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Fan Y, Zhou Z, Liu F, Qian L, Yu X, Huang F, Hu R, Su H, Gu H, Yan Q, He Z, Wang C. The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes. WATER RESEARCH 2024; 262:122113. [PMID: 39032335 DOI: 10.1016/j.watres.2024.122113] [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: 03/22/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.
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Affiliation(s)
- Yijun Fan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengyuan Zhou
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lu Qian
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fangjuan Huang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruiwen Hu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hualong Su
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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Chen H, Wei YQ, Xu MY, Zhu MW, Liu J, Yong YC, Fang Z. Artificial and Biosynthetic Nanoparticles Boost Bioelectrochemical Reactions via Efficient Bidirectional Electron Transfer of Shewanella loihica. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400962. [PMID: 38511578 DOI: 10.1002/smll.202400962] [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: 02/05/2024] [Revised: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Bioelectrochemical reactions using whole-cell biocatalysts are promising carbon-neutral approaches because of their easy operation, low cost, and sustainability. Bidirectional (outward or inward) electron transfer via exoelectrogens plays the main role in driving bioelectrochemical reactions. However, the low electron transfer efficiency seriously inhibits bioelectrochemical reaction kinetics. Here, a three dimensional and artificial nanoparticles-constituent inverse opal-indium tin oxide (IO-ITO) electrode is fabricated and employed to connect with exoelectrogens (Shewanella loihica PV-4). The above electrode collected 128-fold higher cell density and exhibited a maximum current output approaching 1.5 mA cm-2 within 24 h at anode mode. By changing the IO-ITO electrode to cathode mode, the exoelectrogens exhibited the attractive ability of extracellular electron uptake to reduce fumarate and 16 times higher reverse current than the commercial carbon electrode. Notably, Fe-containing oxide nanoparticles are biologically synthesized at both sides of the outer cell membrane and probably contributed to direct electron transfer with the transmembrane c-type cytochromes. Owing to the efficient electron exchange via artificial and biosynthetic nanoparticles, bioelectrochemical CO2 reduction is also realized at the cathode. This work not only explored the possibility of augmenting bidirectional electron transfer but also provided a new strategy to boost bioelectrochemical reactions by introducing biohybrid nanoparticles.
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Affiliation(s)
- Han Chen
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yu-Qing Wei
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Meng-Yuan Xu
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Ma-Wei Zhu
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Junying Liu
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zhen Fang
- Biofuels Institute, School of Emergency Management, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
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Gao X, Li X, Wang Y, Lin C, Zuo Y, Li X, Xing W. Does invasive submerged macrophyte diversity affect dissimilatory nitrate reduction processes in sediments with varying microplastics? JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134510. [PMID: 38704909 DOI: 10.1016/j.jhazmat.2024.134510] [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: 02/20/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
Nitrogen removal is essential for restoring eutrophic lakes. Microorganisms and aquatic plants in lakes are both crucial for removing excess nitrogen. However, microplastic (MP) pollution and the invasion of exotic aquatic plants have become increasingly serious in lake ecosystems due to human activity and plant-dominant traits. This field mesocosm study explored how the diversity of invasive submerged macrophytes affects denitrification (DNF), anammox (ANA), and dissimilatory nitrate reduction to ammonium (DNRA) in lake sediments with varying MPs. Results showed that invasive macrophytes suppressed DNF rates, but DNRA and ANA were less sensitive than DNF to the diversity of invasive species. Sediment MPs increased the biomass of invasive species more than native species, but did not affect microbial processes. The effects of MPs on nitrate dissimilatory reduction were process-specific. MPs increased DNF rates and the competitive advantage of DNF over DNRA by changing the sediment environment. The decoupling of DNF and ANA was also observed, with increased DNF rates and decreased ANA rates. The study findings suggested new insights into how the invasion of exotic submerged macrophytes affects the sediment nitrogen cycle complex environments.
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Affiliation(s)
- Xueyuan Gao
- CAS 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 100039, China
| | - Xiaowei Li
- CAS 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 100039, China
| | - Yingcai Wang
- Eco-Environment Monitoring and Scientific Research Center, Changjiang Basin Ecology and Environment Administration, Ministry of Ecology and Environment, Wuhan 430010, China.
| | - Cheng Lin
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resource and Environment, Hubei University, Wuhan 430062, China
| | - Yanxia Zuo
- Analysis and Testing Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaolu Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wei Xing
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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Shao B, Niu L, Xie YG, Zhang R, Wang W, Xu X, Sun J, Xing D, Lee DJ, Ren N, Hua ZS, Chen C. Overlooked in-situ sulfur disproportionation fuels dissimilatory nitrate reduction to ammonium in sulfur-based system: Novel insight of nitrogen recovery. WATER RESEARCH 2024; 257:121700. [PMID: 38705068 DOI: 10.1016/j.watres.2024.121700] [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: 02/28/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/07/2024]
Abstract
Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %-61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7-210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus, and Rubrivivax, harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology.
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Affiliation(s)
- Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Li Niu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Yuan-Guo Xie
- Department of Environmental Science and Engineering, Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, University of Science and Technology of China, Hefei 230026, PR China
| | - Ruochen Zhang
- School of Civil and Transportation, Hebei University of Technology, Tianjin 300401, PR China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan 410083, PR China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, PR China; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, University of Science and Technology of China, Hefei 230026, PR China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China.
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Pflüger T, Gschell M, Zhang L, Shnitsar V, Zabadné AJ, Zierep P, Günther S, Einsle O, Andrade SLA. How sensor Amt-like proteins integrate ammonium signals. SCIENCE ADVANCES 2024; 10:eadm9441. [PMID: 38838143 DOI: 10.1126/sciadv.adm9441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.
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Affiliation(s)
- Tobias Pflüger
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Mathias Gschell
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Lin Zhang
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Volodymyr Shnitsar
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Annas J Zabadné
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Paul Zierep
- Faculty of Chemistry and Pharmacy, Institute for Pharmaceutical Sciences, University Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Stefan Günther
- Faculty of Chemistry and Pharmacy, Institute for Pharmaceutical Sciences, University Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Oliver Einsle
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University Freiburg, Schänzlerstr. 1, 79104 Freiburg, Germany
| | - Susana L A Andrade
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University Freiburg, Schänzlerstr. 1, 79104 Freiburg, Germany
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6
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Cheng J, Robles-Lecompte A, McKenna AM, Chang NB. Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system. CHEMOSPHERE 2024; 357:142042. [PMID: 38621490 DOI: 10.1016/j.chemosphere.2024.142042] [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: 02/23/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.
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Affiliation(s)
- Jinxiang Cheng
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Alejandra Robles-Lecompte
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA
| | - Amy M McKenna
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ni-Bin Chang
- Department of Civil, Environmental, and Construction Engineering, University of Central Florida, Orlando, FL, USA.
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Chen T, Zhang Y, Xia M, Wang Q. Soil properties and functional genes in nitrogen removal process of bioretention. ENVIRONMENTAL TECHNOLOGY 2024; 45:2268-2283. [PMID: 36779295 DOI: 10.1080/09593330.2023.2172616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
The effects of different soil properties on hydrology and nitrogen removal were studied in a simulated bioretention system. Soil capacity of permeability and water retention, changes in the soil environment, leachate concentrations at the surface and bottom layers, quantification of N removal from soil, microorganism and plant by 15N isotope tracer technique, and functional genes abundance at different depths were evaluated. The results showed that shallow root plants, soil compaction, and low organic matter content were not conducive to the infiltration of bioretention systems. In the 72 h experiment, compaction (especially surface compaction) and planting of herbaceous plants (Ophiopogon japonicus) were not beneficial to the removal of TN, TP, and COD. Adding an appropriate amount of organic matter also affects nitrogen and phosphorus removal. In the process of denitrification, the order of the ability to remove nitrogen is soil adsorption > microbial assimilation > plant uptake. The contribution of soil denitrification is affected by soil compaction, compaction location, plant species and organic matter content. The abundance of 16S rRNA, nitrifying, denitrifying and nrfA genes decreased with soil depth. More copies of genes in topsoil were thought to be due to sufficient nutrients, aerobic condition, anaerobic microsites and submerged state. Soil compaction, organic matter content and plant species affected nitrification, denitrification and DNRA gene characteristics.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yafu Zhang
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Mengmeng Xia
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Qianpeng Wang
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
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Dong B, Lu J, Liu Y, Zhang R, Xing B. A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar. ENVIRONMENT INTERNATIONAL 2024; 183:108435. [PMID: 38217902 DOI: 10.1016/j.envint.2024.108435] [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: 09/17/2023] [Revised: 12/13/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.
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Affiliation(s)
- Biya Dong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuexian Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ruili Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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9
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Sun Y, Yin Y, He G, Cha G, Ayala-del-Río HL, González G, Konstantinidis KT, Löffler FE. pH selects for distinct N 2O-reducing microbiomes in tropical soil microcosms. ISME COMMUNICATIONS 2024; 4:ycae070. [PMID: 38808123 PMCID: PMC11131594 DOI: 10.1093/ismeco/ycae070] [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: 11/29/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.
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Affiliation(s)
- Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA 02148, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Grizelle González
- USDA Forest Service, International Institute of Tropical Forestry, San Juan 00926, Puerto Rico
| | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
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10
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Mosley OE, Gios E, Handley KM. Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers. ISME COMMUNICATIONS 2024; 4:ycae047. [PMID: 38650708 PMCID: PMC11033732 DOI: 10.1093/ismeco/ycae047] [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: 01/17/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.
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Affiliation(s)
- Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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11
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Pan D, Chen P, Yang G, Niu R, Bai Y, Cheng K, Huang G, Liu T, Li X, Li F. Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21156-21167. [PMID: 38064275 DOI: 10.1021/acs.est.3c06337] [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: 12/20/2023]
Abstract
Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2- accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4+ to the reduced NO3- were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2--to-NH4+ reduction in the cytoplasm. Dechloromonas dominated the NO2--to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2--to-NH4+ during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4+ production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.
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Affiliation(s)
- Dandan Pan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Pengcheng Chen
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guang Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Rumiao Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yan Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Kuan Cheng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guoyong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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12
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Saghaï A, Pold G, Jones CM, Hallin S. Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Nat Commun 2023; 14:8249. [PMID: 38086813 PMCID: PMC10716430 DOI: 10.1038/s41467-023-44022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.
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Affiliation(s)
- Aurélien Saghaï
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Grace Pold
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden.
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13
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Brescia F, Sillo F, Franchi E, Pietrini I, Montesano V, Marino G, Haworth M, Zampieri E, Fusini D, Schillaci M, Papa R, Santamarina C, Vita F, Chitarra W, Nerva L, Petruzzelli G, Mennone C, Centritto M, Balestrini R. The 'microbiome counterattack': Insights on the soil and root-associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:459-483. [PMID: 37226644 PMCID: PMC10667653 DOI: 10.1111/1758-2229.13167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023]
Abstract
Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root-associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype-specific one. A higher number of specific bacterial taxa and an enhanced tolerance to fungal diseases characterized a lentil landrace compared to the commercial varieties. This outcome supported the hypothesis that locally adapted landraces might have a high recruiting efficiency of beneficial soil microbes.
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Affiliation(s)
- Francesca Brescia
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Fabiano Sillo
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Elisabetta Franchi
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Ilaria Pietrini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Vincenzo Montesano
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyBernalda (MT)Italy
| | - Giovanni Marino
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Matthew Haworth
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
| | - Elisa Zampieri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Danilo Fusini
- Eni S.p.A.R&D Environmental & Biological LaboratoriesSan Donato MilaneseItaly
| | - Martino Schillaci
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Chiara Santamarina
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Federico Vita
- Department of Bioscience, Biotechnology and EnvironmentUniversity of Bari Aldo MoroBariItaly
| | - Walter Chitarra
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | - Luca Nerva
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and EconomicsConeglianoItaly
| | | | - Carmelo Mennone
- Azienda Pantanello, ALSIA Research Center Metapontum AgrobiosBernalda (MT)Italy
| | - Mauro Centritto
- Institute for Sustainable Plant ProtectionNational Research Council of ItalySesto FiorentinoItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
| | - Raffaella Balestrini
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyTurinItaly
- ENI‐CNR Water Research Center ‘Hypatia of Alexandria’ALSIA Research Center Metapontum AgrobiosBernaldaItaly
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14
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Niu Y, An Z, Gao D, Chen F, Zhou J, Liu B, Qi L, Wu L, Lin Z, Yin G, Liang X, Dong H, Liu M, Hou L, Zheng Y. Tidal dynamics regulates potential coupling of carbon‑nitrogen‑sulfur cycling microbes in intertidal flats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165663. [PMID: 37474052 DOI: 10.1016/j.scitotenv.2023.165663] [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: 05/05/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.
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Affiliation(s)
- Yuhui Niu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, China
| | - Zhirui An
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Bolin Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Lin Qi
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Zhuke Lin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China.
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15
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Yoon S, Heo H, Han H, Song DU, Bakken LR, Frostegård Å, Yoon S. Suggested role of NosZ in preventing N 2O inhibition of dissimilatory nitrite reduction to ammonium. mBio 2023; 14:e0154023. [PMID: 37737639 PMCID: PMC10653820 DOI: 10.1128/mbio.01540-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.
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Affiliation(s)
- Sojung Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hokwan Heo
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Dong-Uk Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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16
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Sorokin DY, Tikhonova TV, Koch H, van den Berg EM, Hinderks RS, Pabst M, Dergousova NI, Soloveva AY, Kuenen GJ, Popov VO, van Loosdrecht MCM, Lücker S. Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia. THE ISME JOURNAL 2023; 17:1639-1648. [PMID: 37443340 PMCID: PMC10504241 DOI: 10.1038/s41396-023-01473-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.
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Affiliation(s)
- Dimitry Y Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
| | - Tamara V Tikhonova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | | | - Renske S Hinderks
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Natalia I Dergousova
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Y Soloveva
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Gijs J Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Vladimir O Popov
- Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
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17
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Liu B, Dai Y, Cheng X, He X, Bei Q, Wang Y, Zhou Y, Zhu B, Zhang K, Tian X, Duan M, Xie X, Wang L. Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field. Front Microbiol 2023; 14:1217966. [PMID: 37533822 PMCID: PMC10391546 DOI: 10.3389/fmicb.2023.1217966] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.
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Affiliation(s)
- Bangyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yisha Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xin Cheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xian He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Yifan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yuling Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Bo Zhu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Kangping Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoqin Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Meichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoyu Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Longchang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
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18
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Zhao L, Fu G, Pang W, Li X, Pan C, Hu Z. A novel autotrophic denitrification and nitrification integrated constructed wetland process for marine aquaculture wastewater treatment. CHEMOSPHERE 2023; 321:138157. [PMID: 36796520 DOI: 10.1016/j.chemosphere.2023.138157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/29/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
We undertook a lab-scale evaluation of a novel autotrophic denitrification and nitrification integrated constructed wetland (ADNI-CW) for improved carbon (C), nitrogen (N), and sulfur (S) cycling to treat mariculture wastewater. The process involved an up-flow autotrophic denitrification constructed wetland unit (AD-CW) for sulfate reduction and autotrophic denitrification, and an autotrophic nitrification constructed wetland unit (AN-CW) for nitrification. The 400-day experiment investigated the performance of the AD-CW, AN-CW, and entire ADNI-CW processes under various hydraulic retention times (HRTs), nitrate concentrations, dissolved oxygen levels, and recirculation ratios. Under various HRTs, the AN-CW achieved a nitrification performance exceeding 92%. Correlation analysis of the chemical oxygen demand (COD) revealed that, on average, approximately 96% of COD was removed by sulfate reduction. Under different HRTs, increases in influent NO3--N concentrations caused the amount of sulfide to gradually decrease from sufficient to deficient, and the autotrophic denitrification rate also decreased from 62.18 to 40.93%. In addition, when the NO3--N load rate was above 21.53 g N/m2·d, the transformation of organic N by mangrove roots may have increased NO3--N in the top effluent of the AD-CW. The coupling of N and S metabolic processes mediated by various functional microorganisms (Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and unclassified_d__Bacteria) enhanced N removal. We intensively explored the effects of changing inputs as culture species developed on the physical, chemical, and microbial changes of CW to ensure a consistent and effective management of C, N, and S. This study lays the foundation for green and sustainable mariculture development.
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Affiliation(s)
- Lin Zhao
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China
| | - Guiping Fu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Weicheng Pang
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xiaxin Li
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Chao Pan
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhangli Hu
- Guangdong Technology Research Center for Marine Algal Bioengineering, Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China; Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen, 518055, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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19
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Bello A, Liu W, Chang N, Erinle KO, Deng L, Egbeagu UU, Babalola BJ, Yue H, Sun Y, Wei Z, Xu X. Deciphering biochar compost co-application impact on microbial communities mediating carbon and nitrogen transformation across different stages of corn development. ENVIRONMENTAL RESEARCH 2023; 219:115123. [PMID: 36549490 DOI: 10.1016/j.envres.2022.115123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/27/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Under current climatic conditions, developing eco-friendly and climate-smart fertilizers has become increasingly important.The co-application of biochar and compost on agricultural soils has received considerable attention recently.Unfortunately, little is known about its effects on specific microbial taxa involved in carbon and nitrogen transformation in the soil.Herein, we report the efficacy of applying biochar-based amendments on soil physicochemical indices, enzymatic activity, functional genes, bacterial community, and their network patterns in corn rhizosphere at seedling (SS), flowering (FS), and maturity (MS) stages.The applied treatments were: compost alone (COM), biochar alone (BIOC), composted biochar (CMB), fortified compost (CMWB), and the control (no fertilizer (CNTRL).The non-metric multidimensional scaling (NMDS) indicated total nitrogen (TN), pH, NO3--N, urease, protease, and microbial biomass C (MBC) as the dominant environmental factors driving soil bacteria in this study.The dominant N mediating genes belonged to nitrate reductase (narG) and nitronate monooxygenase (amo), while beta-galactosidase, catalase, and alpha-amylase were the dominant genes observed relating to C cycling.Interestingly, the abundance of these genes was higher in COM, CMWB, and CMB compared with the CNTRL and BIOC treatments.The bacteria network properties of CWMB and CMB indicated robust niche overlap associated with high cross-feeding between bacterial communities compared to other treatments.Path and stepwise regression analyses revealed norank_Reyranellaceae and Sphingopyxis in CMWB as the major bacterial genera and the major predictive indices mediating soil organic C (SOC), NH4+-N, NO3--N, and TN transformation.Overall, biochar with compost amendments improved soil nutrient conditions, regulated the composition of the bacterial community, and benefited C/N cycling in the soil ecosystem.
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Affiliation(s)
- Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China; College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Wanying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Nuo Chang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Kehinde Olajide Erinle
- School of Agriculture, Food and Wine, Faculty of Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Liting Deng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ugochi Uzoamaka Egbeagu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Busayo Joshua Babalola
- Department of Plant Biology and Plant Pathology, University of Georgia, Athens, Georgia, 30602, USA
| | - Han Yue
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
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20
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Semedo M, Song B. Sediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159496. [PMID: 36257428 DOI: 10.1016/j.scitotenv.2022.159496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA 23062, USA; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA 23062, USA
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21
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Pizarro L, Magalhães C, Almeida CMR, Carvalho MDF, Semedo M. Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4. FEMS Microbiol Lett 2023; 370:fnad047. [PMID: 37279908 PMCID: PMC10337742 DOI: 10.1093/femsle/fnad047] [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: 01/31/2023] [Revised: 05/19/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023] Open
Abstract
Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.
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Affiliation(s)
- Leonor Pizarro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Faculty of Biotechnology, Catholic University of Portugal, Porto 4169-005, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Biology, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences (FCUP), University of Porto, Porto 4169-007, Portugal
| | - Maria de Fátima Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto 4050-313, Portugal
| | - Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4450-208, Portugal
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22
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Rempfert KR, Nothaft DB, Kraus EA, Asamoto CK, Evans RD, Spear JR, Matter JM, Kopf SH, Templeton AS. Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman. Front Microbiol 2023; 14:1139633. [PMID: 37152731 PMCID: PMC10160414 DOI: 10.3389/fmicb.2023.1139633] [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: 01/07/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H2) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg2+- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca2+-OH- fluids comprised primarily of ammonia (NH3). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ18O ~ 22‰, Δ17O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ18O of 53.7‰, Δ17O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ18O and Δ17O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH3 (>100 μM) with little NO 3 - detectable. We interpret that NH3 in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation (18ε / 15ε) measured in Samail Ophiolite NO 3 - was close to unity (18ε / 15ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.
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Affiliation(s)
- Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- *Correspondence: Kaitlin R. Rempfert
| | - Daniel B. Nothaft
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Emily A. Kraus
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Ciara K. Asamoto
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - R. Dave Evans
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, CO, United States
| | - Juerg M. Matter
- National Oceanography Centre, University of Southampton, Southampton, United Kingdom
| | - Sebastian H. Kopf
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
- Alexis S. Templeton
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23
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Li X, Deng Q, Zhang Z, Bai D, Liu Z, Cao X, Zhou Y, Song C. The role of sulfur cycle and enzyme activity in dissimilatory nitrate reduction processes in heterotrophic sediments. CHEMOSPHERE 2022; 308:136385. [PMID: 36096301 DOI: 10.1016/j.chemosphere.2022.136385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
The dissimilatory nitrate (NO3-) reduction processes (DNRPs) play an important role in regulating the nitrogen (N) balance of aquatic ecosystem. Organic carbon (OC) and sulfur are important factors that influence the DNRPs. In this study, we investigated the effects of sulfur cycle and enzyme activity on DNRPs in the natural and human-modified heterotrophic sediments. Quarterly monitoring of anaerobic ammonium oxidation, denitrification (DNF), and dissimilatory NO3- reduction to ammonium (DNRA) in sediments was conducted using 15N isotope tracing method. qPCR and high-throughput sequencing were applied to characterize the DNF and DNRA microbial abundances and communities. Results showed that instead of the OC, the glucosidase activity (GLU) was the key driver of the DNRPs. Furthermore, instead of the ratio of OC to NO3-, the GLU and the ratio of OC to sulfide (C/S) correctly indicated the partitioning of DNRPs in this study. We deduced that the sulfur reduction processes competed with the DNRPs for the available OC. In addition, the inhibitory effect of sulfide (final product of the sulfur reduction processes) on the DNRPs bacterial community were observed, which suggested a general restrictive role of the sulfur cycle in the regulation and partitioning of the DNRPs in heterotrophic sediments.
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Affiliation(s)
- Xiaowen Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Qinghui Deng
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, PR China; Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, PR China.
| | - Zhimin Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Dong Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China.
| | - Zhenghan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China.
| | - Xiuyun Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Yiyong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Chunlei Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
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24
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Li L, Li S, Ma X, Yan Y. Effects of Urban Green Infrastructure Designs on Soil Bacterial Community Composition and Function. Ecosystems 2022. [DOI: 10.1007/s10021-022-00797-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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25
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Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle. World J Microbiol Biotechnol 2022; 38:168. [DOI: 10.1007/s11274-022-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
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26
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Zhao X, Guo M, Chen J, Zhuang Z, Zhang T, Wang X, Li C, Hou N, Bai S. Successional dynamics of microbial communities in response to concentration perturbation in constructed wetland system. BIORESOURCE TECHNOLOGY 2022; 361:127733. [PMID: 35932946 DOI: 10.1016/j.biortech.2022.127733] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Constructed wetlands (CWs) are widely considered as resilient systems able to adapt to environmental perturbations. Little attention has been paid, however, to microbial dynamics when CWs withstand and recover from external shock. To understand the resilience of CWs, this study investigated rhizosphere microbial dynamics when CWs were subjected to influent COD perturbation (200 mg/L-1600 mg/L). Results demonstrated that CWs had strong adaptability to different influent perturbations, characterized by transitions from fluctuating to stable pollutant removal. Microbial analysis showed that rhizosphere microorganisms competed for niches in response to increased COD concentrations, and Trichococcus played key roles in resisting concentration perturbations. Structural equation modeling indicated that rhizosphere community succession and microbial energy metabolism were shaped by pH and DO. These findings provide insights into the mechanism for CW stability maintenance when facing concentration perturbations.
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Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Juntong Chen
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Zhixuan Zhuang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Tuoshi Zhang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xiaohui Wang
- Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunyan Li
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ning Hou
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Shunwen Bai
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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27
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Tang Z, Liu X, Li G, Liu X. Mechanism of biochar on nitrification and denitrification to N 2O emissions based on isotope characteristic values. ENVIRONMENTAL RESEARCH 2022; 212:113219. [PMID: 35390305 DOI: 10.1016/j.envres.2022.113219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/13/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
To clarify the mechanism of biochar on nitrification and denitrification to N2O emissions in farmland soil, the effects of combined application of biochar and different nitrogen sources on the contributions of nitrification and denitrification to N2O emissions were studied using isotope characteristic values. The results showed that the soil N2O emissions from ammonium nitrogen fertilizer treatments were significantly higher than that from nitrate nitrogen fertilizer treatments. The biochar combined with ammonium nitrogen fertilizer reduced soil N2O emissions by 31.0%-30.8%, and biochar combined with nitrate nitrogen fertilizer reduced soil N2O emissions by 70.6%-63.0%. The isotope model showed that the application of ammonium nitrogen fertilizer was more favorable for soil nitrification in the early stage of the experiment (0-2 d), and more favorable for denitrification in the middle and later stages of the experiment (3-17 d). Application of nitrate nitrogen fertilizer enhanced the nitrification of soil nitrifying bacteria in the early and middle stages of the experiment (0-8 d), and the denitrification of soil denitrifying bacteria in the later stage of the experiment (9-17 d). The effects of biochar on N2O emissions were mainly in the middle and later stages of the experiment by promoting the nitrification of nitrifying bacteria and inhibiting denitrification of denitrifying bacteria, so as to reduce N2O emission in soil. These results may help to understand the mitigation mechanism of biochar on N2O emission in upland soil.
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Affiliation(s)
- Zhanming Tang
- Agricultural Clean Watershed Research Group, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingren Liu
- Agricultural Clean Watershed Research Group, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guichun Li
- Agricultural Clean Watershed Research Group, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowan Liu
- Agricultural Clean Watershed Research Group, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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28
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Mosley OE, Gios E, Close M, Weaver L, Daughney C, Handley KM. Nitrogen cycling and microbial cooperation in the terrestrial subsurface. THE ISME JOURNAL 2022; 16:2561-2573. [PMID: 35941171 PMCID: PMC9562985 DOI: 10.1038/s41396-022-01300-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
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Shewanella sp. T2.3D-1.1 a Novel Microorganism Sustaining the Iron Cycle in the Deep Subsurface of the Iberian Pyrite Belt. Microorganisms 2022; 10:microorganisms10081585. [PMID: 36014003 PMCID: PMC9415397 DOI: 10.3390/microorganisms10081585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The Iberian Pyrite Belt (IPB) is one of the largest deposits of sulphidic minerals on Earth. Río Tinto raises from its core, presenting low a pH and high metal concentration. Several drilling cores were extracted from the IPB’s subsurface, and strain T2.3D-1.1 was isolated from a core at 121.8 m depth. We aimed to characterize this subterranean microorganism, revealing its phylogenomic affiliation (Average Nucleotide Identity, digital DNA-DNA Hybridization) and inferring its physiology through genome annotation, backed with physiological experiments to explore its relationship with the Fe biogeochemical cycle. Results determined that the isolate belongs to the Shewanella putrefaciens (with ANI 99.25 with S. putrefaciens CN-32). Its genome harbours the necessary genes, including omcA mtrCAB, to perform the Extracellular Electron Transfer (EET) and reduce acceptors such as Fe3+, napAB to reduce NO3− to NO2−, hydAB to produce H2 and genes sirA, phsABC and ttrABC to reduce SO32−, S2O32− and S4O62−, respectively. A full CRISPR-Cas 1F type system was found as well. S. putrefaciens T2.3D-1.1 can reduce Fe3+ and promote the oxidation of Fe2+ in the presence of NO3− under anaerobic conditions. Production of H2 has been observed under anaerobic conditions with lactate or pyruvate as the electron donor and fumarate as the electron acceptor. Besides Fe3+ and NO3−, the isolate also grows with Dimethyl Sulfoxide and Trimethyl N-oxide, S4O62− and S2O32− as electron acceptors. It tolerates different concentrations of heavy metals such as 7.5 mM of Pb, 5 mM of Cr and Cu and 1 mM of Cd, Co, Ni and Zn. This array of traits suggests that S. putrefaciens T2.3D-1.1 could have an important role within the Iberian Pyrite Belt subsurface participating in the iron cycle, through the dissolution of iron minerals and therefore contributing to generate the extreme conditions detected in the Río Tinto basin.
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Li S, Jiang Z, Ji G. Effect of sulfur sources on the competition between denitrification and DNRA. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119322. [PMID: 35447253 DOI: 10.1016/j.envpol.2022.119322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
The fate of nitrogen is controlled by the competition between nitrate reduction pathways. Denitrification removes nitrogen in the system to the atmosphere, whereas dissimilatory nitrate reduction to ammonia (DNRA) retains nitrate in the form of ammonia. Different microbes specialize in the oxidation of different electron donors, thus electron donors might influence the outcomes of the competition. Here, we investigated the fate of nitrate with five forms of sulfur as electron donors. Chemoautotrophic nitrate reduction did not continue after the passages of the enrichments with sulfide, sulfite and pyrite. Nitrate reduction rate was the highest in the enrichment with thiosulfate. Denitrification was stimulated and no DNRA was observed with thiosulfate, while both denitrification and DNRA were stimulated with elemental sulfur. Metagenomes of the enrichments were assembled and binned into ten genomes. The enriched populations with thiosulfate included Thiobacillus, Lentimicrobium, Sulfurovum and Hydrogenophaga, all of which contained genes involved in sulfur oxidation. Elemental sulfur-based DNRA was performed by Thiobacillus (with NrfA and NirB) and Nocardioides (with only NirB). Our study established a link between sulfur sources, nitrate reduction pathways and microbial populations.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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Upreti K, Rivera-Monroy VH, Maiti K, Giblin AE, Castañeda-Moya E. Dissimilatory nitrate reduction to ammonium (DNRA) is marginal relative to denitrification in emerging-eroding wetlands in a subtropical oligohaline and eutrophic coastal delta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152942. [PMID: 35007602 DOI: 10.1016/j.scitotenv.2022.152942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Nitrate (NO3-) and ammonium (NH4+) are reactive nitrogen (Nr) forms that can exacerbate eutrophication in coastal regions. NO3- can be lost to the atmosphere as N2 gas driven by direct denitrification, coupled nitrification-denitrification and annamox or retained within the ecosystems through conversion of NO3- to NH4+ via dissimilatory nitrate reduction to ammonium (DNRA). Denitrification and DNRA are competitive pathways and hence it is critical to evaluate their functional biogeochemical role. However, there is limited information about the environmental factors driving DNRA in oligohaline habitats, especially within deltaic regions where steep salinity gradients define wetland spatiotemporal distribution. Here we use the Isotope Pairing Technique to evaluate the effect of temperature (10, 20, 30 °C) and in situ soil/sediment organic matter (OM%) on total denitrification (Dtotal = direct + coupled nitrification) and DNRA rates in oligohaline forested/marsh wetlands soils and benthic sediment habitats at two sites representing prograding (Wax Lake Delta, WLD) and eroding (Barataria- Lake Cataouatche, BLC) deltaic stages in the Mississippi River Delta Plain (MRDP). Both sites receive MR water with high NO3- (>40 μM) concentrations during the year via river diversions. Denitrification rates were significantly higher (range: 18.0 ± 0.4-113.0 ± 10.6 μmol m-2 h-1) than DNRA rates (range: 0.7 ± 0.2-9.2 ± 0.3 μmol m-2 h-1). Therefore, DNRA represented on average < 10% of the total NO3- reduction (DNRA + Dtotal). Unlike denitrification, DNRA showed no consistent response to temperature. These results indicate that DNRA in wetland soils and benthic sediment is not a major nitrogen transformation in oligohaline regions across the MRDP regardless of wide range of OM% content in these eroding and prograding delta lobes.
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Affiliation(s)
- Kiran Upreti
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Victor H Rivera-Monroy
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA.
| | - Kanchan Maiti
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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Zhang H, Chen X, Song L, Liu S, Li P. The mechanism by which Enteromorpha Linza polysaccharide promotes Bacillus subtilis growth and nitrate removal. Int J Biol Macromol 2022; 209:840-849. [PMID: 35439475 DOI: 10.1016/j.ijbiomac.2022.04.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/15/2022]
Abstract
In this study, we discussed the relationship between Entermorpha linza polysaccharide (EP) and Bacillus subtilis, which can transform nitrate. A sole carbon source experiment showed that Bacillus subtilis could utilize EP, and the bacterial density was maximally increased by 54.43% in the EP groups. The results of reducing sugar determination proved the secretion of polysaccharide-degrading enzymes. Scanning electron microscopy (SEM) showed that the EP groups had fewer spores and shrunken bacteria, indicating that EP could improve the growth environment and maintain bacterial integrity. Additionally, the ratios of periplasmic nitrate reductase (NAP), nitrite reductase (NIR), and dissimilatory nitrate reductase (D-NRase) in the EP groups were maximally increased by 107.22%, 84.70% and 36.10%, respectively. Transcriptome analysis further confirmed the above mentioned results. For example, the high expression of quorum sensing genes indicated that EP groups had higher bacterial density. Moreover, the high expression of antioxidant genes in the EP groups may be related to morphological integrity. Our study provides a basis for further discussion of the mechanism.
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Affiliation(s)
- Hui Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolin Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
| | - Lin Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
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Altshuler I, Raymond-Bouchard I, Magnuson E, Tremblay J, Greer CW, Whyte LG. Unique high Arctic methane metabolizing community revealed through in situ 13CH 4-DNA-SIP enrichment in concert with genome binning. Sci Rep 2022; 12:1160. [PMID: 35064149 PMCID: PMC8782848 DOI: 10.1038/s41598-021-04486-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada.
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences NMBU, Universitetstunet 3, 1430, Ås, Norway.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
- Energy, Mining and Environment Research Centre, National Research Council of Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, QC, H9X 3V9, Canada
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Response to substrate limitation by a marine sulfate-reducing bacterium. THE ISME JOURNAL 2022; 16:200-210. [PMID: 34285365 PMCID: PMC8692349 DOI: 10.1038/s41396-021-01061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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35
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Huang X, Tie W, Xie D, Jiang D, Li Z. Certain Environmental Conditions Maximize Ammonium Accumulation and Minimize Nitrogen Loss During Nitrate Reduction Process by Pseudomonas putida Y-9. Front Microbiol 2021; 12:764241. [PMID: 34966364 PMCID: PMC8710668 DOI: 10.3389/fmicb.2021.764241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/11/2021] [Indexed: 11/17/2022] Open
Abstract
Realizing the smallest nitrogen loss is a challenge in the nitrate reduction process. Dissimilatory nitrate reduction to ammonium (DNRA) and nitrate assimilation play crucial roles in nitrogen retention. In this study, the effects of the carbon source, C/N ratio, pH, and dissolved oxygen on the multiple nitrate reduction pathways conducted by Pseudomonas putida Y-9 are explored. Strain Y-9 efficiently removed nitrate (up to 89.79%) with glucose as the sole carbon source, and the nitrogen loss in this system was 15.43%. The total nitrogen decrease and ammonium accumulation at a C/N ratio of 9 were lower than that at 12 and higher than that at 15, respectively (P < 0.05). Besides, neutral and alkaline conditions (pH 7–9) favored nitrate reduction. Largest nitrate removal (81.78%) and minimum nitrogen loss (10.63%) were observed at pH 7. The nitrate removal and ammonium production efficiencies of strain Y-9 increased due to an increased shaking speed. The expression patterns of nirBD (the gene that controls nitrate assimilation and DNRA) in strain Y-9 were similar to ammonium patterns of the tested incubation conditions. In summary, the following conditions facilitated nitrate assimilation and DNRA by strain Y-9, while reducing the denitrification: glucose as the carbon source, a C/N ratio of 9, a pH of 7, and a shaking speed of 150 rpm. Under these conditions, nitrate removal was substantial, and nitrogen loss from the system was minimal.
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Affiliation(s)
- Xuejiao Huang
- Key Laboratory of (Guang Xi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China.,Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
| | - Wenzhou Tie
- Key Laboratory of (Guang Xi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
| | - Daihua Jiang
- Key Laboratory of (Guang Xi) Agricultural Environment and Products Safety, College of Agronomy, Guangxi University, Nanning, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing, China
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Wang P, Li J, Luo X, Ahmad M, Duan L, Yin L, Fang B, Li S, Yang Y, Jiang L, Li W. Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13949] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Jia‐Ling Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Xiao‐Qing Luo
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Li Duan
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Ling‐Zi Yin
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
| | - Shan‐Hui Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Lin Jiang
- School of Biological Sciences Georgia Institute of Technology Atlanta GA USA
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
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Yu Y, Liu L, Wang J, Zhang Y, Xiao C. Effects of warming on the bacterial community and its function in a temperate steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148409. [PMID: 34146803 DOI: 10.1016/j.scitotenv.2021.148409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
As a significant environmental issue, global warming will have a significant impact on soil microorganisms, especially soil bacteria. However, the effects of warming on the network structure of bacterial communities and the function of ecosystems remain unclear. Therefore, we examined the effects of three-year simulated field warming on the complexity of soil bacterial communities and predicted functions in a temperate steppe of Inner Mongolia. Warming significantly increased the α-diversity of bacteria in 2018 but did not affect it in 2019 and 2020. Warming increased network complexity and stability and keystone taxa, and these bacterial taxa also associated more closely with each other, indicating that the protection of interactions between bacterial taxa is very important for the conservation of biodiversity. Warming significantly increased aerobic chemoheterotrophy, ureolysis, and chemoheterotrophy, suggesting that warming increased the ability of bacteria to decompose organic matter and the emission of greenhouse gases, such as CO2 and CH4. Collectively, warming will alter soil bacterial community structure and its potential functions, further affecting key functions in grassland belowground ecosystems.
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Affiliation(s)
- Yang Yu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Lu Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jing Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yushu Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China.
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Hu Y, Hong Y, Ye J, Wu J, Wang Y, Ye F, Chang X, Long A. Shift of DNRA bacterial community composition in sediment cores of the Pearl River Estuary and the impact of environmental factors. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1689-1703. [PMID: 33411163 DOI: 10.1007/s10646-020-02321-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) process, competing with denitrification and anaerobic ammonia oxidation (anammox) for nitrate, is an important nitrogen retention pathway in the environment. Previous studies on DNRA bacterial diversity and composition focused on the surface sediments in estuaries, but studies on the deep sediments are limited, and the linkage between DNRA community structure and complex estuarine environment remains unclear. In this study, through high-throughput sequencing of nrfA gene followed by high-resolution sample inference, we examined spatially and temporally the composition and diversity of DNRA bacteria along a salinity gradient in five sediment cores of the Pearl River Estuary (PRE). We found a higher diversity and richness of DNRA bacteria in sediments with lower organic carbon, where sea water intersects fresh water. Moreover, the DNRA bacterial communities had the specific spatially distribution coupling with their metabolic difference along the salinity gradient of the Pearl River Estuary, but no obvious difference along the sediment depth. The distribution of DNRA bacteria in the PRE was largely driven by various environmental factors, including salinity, Oxidation-Reduction Potential (ORP), ammonium, nitrate and Corg/NO3-. Furthermore, dominant DNRA bacteria were found to be the key populations of DNRA communities in the PRE sediments by network analysis. Collectively, our results showed that niche difference of DNRA bacteria indeed occurs in the Pearl River Estuary.
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Affiliation(s)
- Yaohao Hu
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, PR China
- University of Chinese Academy of Sciences, 100049, Beijing, PR 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, 510006, Guangzhou, PR China.
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, PR 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, 510006, Guangzhou, PR China
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, PR 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, 510006, Guangzhou, PR China
| | - Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, PR China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, 510006, Guangzhou, PR China
| | - Xiangyang Chang
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, PR China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510301, Guangzhou, PR China.
- University of Chinese Academy of Sciences, 100049, Beijing, PR China.
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Huang X, Tie W, Xie D, Li Z. Low C/N Ratios Promote Dissimilatory Nitrite Reduction to Ammonium in Pseudomonas putida Y-9 under Aerobic Conditions. Microorganisms 2021; 9:microorganisms9071524. [PMID: 34361959 PMCID: PMC8305387 DOI: 10.3390/microorganisms9071524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
The biogeochemical consequences of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) have a significant influence on nitrogen (N) cycling in the ecosystem. Many researchers have explored these two pathways in soil and sediment ecosystems under anaerobic conditions. However, limited information is available regarding the influence of external environmental conditions on these two pathways in a well-defined experimental system under aerobic conditions. In this study, the impacts of the external environmental factors (carbon source, C/N ratio, pH, and dissolved oxygen) on nitrite reduction through the denitrification and DNRA routes in Pseudomonas putida Y-9 were studied. Results found that sodium citrate and sodium acetate favored denitrification and DNRA, respectively. Furthermore, neutral pH and aerobic conditions both facilitated DNRA and denitrification. Especially, low C/N ratios motivated the DNRA while high C/N ratios stimulated the denitrification, which was opposite to the observed phenomena under anaerobic conditions.
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Affiliation(s)
- Xuejiao Huang
- College of Agronomy, Guangxi University, Nanning 530004, China;
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China;
- Correspondence: (X.H.); (Z.L.); Tel.: +86-19978544987 (X.H.); +86-13883372713 (Z.L.)
| | - Wenzhou Tie
- College of Agronomy, Guangxi University, Nanning 530004, China;
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China;
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China;
- Correspondence: (X.H.); (Z.L.); Tel.: +86-19978544987 (X.H.); +86-13883372713 (Z.L.)
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Röthig T, Puntin G, Wong JCY, Burian A, McLeod W, Baker DM. Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish. MICROBIOME 2021; 9:127. [PMID: 34078452 PMCID: PMC8173792 DOI: 10.1186/s40168-021-01075-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/07/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana. METHODS Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae. RESULTS C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae. CONCLUSION Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.
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Affiliation(s)
- Till Röthig
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Giulia Puntin
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
- Department of Animal Ecology & Systematics, Justus Liebig University, Giessen, Germany
| | - Jane C. Y. Wong
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - Alfred Burian
- Marine Ecology Department, Lurio University, Nampula, Mozambique
- Department of Computational Landscape Ecology, UFZ– Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Wendy McLeod
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
| | - David M. Baker
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong, SAR of China
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Asamoto CK, Rempfert KR, Luu VH, Younkin AD, Kopf SH. Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5537-5546. [PMID: 33687201 DOI: 10.1021/acs.est.0c07816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (14N, 15N) and oxygen (16O, 18O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (18ε/15ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the 18ε/15ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of 18ε/15ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an 18ε/15ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in 18ε/15ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar 18ε/15ε signatures.
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Affiliation(s)
- Ciara K Asamoto
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Kaitlin R Rempfert
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Victoria H Luu
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Adam D Younkin
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
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Pang Y, Wang J, Li S, Ji G. Long-term sulfide input enhances chemoautotrophic denitrification rather than DNRA in freshwater lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116201. [PMID: 33321438 DOI: 10.1016/j.envpol.2020.116201] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Partitioning between nitrate reduction pathways, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) determines the fate of nitrate removal and thus it is of great ecological importance. Sulfide (S2-) is a potentially important factor that influences the role of denitrification and DNRA. However, information on the impact of microbial mechanisms for S2- on the partitioning of nitrate reduction pathways in freshwater environments is still lacking. This study investigated the effects of long-term (108 d) S2- addition on nitrate reduction pathways and microbial communities in the sediments of two different freshwater lakes. The results show that the increasing S2- addition enhanced the coupling of S2- oxidation with denitrification instead of DNRA. The sulfide-oxidizing denitrifier, Thiobacillus, was significantly enriched in the incubations of both lake samples with S2- addition, which indicates that it may be the key genus driving sulfide-oxidizing denitrification in the lake sediments. During S2- incubation of the Hongze Lake sample, which had lower inherent organic carbon (C) and sulfate (SO42-), Thiobacillus was more enriched and played a dominant role in the microbial community; while during that of the Nansi Lake sample, which had higher inherent organic C and SO42-, Thiobacillus was less enriched, but increasing abundances of sulfate reducing bacteria (Desulfomicrobium, Desulfatitalea and Geothermobacter) were observed. Moreover, sulfide-oxidizing denitrifiers and sulfate reducers were enriched in the Nansi Lake control treatment without external S2- input, which suggests that internal sulfate release may promote the cooperation between sulfide-oxidizing denitrifiers and sulfate reducers. This study highlights the importance of sulfide-driven denitrification and the close coupling between the N and S cycles in freshwater environments, which are factors that have often been overlooked.
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Affiliation(s)
- Yunmeng Pang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, PR China; Laboratory of Environmental Technology, INET, Tsinghua University, Beijing, 100084, PR China
| | - Jianlong Wang
- Laboratory of Environmental Technology, INET, Tsinghua University, Beijing, 100084, PR China
| | - Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, PR China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, PR China.
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Nie WB, Ding J, Xie GJ, Yang L, Peng L, Tan X, Liu BF, Xing DF, Yuan Z, Ren NQ. Anaerobic Oxidation of Methane Coupled with Dissimilatory Nitrate Reduction to Ammonium Fuels Anaerobic Ammonium Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1197-1208. [PMID: 33185425 DOI: 10.1021/acs.est.0c02664] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is critical for mitigating methane emission and returning reactive nitrogen to the atmosphere. The genomes of n-DAMO archaea show that they have the potential to couple anaerobic oxidation of methane to dissimilatory nitrate reduction to ammonium (DNRA). However, physiological details of DNRA for n-DAMO archaea were not reported yet. This work demonstrated n-DAMO archaea coupling the anaerobic oxidation of methane to DNRA, which fueled Anammox in a methane-fed membrane biofilm reactor with nitrate as only electron acceptor. Microelectrode analysis revealed that ammonium accumulated where nitrite built up in the biofilm. Ammonium production and significant upregulation of gene expression for DNRA were detected in suspended n-DAMO culture with nitrite exposure, indicating that nitrite triggered DNRA by n-DAMO archaea. 15N-labeling batch experiments revealed that n-DAMO archaea produced ammonium from nitrate rather than from external nitrite. Localized gradients of nitrite produced by n-DAMO archaea in biofilms induced ammonium production via the DNRA process, which promoted nitrite consumption by Anammox bacteria and in turn helped n-DAMO archaea resist stress from nitrite. As biofilms predominate in various ecosystems, anaerobic oxidation of methane coupled with DNRA could be an important link between the global carbon and nitrogen cycles that should be investigated in future research.
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Affiliation(s)
- Wen-Bo Nie
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Jie Ding
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Guo-Jun Xie
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Lu Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551, Singapore
| | - Lai Peng
- School of Resources and Environmental Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xin Tan
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Bing-Feng Liu
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - De-Feng Xing
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nan-Qi Ren
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang, Harbin 150090, Heilongjiang, China
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Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4. Appl Environ Microbiol 2021; 87:AEM.01964-20. [PMID: 33158888 DOI: 10.1128/aem.01964-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Under anoxic conditions, many bacteria, including Shewanella loihica strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in S. loihica PV-4 and several other denitrifying Shewanella species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of crp1 could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and N2O gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions.IMPORTANCE Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of N2O, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in S. loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N2O emission from nitrate-rich and carbon source-poor waters and soils.
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Nordström A, Hellman M, Hallin S, Herbert RB. Microbial controls on net production of nitrous oxide in a denitrifying woodchip bioreactor. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:228-240. [PMID: 33270921 DOI: 10.1002/jeq2.20181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
Denitrifying woodchip bioreactors are potential low-cost technologies for the removal of nitrate (NO3 - ) in water through denitrification. However, if environmental conditions do not support microbial communities performing complete denitrification, other N transformation processes will occur, resulting in the export of nitrite (NO2 - ), nitrous oxide (N2 O), or ammonium (NH4 + ). To identify the factors controlling the relative accumulation of NO2 - , N2 O, and/or NH4 + in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO3 - from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N2 O reduction, and dissimilatory NO3 - reduction to NH4 + were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly correlated with increases in porewater N2 O concentrations and indicated the preferential selection of incomplete denitrifying pathways ending with N2 O. Temperature and the total organic carbon/NO3 - ratio were strongly correlated with NH4 + concentrations and inversely correlated with the ratio between denitrification genes and the genes indicative of ammonification (Σnir/nrfA), suggesting an environmental control on NO3 - transformations. Overall, our results for a denitrifying woodchip bioreactor operated at hydraulic residence times of 1.0-2.6 d demonstrate the temporal development in the microbial community and indicate an increased potential for N2 O emissions with time from the denitrifying woodchip bioreactor.
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Affiliation(s)
- Albin Nordström
- Dep. of Earth Sciences, Uppsala Univ., Villavägen 16, Uppsala, SE-752 36, Sweden
| | - Maria Hellman
- Dep. of Forest Mycology and Plant, Pathology, Swedish Univ. of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Sara Hallin
- Dep. of Forest Mycology and Plant, Pathology, Swedish Univ. of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
| | - Roger B Herbert
- Dep. of Earth Sciences, Uppsala Univ., Villavägen 16, Uppsala, SE-752 36, Sweden
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Li Q, Bu C, Ahmad HA, Guimbaud C, Gao B, Qiao Z, Ding S, Ni SQ. The distribution of dissimilatory nitrate reduction to ammonium bacteria in multistage constructed wetland of Jining, Shandong, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4749-4761. [PMID: 32951167 DOI: 10.1007/s11356-020-10709-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA) is an important process of nitrate reduction in the environment. The distribution of DNRA bacteria and the relationships with environmental factors in multistage constructed wetland were investigated in this study. The quantitative real-time polymerase chain reaction analysis showed that the abundance of DNRA bacteria at all sites ranged from 2.10 × 1010 to 1.10 × 1011 copies/g of dry sediments. The Anaeromyxobacter (belong to Deltaproteobacteria) was the most abundant DNRA bacteria at all sites. The Geobater known as DNRA bacteria was also identified in this study. The abundances of DNRA bacteria, denitrifying bacteria, and anammox bacteria were conspicuously negatively correlated with Eh and positively correlated with the NO3--N removal efficency by statistical analysis.
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Affiliation(s)
- Qianxia Li
- State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, People's Republic of China
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, No. 72 Binhai Road, Qingdao, 266237, Shandong, People's Republic of China
| | - Cuina Bu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, No. 72 Binhai Road, Qingdao, 266237, Shandong, People's Republic of China
| | - Hafz Adeel Ahmad
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, No. 72 Binhai Road, Qingdao, 266237, Shandong, People's Republic of China
| | - Christophe Guimbaud
- Laboratoire de Physique et de Chimie de l'Environnement et de l'Espace (LPC2E), CNRS et Université d'Orléans (UMR 7328), 45071, Orléans Cedex 2, France
| | - Baoyu Gao
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, No. 72 Binhai Road, Qingdao, 266237, Shandong, People's Republic of China
| | - Zhuangming Qiao
- Shandong Meiquan Environmental Protection Technology Co., Ltd., Jinan, People's Republic of China
| | - Shaowu Ding
- Shandong Wanhao Fertilizer Co., Ltd., Jinan, People's Republic of China
| | - Shou-Qing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, No. 72 Binhai Road, Qingdao, 266237, Shandong, People's Republic of China.
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Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers. Appl Environ Microbiol 2020; 87:e0230120. [PMID: 33355098 DOI: 10.1128/aem.02301-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N2O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N2O production, with more pronounced responses observed for soils with lower copper content. The N2O emission-enhancing effect of the soil's native mbnA-expressing Methylocystaceae methanotrophs on the native denitrifiers was then experimentally verified with a Methylocystaceae-dominant chemostat culture prepared from a rice paddy microbial consortium as the inoculum. Lastly, with microcosms amended with varying cell numbers of methanobactin-producing Methylosinus trichosporium OB3b before CH4 enrichment, microbiomes with different ratios of methanobactin-producing Methylocystaceae to gammaproteobacterial methanotrophs incapable of methanobactin production were simulated. Significant enhancement of N2O production from denitrification was evident in both Methylocystaceae-dominant and Methylococcaceae-dominant enrichments, albeit to a greater extent in the former, signifying the comparative potency of methanobactin-mediated copper sequestration while implying the presence of alternative copper abstraction mechanisms for Methylococcaceae These observations support that copper-mediated methanotrophic enhancement of N2O production from denitrification is plausible where methanotrophs and denitrifiers cohabit.IMPORTANCE Proteobacterial methanotrophs, groups of microorganisms that utilize methane as source of energy and carbon, have been known to utilize unique mechanisms to scavenge copper, namely utilization of methanobactin, a polypeptide that binds copper with high affinity and specificity. Previously the possibility that copper sequestration by methanotrophs may lead to alteration of cuproenzyme-mediated reactions in denitrifiers and consequently increase emission of potent greenhouse gas N2O has been suggested in axenic and co-culture experiments. Here, a suite of experiments with rice paddy soil slurry cultures with complex microbial compositions were performed to corroborate that such copper-mediated interplay may actually take place in environments co-habited by diverse methanotrophs and denitrifiers. As spatial and temporal heterogeneity allow for spatial coexistence of methanotrophy (aerobic) and denitrification (anaerobic) in soils, the results from this study suggest that this previously unidentified mechanism of N2O production may account for significant proportion of N2O efflux from agricultural soils.
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Tatariw C, Mortazavi B, Ledford TC, Starr SF, Smyth E, Griffin Wood A, Simpson LT, Cherry JA. Nitrate reduction capacity is limited by belowground plant recovery in a 32‐year‐old created salt marsh. Restor Ecol 2020. [DOI: 10.1111/rec.13300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Corianne Tatariw
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Behzad Mortazavi
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
- Alabama Water Institute The University of Alabama Tuscaloosa AL 35487 U.S.A
- Center for Complex Hydrosystems Research The University of Alabama Tuscaloosa AL 35487 U.S.A
| | - Taylor C. Ledford
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Sommer F. Starr
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Erin Smyth
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Abigail Griffin Wood
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Loraé T. Simpson
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
| | - Julia A. Cherry
- Department of Biological Sciences The University of Alabama 1325 Science and Engineering Complex (SEC), 300 Hackberry Lane Tuscaloosa AL 35487 U.S.A
- New College, The University of Alabama 201 Lloyd Hall, 503 6th Avenue Tuscaloosa AL 35487 U.S.A
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Jia M, Winkler MKH, Volcke EIP. Elucidating the Competition between Heterotrophic Denitrification and DNRA Using the Resource-Ratio Theory. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13953-13962. [PMID: 33095565 DOI: 10.1021/acs.est.0c01776] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Heterotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes competing for two shared resources, namely, nitrate and organic carbon (COD). Their competition has great implications for nitrogen loss, conservation, and greenhouse gas emissions. Nevertheless, a comprehensive and mechanistic understanding of the governing factors for this competition is still lacking. We applied the resource-ratio theory to study this competition and validated the theory with experimental data from continuous cultures reported in the literature. Based on this theory, we revealed that influent COD/N ratio alone was not sufficient to predict the competition outcome as the boundary values for different competition outcomes changed substantially with influent resource concentrations. The stoichiometry of the two processes was determinative for the boundaries, whereas the affinity for the shared resources (KS), maximum specific growth rate (μmax) of the two species, and the dilution rate had significant impacts as well but mainly at low influent resource concentrations (e.g., <100 μM nitrate). The presented approach allows for a more comprehensive understanding of the parameters controlling microbial competition. The computational comparison between continuous and batch cultures could explain seemingly conflicting experimental results as to the impact of the COD/N ratio. The results also include testable hypotheses and tools for understanding and managing the fate of nitrate in ecosystems, which could also be applied more widely to other species competing for two shared resources.
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Affiliation(s)
- Mingsheng Jia
- BioCo Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195-2700, United States
| | - Eveline I P Volcke
- BioCo Research Group, Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
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50
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Kim DD, Park D, Yoon H, Yun T, Song MJ, Yoon S. Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses. WATER RESEARCH 2020; 185:116261. [PMID: 32791454 DOI: 10.1016/j.watres.2020.116261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/14/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Substantial N2O emission results from activated sludge nitrogen removal processes. N2O-reducing organisms possessing NosZ-type N2O reductases have been recognized to play crucial roles in suppressing emission of N2O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N2O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.
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Affiliation(s)
- Daehyun D Kim
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea
| | - Doyoung Park
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea
| | - Hyun Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea; Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Taeho Yun
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea
| | - Min Joon Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 350-701, Korea.
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