both water and sediment; the mean relative errors were all lower than 40%. The model emphasized the importance of transport processes, which contributed more than 90% to gene abundances and chemical concentrations. Moreover, the simulation of reaction rates exhibited the specific nitrogen transformation processes in the confluence. The sulfide oxidation and the nitrate reduction and anaerobic ammonium oxidation, with the participation of the genes nap and hzo, respectively, were promoted as the main processes of nitrate and nitrite reduction.
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Affiliation(s)
- Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Gang Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Haolan Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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Nguyen VQ, Van HT, Sy HL, Nguyen TML, Nguyen DK. Application of Mussell-derived biosorbent to remove NH4+ from aqueous solution: Equilibrium and Kinetics. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04462-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
AbstractMussel shells are often considered an abundant waste with no use. This study shows that the employment of mussel shells as a biosorbent for ammonium from water environment is completely possible. By using batch experimental method, optimal conditions for the ammonium adsorption onto mussel shells were determined. Specifically, those include a pH level of 8, contact time of 90 min, an initial ammonium concentration of 40 mg/l and the adsorbent dose of 700 mg/25 ml. With such operating conditions, experiments in laboratory aqueous solutions resulted in a maximum adsorption capacity of 2.33 mg/g, corresponded by 46.575% of efficiency. Adsorption isotherms and kinetics were well described with the Freundlich isothermal model, suggesting a heterogeneous adsorption process occurring on multilayers and both the pseudo-first-order and the pseudo-second-order, implying that the operational fundament was based on chemisorption. Analyses regarding SEM, EDS and FTIR were also implemented to identify the morphology, composition and functional groups of the adsorbent.
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