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Zhu H, Liu Y, Peng Z, Liu Q, Pan X, Yang B. Enhanced nitrogen removal by an isolated aerobic denitrifying strain in a vertical-flow constructed wetland. CHEMOSPHERE 2024; 359:142131. [PMID: 38697574 DOI: 10.1016/j.chemosphere.2024.142131] [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: 01/05/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
The addition of bacterial agents is an effective method for improving nitrogen removal from wetlands. Herein, an aerobic denitrifier, RC-15, was added to a vertical-flow constructed wetland (CW), and the presence of functional genes and microbial communities was investigated at different CW depths. For the RC-15-treated CW, the removal of NO3- and TN during the process was significantly greater than in the control. Quantitative PCR revealed that nirS is a dominant denitrifying gene for treating WWTP tailwater. Moreover, the presence of the RC-15 strain significantly enhanced the abundance of the napA gene and nirK gene in the CWs. The napA gene was concentrated in the upper layer of the CWs, and the nirK gene was concentrated in the middle and bottom layers. Compared to the control, the addition of the bacterial agent Trial resulted in a more diverse denitrification pathway, a greater abundance of 16Sr RNA, and a greater number of denitrifying strains. According to the microbial community analysis, Proteobacteria and Chloroflexi dominated denitrification in the CWs. Greater abundances of Thauera, Aeromonas and Ardenticatenales were found at the genus level, indicating that these genera have potential applications in future nitrogen removal projects.
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Affiliation(s)
- Hongxu Zhu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; Kunming Metallurgical Research Institute Co., Ltd., Kunming, 650031, China
| | - Yanmei Liu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China; College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Zhenghua Peng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Qiuyun Liu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Benqin Yang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650500, China
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2
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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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3
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Zhao C, Li W, Shang D, Ma Q, Liu L, Xu J, Meng J, Zhang T, Wang Q, Wang X, Zhang J, Kong Q. Influence of nitrogen sources on wastewater treatment performance by filamentous algae in constructed wetland system. ENVIRONMENTAL RESEARCH 2023; 235:116638. [PMID: 37442256 DOI: 10.1016/j.envres.2023.116638] [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: 05/01/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Although filamentous algae have the characteristics of high nutrient assimilation ability, and adaptation to different conditions, studies on their role in water purification of constructed wetlands (CWs) are limited. In this study, the wastewater treatment capacity under different nitrogen sources was explored by constructing a filamentous algal CW (FACW) system. Results confirmed the fast and stable operation efficiency of the FACW system. Ammonia nitrogen was preferred in Cladophora sp. absorption and assimilation. The nutrient consumption rate (NCR) for total nitrogen (TN) of AG was 2.65 mg g-1 d-1, much higher than that of nitrate nitrogen (NG) (0.89 mg g-1 d-1). The symbiosis of bacteria and Cladophora sp. Contributed to pollutant removal. A stable and diverse community of microorganisms was found on Cladophora sp. Surface, which revealed different phylogenetic relationships and functional bacterial proportions with those attached on sediment surface. In addition, temperature and light intensity have great influence on the purification ability of plants, and low hydraulic retention time is beneficial to the cost-effective operation of the system. This study provides a method to expand the utilization of wetland plants and apply large filamentous algae to the purification of wetland water quality.
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Affiliation(s)
- Congcong Zhao
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China; Dongying Institute, Shandong Normal University, Dongying 257092, Shandong, PR China
| | - Wenying Li
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Dawei Shang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Qilong Ma
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Luxing Liu
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Jingtao Xu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, PR China
| | - Jiashuo Meng
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Tao Zhang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Qian Wang
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China
| | - Xiaofei Wang
- Shandong Academy of Environmental Sciences CO., LTD, No. 50, Lishan Road, Lixia District, Jinan City, Shandong Province, PR China
| | - Jian Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, PR China
| | - Qiang Kong
- College of Geography and Environment, Shandong Normal University, Jinan, 250014, PR China; Dongying Institute, Shandong Normal University, Dongying 257092, Shandong, PR China.
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4
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Wei T, Wang Z, Yang Y, Xiang W, Liu Y, Wu B, Cui X, Guo B, Zhou Y. Microbial niches and dynamics of antibiotic resistance genes in a bio-enhanced granular-activated carbon biofilm treating greywater. CHEMOSPHERE 2023; 331:138774. [PMID: 37100251 DOI: 10.1016/j.chemosphere.2023.138774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/30/2023] [Accepted: 04/22/2023] [Indexed: 05/03/2023]
Abstract
Accumulation and transmission of antibiotic resistance genes (ARGs) in greywater treatment systems present risks for its reuse. In this study, a gravity flow self-supplying oxygen (O2) bio-enhanced granular activated carbon dynamic biofilm reactor (BhGAC-DBfR) was developed to treat greywater. Maximum removal efficiencies were achieved at saturated/unsaturated ratios (RSt/Ust) of 1:1.1 for chemical oxygen demand (97.6 ± 1.5%), linear alkylbenzene sulfonates (LAS) (99.2 ± 0.5%), NH4+-N (99.3 ± 0.7%) and total nitrogen (85.3 ± 3.2%). Microbial communities were significantly different at various RSt/Ust and reactor positions (P < 0.05). The unsaturated zone with low RSt/Ust showed more abundant microorganisms than the saturated zone with high RSt/Ust. The reactor-top community was predominant by aerobic nitrification (Nitrospira) and LAS biodegradation (Pseudomonas, Rhodobacter and Hydrogenophaga) related genera; but reactor-bottom community was predominant by anaerobic denitrification and organics removal related genera (Dechloromonas and Desulfovibrio). Most of the ARGs (e.g., intI-1, sul1, sul2 and korB) were accumulated in the biofilm, which were closely associated with microbial communities at reactor top and stratification. The saturated zone can achieve over 80% removal of the tested ARGs at all operation Phases. Results suggested that BhGAC-DBfR can provide assistance in blocking the environment dissemination of ARGs during greywater treatment.
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Affiliation(s)
- Ting Wei
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziqi Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Yang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wanchen Xiang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Beibei Wu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaocai Cui
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Guo
- Department of Civil and Environmental Engineering, University of Surrey, Surrey, GU2 7XH, United Kingdom.
| | - Yun Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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5
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Bai Y, Wang S, Zhussupbekova A, Shvets IV, Lee PH, Zhan X. High-rate iron sulfide and sulfur-coupled autotrophic denitrification system: Nutrients removal performance and microbial characterization. WATER RESEARCH 2023; 231:119619. [PMID: 36689879 DOI: 10.1016/j.watres.2023.119619] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/06/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Iron sulfides-based autotrophic denitrification (IAD) is a promising technology for nitrate and phosphate removal from low C:N ratio wastewater due to its cost-effectiveness and low sludge production. However, the slow kinetics of IAD, compared to other sulfur-based autotrophic denitrification (SAD) processes, limits its engineering application. This study constructed a co-electron-donor (FeS and S0 with a volume ratio of 2:1) iron sulfur autotrophic denitrification (ISAD) biofilter and operated at as short as 1 hr hydraulic retention time (HRT). Long-term operation results showed that the superior total nitrogen and phosphate removals of the ISAD biofilter were 90-100% at 1-12 h HRT, with the highest denitrification rate up to 960 mg/L/d. Considering low sulfate production, HRT of 3 h could be the optimal condition. Such superior performance in the ISAD biofilter was achieved due to the interactions between FeS and S0, which accelerated the denitrification process and maintained the acidity-alkalinity balance. Metagenomic analysis found that the enriched nitrate-dependent iron-oxidizing (NDFO) bacteria (Acinetobacter and Acidovorax), sulfur-oxidizing bacteria (SOB), and dissimilatory nitrate reduction to ammonia (DNRA) bacteria likely supported stable nitrate reduction. The metabolic pathway analysis showed that completely denitrification and DNRA, coupled with sulfur oxidation, disproportionation, iron oxidation and phosphate precipitation with FeS and S0 as co-electron donors, were responsible for the high-rate nitrate and phosphate removal. This study provides the potential of ISAD as a highly efficient post-denitrification technology and sheds light on the balanced microbial S-N-Fe transformation.
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Affiliation(s)
- Yang Bai
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Shun Wang
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | | | - Igor V Shvets
- CRANN, School of Physics, Trinity College Dublin, Dublin 2, Ireland
| | - Po-Heng Lee
- Imperial College London, London SW7 2AZ, United Kingdom
| | - Xinmin Zhan
- Civil Engineering, School of Engineering, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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6
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Yuan X, Cui K, Chen Y, Xu W, Li P, He Y. Response of microbial community and biological nitrogen removal to the accumulation of nonylphenol in sequencing batch reactor. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2023; 20:1-12. [PMID: 36817166 PMCID: PMC9923645 DOI: 10.1007/s13762-023-04825-9] [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: 03/30/2022] [Revised: 08/23/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
The widespread existence of nonylphenol in the environmental rendered from wastewater discharge has become a growing concern for its endocrine disrupting effects on microorganisms. In this study, the performance of nitrifying and denitrifying microbial community in a sequencing batch reactor (SBR) was investigated under different nonylphenol concentrations. The SBR was shown to be less effective in nitrogen removal at higher concentration of nonylphenol. Proteobacteria, Bacteroidetes, and Actinobacteria were characterized by 454 pyrosequencing as the dominant bacteria, nitrogen removal functional bacteria in these three phyla were inhibited by nonylphenol, and Proteobacteria and Actinobacteria were more sensitive to nonylphenol. With the accumulation of nonylphenol, the population of the most abundant denitrifying bacteria (Thauera spp.) and nitrifying bacteria (Nitrosomonas spp.) significantly reduced. Microbial diversity increased due to nonylphenol perturbation, which is indicated by the changes in microbial alpha diversity. Principal component analysis showed high similarity between microbial community in low and high concentration of nonylphenol, and the core genera involved in nitrogen removal had a low correlation with other genera shown in co-occurrence network. Moreover, linear discriminant analysis effect size analysis revealed intergroup differences in microorganisms. The mechanism of accumulated NP on the diversity and metabolism of the microbial community was examined. This paper established a theoretical foundation for the treatment of NP-containing wastewater and provided hints for further research about NP impact on biological nitrogen removal. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s13762-023-04825-9.
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Affiliation(s)
- X. Yuan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 246011 China
| | - K. Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 246011 China
| | - Y. Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, 246011 China
| | - W. Xu
- Zhejiang Lab, Hangzhou, 310012 China
| | - P. Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Y. He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
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7
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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Liu Y, Xu F, Ding L, Zhang G, Bai B, Han Y, Xiao L, Song Y, Li Y, Wan S, Li G. Microplastics reduce nitrogen uptake in peanut plants by damaging root cells and impairing soil nitrogen cycling. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130384. [PMID: 36444071 DOI: 10.1016/j.jhazmat.2022.130384] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Microplastic (MP) pollution severely impairs the sustainable development of modern agriculture. However, the mechanisms underlying the effects of MP contaminants on nutrient cycles in agroecosystems are poorly understood. In this study, we examined the impacts of two types of MPs, polypropylene (PP) and rubber crumb (RC), on nitrogen (N) transformation and N cycling in soil-peanut system. High concentrations of PP (1% w/w) and RC (1% w/w) inhibited vegetative growth and N uptake in peanut plants by damaging root cells and disturbing soil N cycling. These MPs damaged the plasma membranes of root cells and caused oxidative stress, as evidenced by the decreased number of xylem vessels, which in turn inhibited N uptake by roots. Integrated metagenomic and metabolomic analyses revealed that the differential soil metabolite levels in response to MP treatment affected the microbial community structure in the rhizosphere and the expression of key N cycling-related genes, resulting in altered N transformation and the decreased availability of N in rhizosphere soil. These findings provide the first evidence of the effects of MPs on N uptake in peanut plants and shed light on the importance of rational management of MPs for crop growth and yield in agroecosystems.
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Affiliation(s)
- Yiyang Liu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fangji Xu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liping Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guanchu Zhang
- Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao 266100, China
| | - Bo Bai
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yan Han
- Shandong Academy of Grape, Jinan 250199, China
| | - Lina Xiao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yan Song
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shubo Wan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
| | - Guowei Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
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Nie Y, Lau SYL, Tan X, Lu X, Liu S, Tahvanainen T, Isoda R, Ye Q, Hashidoko Y. Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions. FRONTIERS IN PLANT SCIENCE 2022; 13:974251. [PMID: 36160957 PMCID: PMC9490422 DOI: 10.3389/fpls.2022.974251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.
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Affiliation(s)
- Yanxia Nie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sharon Yu Ling Lau
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Sarawak Tropical Peat Research Institute, Kota Samarahan, Malaysia
| | - Xiangping Tan
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiankai Lu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Suping Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Teemu Tahvanainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Reika Isoda
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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10
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions. NITROGEN 2022. [DOI: 10.3390/nitrogen3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.
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Zhou Y, Anwar MN, Guo B, Huang W, Liu Y. Response of antibiotic resistance genes and microbial niches to dissolved oxygen in an oxygen-based membrane biofilm reactor during greywater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155062. [PMID: 35395308 DOI: 10.1016/j.scitotenv.2022.155062] [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: 03/09/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Linear alkylbenzene sulfonates (LAS) in greywater (GW) will simulate antibiotic resistance genes (ARGs) production in the biofilm-based system. Our study emphasizes the dissolved oxygen (DO)-dependent ARGs accumulation and microbial niches succession in an oxygen-based membrane biofilm reactor (O2-MBfR) treating GW, as well as revealing the key roles of EPS. Changing DO concentrations led to significant differences in ARGs production, EPS secretion and microbial communities, as well as the organics and nitrogen removal efficiency. Increasing DO concentration from 0.2 to 0.4 mg/L led to improved organics (> 90%) and nitrogen removal, as well as less EPS (especially for proteins and carbohydrates) and ARGs accumulation (e.g., intI-1, korB and sul-2) in the biofilm; the high-DO-concentration accumulated microbial niches, including Flavobacteriaceae and Cyanobacteria that revealed by LEfSe analysis, contributed to both nitrogen reduction and organics biodegradation. While, the inefficient electron acceptor at low DO conditions (0.2 mg/L) reduced the organics and nitrogen removal efficiency, as well as the improved accumulation of EPS in biofilm; high EPS enabled the capture of residual LAS from the liquid phase, which stimulated the production of ARGs by the distinct microbial community compositions. These findings suggested the DO-based ARGs reduction regulation strategy in the O2-MBfR treating GW.
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Affiliation(s)
- Yun Zhou
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta T6G 1H9, Canada
| | - Mian Nabeel Anwar
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta T6G 1H9, Canada
| | - Bing Guo
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta T6G 1H9, Canada; Centre for Environmental Health and Engineering (CEHE), Department of Civil and Environmental Engineering, University of Surrey, Surrey GU2 7XH, United Kingdom.
| | - Wendy Huang
- Department of Civil Engineering, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Yang Liu
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta T6G 1H9, Canada.
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Song L, Zang S, Lin L, Lu B, Sun C, Jiao Y, Wang H. Responses of nitrous oxide fluxes to autumn freeze-thaw cycles in permafrost peatlands of the Da Xing'an Mountains, Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:31700-31712. [PMID: 35013975 DOI: 10.1007/s11356-022-18545-z] [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: 07/13/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Climate warming has intensified changes of permafrost freeze-thaw process and postponed the starting period of soil freezing, which significantly affected the processes of N2O production and emission from the soils. However, responses of soil N2O fluxes to freeze-thaw cycles (FTCS) during autumn freezing period in permafrost peatlands in field remain unclear. Therefore, the static chamber-GC techniques were used to explore the effects of autumn FTCS on N2O fluxes in the three permafrost peatlands [Calamagrostis angustifolia peatland (CA), Larix gmelini-Sphagnum swamp (LS), and Eriophorum vaginatum peatland (EV)] in Da Xing'an Mountains, Northeast China, from September to November 2019. The response peaks of N2O fluxes to autumn FTCS in CA (29.22 ± 14.90 μg m-2 h-1) and EV (19.70 ± 7.26 μg m-2 h-1) occurred in the autumn FTCS prophase, whereas LS (11.33 ± 0.90 μg m-2 h-1) appeared in the autumn FTCS metaphase. CA (394.90 μg m-2) and EV (497.82 μg m-2) acted as a N2O source, and LS (- 1321.43 μg m-2) was a N2O sink. The effects of autumn FTCS on N2O fluxes were significantly different (p < 0.001) in the three permafrost peatlands. N2O emissions during autumn FTCS were mainly driven by soil NH4+-N0-50 cm, DOC30-40 cm and 40-50 cm content and soil NO3--N0-50 cm content. The results implied that autumn FTCS could stimulate soil N2O emissions in permafrost peatlands and confirmed the important contribution of N2O emissions during autumn FTCS to annual nitrogen budget. This study could improve the accuracy of regional estimates of annual nitrogen budget.
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Affiliation(s)
- Liquan Song
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Shuying Zang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China.
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China.
| | - Lin Lin
- College of Foreign Languages, Jiamusi University, Jiamusi, 154007, China
| | - Boquan Lu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Chaofeng Sun
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Yaqing Jiao
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Hanxi Wang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China.
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China.
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun, 130117, China.
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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Biswal BK, Vijayaraghavan K, Tsen-Tieng DL, Balasubramanian R. Biochar-based bioretention systems for removal of chemical and microbial pollutants from stormwater: A critical review. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126886. [PMID: 34419842 DOI: 10.1016/j.jhazmat.2021.126886] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 05/14/2023]
Abstract
Biochar has been increasingly used as a filter medium in engineered low impact development systems (e.g., bioretention systems) for decontamination of urban stormwater and management of hydrology. This review paper critically analyzes the performance of biochar-based biofiltration systems for removal of chemical and microbial pollutants present in urban runoff. Biochar-amended biofiltration systems efficiently remove diverse pollutants such as total nitrogen (32 - 61%), total phosphorus: (45 - 94%), heavy metals (27 - 100%), organics (54 - 100%) and microbial pollutants (log10 removal: 0.78 - 4.23) from urban runoff. The variation of biofiltration performance is due to changes in biochar characteristics, the abundance of dissolved organic matter and/or stormwater chemistry. The dominant mechanisms responsible for removal of chemical pollutants are sorption, ion exchange and/or biotransformation, whereas filtration/straining is the major mechanism for bacteria removal. The pseudo-second order and Langmuir isotherm are the best models that describe the kinetics and chemical equilibrium of pollutants, respectively. This critical review provides the fundamental scientific knowledge for designing highly efficient biochar-based bioretention systems for removal of diverse pollutants from urban stormwater. The key knowledge gaps that should be addressed in future research include long-term field-scale bioretention study, development of novel methods for filter media regeneration/reuse, and dynamics of filter media microbial communities.
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Affiliation(s)
- Basanta Kumar Biswal
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Kuppusamy Vijayaraghavan
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Daryl Lee Tsen-Tieng
- Centre for Urban Greenery and Ecology, National Parks Board, 1 Cluny Road, 259563, Singapore
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15
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Takatsu Y, Miyamoto T, Tahvanainen T, Hashidoko Y. Nitrous Oxide Emission in Response to pH from Degrading Palsa Mire Peat Due to Permafrost Thawing. Curr Microbiol 2022; 79:56. [PMID: 34982223 DOI: 10.1007/s00284-021-02690-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
N2O, a greenhouse gas, is increasingly emitted from degrading permafrost mounds of palsa mires because of the global warming effects on microbial activity. In the present study, we hypothesized that N2O emission could be affected by a change in pH conditions because the collapse of acidic palsa mounds (pH 3.4-4.6) may result in contact with minerogenic ground water (pH 4.8-6.3), thereby increasing the pH. We compared the effects of pH change on N2O emission from cultures inoculated with peat suspensions. Peat samples were collected on a transect from a still intact high part to the collapsing edge of a degrading palsa mound in northwestern Finland, assuming the microbial communities could be different. We adjusted the pH of peat suspensions prepared from a collapsing palsa mound and compared the N2O emission in a pH gradient from 4.5 to 8.5. The collapsing edge had the highest N2O emission from the peat suspensions among all points on the transect under natural acidic conditions (pH 4.5). The N2O emission was reduced with a moderate rise in pH (pH 5.0-6.0) by approximately 85% compared with natural acidic level (pH 4.5). The bacterial communities in acidic cultures differed considerably from those in alkaline cultures. When pH was adjusted to alkaline conditions, N2O-emitting bacteria different from those present in acidic conditions appeared to emit N2O. The bacterial communities could be characterized by changing pH conditions after thawing and collapse of permafrost have contrasting impacts on N2O production that calls for further attention in future studies.
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Affiliation(s)
- Yuta Takatsu
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toshizumi Miyamoto
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan.
| | - Teemu Tahvanainen
- Department of Biology, University of Eastern Finland, Joensuu, Finland
| | - Yasuyuki Hashidoko
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Biswal BK, Vijayaraghavan K, Adam MG, Lee Tsen-Tieng D, Davis AP, Balasubramanian R. Biological nitrogen removal from stormwater in bioretention cells: a critical review. Crit Rev Biotechnol 2021; 42:713-735. [PMID: 34486441 DOI: 10.1080/07388551.2021.1969888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Excess nitrogen in stormwater degrades surface water quality via eutrophication and related processes. Bioretention has been recognized as a highly effective low-impact development (LID) technology for the management of high runoff volumes and reduction of nitrogen (N) pollutants through various mechanisms. This paper provides a comprehensive and critical review of recent developments on the biological N removal processes occurring in bioretention systems. The key plant- and microbe-mediated N transformation processes include assimilation (N uptake by plants and microbes), nitrification, denitrification, and anammox (anaerobic ammonia oxidation), but denitrification is the major pathway of permanent N removal. Overall, both laboratory- and field-scale bioretention systems have demonstrated promising N removal performance (TN: >70%). The phyla Bacteroidetes and Proteobacteria are the most abundant microbial communities found to be enriched in biofilter media. Furthermore, the denitrifying communities contain several functional genes (e.g., nirK/nirS, and nosZ), and their concentrations increase near the surface of media depth. The N removal effectiveness of bioretention systems is largely impacted by the hydraulics and environmental factors. When a bioretention system operates at: low hydraulic/N loading rate, containing a saturation zone, vegetated with native plants, having deeper and multilayer biofilter media with warm climate temperature and wet storm events periods, the N removal efficiency can be high. This review highlights shortcomings and current knowledge gaps in the area of total nitrogen removal using bioretention systems, as well as identifies future research directions on this topic.
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Affiliation(s)
- Basanta Kumar Biswal
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Kuppusamy Vijayaraghavan
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Max Gerrit Adam
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Daryl Lee Tsen-Tieng
- Centre for Urban Greenery and Ecology, National Parks Board, Singapore, Singapore
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Rajasekhar Balasubramanian
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures. BIOLOGY 2021; 10:biology10070569. [PMID: 34206701 PMCID: PMC8301126 DOI: 10.3390/biology10070569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. Abstract This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
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Hetz SA, Horn MA. Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra. Front Microbiol 2021; 12:628269. [PMID: 33613495 PMCID: PMC7892595 DOI: 10.3389/fmicb.2021.628269] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/18/2021] [Indexed: 01/23/2023] Open
Abstract
Cryoturbated peat circles (pH 4) in the Eastern European Tundra harbor up to 2 mM pore water nitrate and emit the greenhouse gas N2O like heavily fertilized agricultural soils in temperate regions. The main process yielding N2O under oxygen limited conditions is denitrification, which is the sequential reduction of nitrate/nitrite to N2O and/or N2. N2O reduction to N2 is impaired by pH < 6 in classical model denitrifiers and many environments. Key microbes of peat circles are important but largely unknown catalysts for C- and N-cycling associated N2O fluxes. Thus, we hypothesized that the peat circle community includes hitherto unknown taxa and is essentially unable to efficiently perform complete denitrification, i.e., reduce N2O, due to a low in situ pH. 16S rRNA analysis indicated a diverse active community primarily composed of the bacterial class-level taxa Alphaproteobacteria, Acidimicrobiia, Acidobacteria, Verrucomicrobiae, and Bacteroidia, as well as archaeal Nitrososphaeria. Euryarchaeota were not detected. 13C2- and 12C2-acetate supplemented anoxic microcosms with endogenous nitrate and acetylene at an in situ near pH of 4 were used to assess acetate dependent carbon flow, denitrification and N2O production. Initial nitrate and acetate were consumed within 6 and 11 days, respectively, and primarily converted to CO2 and N2, suggesting complete acetate fueled denitrification at acidic pH. Stable isotope probing coupled to 16S rRNA analysis via Illumina MiSeq amplicon sequencing identified acetate consuming key players of the family Burkholderiaceae during complete denitrification correlating with Rhodanobacter spp. The archaeal community consisted primarily of ammonia-oxidizing Archaea of Nitrososphaeraceae, and was stable during the incubation. The collective data indicate that peat circles (i) host acid-tolerant denitrifiers capable of complete denitrification at pH 4-5.5, (ii) other parameters like carbon availability rather than pH are possible reasons for high N2O emissions in situ, and (iii) Burkholderiaceae are responsive key acetate assimilators co-occurring with Rhodanobacter sp. during denitrification, suggesting both organisms being associated with acid-tolerant denitrification in peat circles.
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Affiliation(s)
- Stefanie A Hetz
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University Hannover, Hannover, Germany
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Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining. Appl Environ Microbiol 2021; 87:AEM.02355-20. [PMID: 33355115 PMCID: PMC8090869 DOI: 10.1128/aem.02355-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using 13C-CH4 to a co-occurrence network analysis derived from the 13C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.
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Wang J, Cui W, Che Z, Liang F, Wen Y, Zhan M, Dong X, Jin W, Dong Z, Song H. Effects of synthetic nitrogen fertilizer and manure on fungal and bacterial contributions to N 2O production along a soil acidity gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:142011. [PMID: 32890881 DOI: 10.1016/j.scitotenv.2020.142011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Reactive nitrogen (Nr) input often induces soil acidification, which may in turn affect bacterial and fungal nitrogen (N) transformations in soil and nitrous oxide (N2O) emissions. However, the interactive effects of soil acidity and Nr on the contributions of bacteria and fungi to N2O emissions remain unclear. We conducted a field experiment to assess the effects of anthropogenic Nr forms (i.e., synthetic N fertilizer and manure) on bacterial and fungal N2O emissions along a soil acidity gradient (soil pH = 6.8, 6.1, 5.2, and 4.2). The abundances and structure of bacterial and fungal communities were analyzed by real-time polymerase chain reaction and high-throughput sequencing techniques, respectively. Soil acidification reduced bacterial but increased fungal contributions to N2O production, corresponding respectively to changes in bacterial and fungal abundance. It also altered bacterial and fungal community structures and soil chemical properties, such as dissolved organic carbon and ammonia concentrations. Structural equation modeling (SEM) analyses showed that the soil properties and fungal community were the most important factors determining bacterial and fungal contributions to N2O emissions, respectively. The fertilizer form markedly affected N2O emissions from bacteria but not from fungi. Compared with synthetic N fertilizer, manure significantly lowered the bacterial contribution to N2O emissions in the soils with pH of 5.2 and 4.2. The manure application significantly increased soil pH but reduced nitrate concentration. The fertilizer form did not significantly alter the bacterial and fungal community structures. The SEM revealed that the fertilizer form affected the bacterial contribution to N2O production by changing the soil chemical properties. Together, these results indicated that soil acidification enhanced fungal dominance for N2O emission, and manure application has limited effects on fungal N2O emission, highlighting the challenges for mitigation of soil N2O emissions under future acid deposition and N enrichment scenarios.
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Affiliation(s)
- Jun Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenli Cui
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhao Che
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fei Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yongkang Wen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Meimei Zhan
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Xiao Dong
- School of Engineering, Anhui Agricultural University, Hefei 230036, China
| | - Wenjun Jin
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Zhaorong Dong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - He Song
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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Yu J, Pavia MJ, Deem LM, Crow SE, Deenik JL, Penton CR. DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil. Front Microbiol 2020; 11:587972. [PMID: 33329461 PMCID: PMC7717982 DOI: 10.3389/fmicb.2020.587972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/08/2020] [Indexed: 12/03/2022] Open
Abstract
The functions and interactions of individual microbial populations and their genes in agricultural soils amended with biochar remain elusive but are crucial for a deeper understanding of nutrient cycling and carbon (C) sequestration. In this study, we coupled DNA stable isotope probing (SIP) with shotgun metagenomics in order to target the active community in microcosms which contained soil collected from biochar-amended and control plots under napiergrass cultivation. Our analyses revealed that the active community was composed of high-abundant and low-abundant populations, including Actinobacteria, Proteobacteria, Gemmatimonadetes, and Acidobacteria. Although biochar did not significantly shift the active taxonomic and functional communities, we found that the narG (nitrate reductase) gene was significantly more abundant in the control metagenomes. Interestingly, putative denitrifier genomes generally encoded one gene or a partial denitrification pathway, suggesting denitrification is typically carried out by an assembly of different populations within this Oxisol soil. Altogether, these findings indicate that the impact of biochar on the active soil microbial community are transient in nature. As such, the addition of biochar to soils appears to be a promising strategy for the long-term C sequestration in agricultural soils, does not impart lasting effects on the microbial functional community, and thus mitigates un-intended microbial community shifts that may lead to fertilizer loss through increased N cycling.
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Affiliation(s)
- Julian Yu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,Swette Center for Environmental Biotechnology, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Lauren M Deem
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Susan E Crow
- Natural Resources and Environmental Management, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Jonathan L Deenik
- Tropical Plant and Soil Sciences, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Christopher Ryan Penton
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States.,College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
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22
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Zhou Y, Guo B, Li R, Zhang L, Xia S, Liu Y. Treatment of grey water (GW) with high linear alkylbenzene sulfonates (LAS) content and carbon/nitrogen (C/N) ratio in an oxygen-based membrane biofilm reactor (O 2-MBfR). CHEMOSPHERE 2020; 258:127363. [PMID: 32554017 DOI: 10.1016/j.chemosphere.2020.127363] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/24/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
Grey water (GW) containing high levels of linear alkylbenzene sulfonates (LAS) can be a threat to the human health and organisms in the environment if not treated properly. Although aerobic treatment may achieve high GW treatment efficacy, conventional aeration can lead to serious foaming. Here, we firstly and systematically evaluated an oxygen-based membrane biofilm reactor (O2-MBfR) for its capacity to simultaneous remove organics and nitrogen from greywater with high LAS levels and carbon/nitrogen (C/N) ratios. After a five-day startup period, multifarious microorganisms formed multifunctional biofilms and the MBfR achieved high removal rates of chemical oxygen demand (COD), LAS, and total nitrogen (TN) of 88.4%, 95.6%, and 80%, respectively, with a hydraulic retention time of 7.86 h. Higher organics loading (5.53 g TCOD/m2-day) caused cell lysis and damaged the O2-MBfR system, leading to a discernible and continuous decline of the reactor performance. The O2-MBfR design completely eliminated foaming formation. LAS -biodegrading-rich genus containing Clostridium, Parvibaculum, Dechloromonas, Desulfovibrio, Mycobacterium, Pseudomonas, and Zoogloea enable the nearly complete removal of LAS even under high C/N conditions. Results demonstrated that the O2-MBfR technology is feasible for treating GW containing high LAS and C/N ratio, while remaining free of foaming formation, and at a low cost due to high O2 utilization rates.
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Affiliation(s)
- Yun Zhou
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Bing Guo
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Ran Li
- College of Petroleum Engineering, Xi'an Shiyou University, Xi'an, 710065, Shaanxi Province, China
| | - Lei Zhang
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Yang Liu
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada.
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23
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Cox AH, Wigginton SK, Amador JA. Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:140362. [PMID: 32758972 DOI: 10.1016/j.scitotenv.2020.140362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.
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Affiliation(s)
- Alissa H Cox
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - Sara K Wigginton
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - José A Amador
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
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24
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Li H, Barber M, Lu J, Goel R. Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake. WATER RESEARCH 2020; 185:116292. [PMID: 33086464 PMCID: PMC7737503 DOI: 10.1016/j.watres.2020.116292] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 05/06/2023]
Abstract
The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06-1.32 µg/L) and MC-RR (0.01-0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2-3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.
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Affiliation(s)
- Hanyan Li
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA
| | - Mike Barber
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA
| | - Ramesh Goel
- Civil & Environmental Engineering, University of Utah, 110 S. Central Campus Drive, 2000 MCE, Salt Lake City, UT 84121, USA.
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25
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Zou Y, Ning D, Huang Y, Liang Y, Wang H, Duan L, Yuan T, He Z, Yang Y, Xue K, Van Nostrand JD, Zhou J. Functional structures of soil microbial community relate to contrasting N 2O emission patterns from a highly acidified forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138504. [PMID: 32302850 DOI: 10.1016/j.scitotenv.2020.138504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 05/23/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas contributing to global climate change. Emissions of N2O from acidic forests are increasing rapidly; however, little is known about the mechanisms driving these emissions. We analyzed soil samples from a high N2O emission area (HEA, 224-601 μg N m-2 h-1) and an adjacent low emission area (LEA, 20-30 μg N m-2 h-1) of a highly acidified forest. HEA showed similar carbon and nitrogen (N) pools and microbial biomass to LEA, but significantly higher moisture and extractable nutrients than LEA did. GeoChip 4 detected 298 gene families (unadjusted P < 0.05; 94, adjusted P < 0.05) showing significantly different structures between HEA and LEA. Both areas had highly diverse N cycling functional genes. However, HEA had higher relative abundances of nor, P450nor, and archaeal nitrifier nirK, which provided evidence for the importance of denitrifiers in N2O emission. HEA also showed significantly higher relative abundances of lignin- and cellulose-degrading genes, oxygen-limitation-response genes and denitrifier ppk, but lower abundances of N- and phosphorus (P) -limitation-response genes especially denitrifier pstS, corresponding to the higher moisture and extractable nutrients conducive to denitrification. The moisture, extractable nutrients and pH explained over 50% variation in microbial communities, and extractable P appeared as the key factor driving community variation and consequently regulated N2O production. CAPSULE ABSTRACT: N2O emission in highly acidified forest soils was related to the diverse N functional genes, especially denitrification genes, and was affected by soil properties.
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Affiliation(s)
- Yina Zou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yuting Liang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
| | - Lei Duan
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA; Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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26
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Zhou Z, Chen J, Gu W, Gu JD. Biogeographic pattern of the nirS gene-targeted anammox bacterial community and composition in the northern South China Sea and a coastal Mai Po mangrove wetland. Appl Microbiol Biotechnol 2020; 104:3167-3181. [PMID: 32036435 DOI: 10.1007/s00253-020-10415-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/19/2020] [Accepted: 01/24/2020] [Indexed: 11/29/2022]
Abstract
Functional genes, namely hzo/hao, nirS, hzs, and ccs gene, are efficient with high specificity for detecting anammox bacteria. Sc-nirS and An-nirS primer sets were proposed for targeting Scalindua/non-Scalindua anammox bacterial groups; previously, they have not been assessed for biogeographic study on marine-terrestrial transitional systems, specifically marine and terrestrial ecosystems. Here, we report phylogenetic distribution pattern of anammox bacteria in both northern South China Sea (nSCS) and Mai Po wetland (a coastal mangrove) using nirS gene-based primers. A well-delineated biogeographic distribution pattern from ocean to continental shelf was evident by combining both gene-based analyses as previously depicted using 16S rRNA as the biomarker. Furthermore, factors affecting the abundance and composition of An-nirS genes in Mai Po wetland were identified as substrate (NO3-/NO2- concentration) and anoxic/oxic condition in association to depth. An-nirS gene abundance was from 2.6 × 103 to 1.2-1.4 × 104 copies/g dry sediment in nSCS; and it was around 5 × 103 and 1-2 × 104 copies/g dry sediment in surface and subsurface sediments of Mai Po wetland, respectively. In addition, nirS gene abundance and distribution pattern of denitrifiers and anammox bacteria in the wetland indicates a competition relationship between them. Mangrove vegetation affected the community composition of An-nirS gene considerably, and a more homogeneous distribution pattern was observed in the mangrove forest than intertidal mudflats. Sc/An-nirS gene-based biogeographic insights on anammox bacteria have shed lights on the compositional and potential functional dynamics and emphasized the importance of molecular tools on refining the current microbial ecological patterns.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Jing Chen
- School of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan Province, People's Republic of China
| | - Wenjie Gu
- Guangdong Academy of Agricultural Sciences, 29 Jinying Road, Guangzhou, 510000, Guangdong Province, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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27
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Zhou Y, Guo B, Zhang L, Zou X, Yang S, Zhang H, Xia S, Liu Y. Anaerobically digested blackwater treatment by simultaneous denitrification and anammox processes: Feeding loading affects reactor performance and microbial community succession. CHEMOSPHERE 2020; 241:125101. [PMID: 31683431 DOI: 10.1016/j.chemosphere.2019.125101] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Source diverted blackwater collected from toilets can be anaerobically digested to recover energy. The anaerobically digested blackwater (ADB) contains high levels of ammonium and low carbon to nitrogen (C/N) ratio. In the present study, ADB was treated by a two-stage nitritation-denitrification/anammox process in an integrated fixed film activated sludge-continuous flow reactor (IFAS-CFR). NH4+-N, NO2--N, total nitrogen (TN), and chemical oxygen demand (COD) removal efficiencies were 80%, 82%, 76%, and 78%, respectively. Anaerobic ammonium oxidation (anammox) and denitrification contributed to 44-48%, and 52-56% of total nitrogen removal, respectively. Both of the protein- and humic acid-like matters were removed during the process. An increase in feed load promoted the sustained growth of anammox bacteria-Candidatus Brocadia in the biofilm, as well as an increase of denitrifiers (Pseudomonas, Thermotonus, Phodanobacter, Caulobacter) in both biofilm and suspended biomass, which remained higher in the suspended biomass than in biofilm. Overall, biofilm had higher nitrogen removal efficiency than suspended biomass, while suspended biomass had a higher COD removal efficiency than biofilm.
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Affiliation(s)
- Yun Zhou
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Bing Guo
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Lei Zhang
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Xin Zou
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Sen Yang
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Huixin Zhang
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Yang Liu
- University of Alberta, Department of Civil and Environmental Engineering, Edmonton, Alberta, T6G 1H9, Canada.
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28
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Zhu A, Chen J, Gao L, Shimizu Y, Liang D, Yi M, Cao L. Combined microbial and isotopic signature approach to identify nitrate sources and transformation processes in groundwater. CHEMOSPHERE 2019; 228:721-734. [PMID: 31071559 DOI: 10.1016/j.chemosphere.2019.04.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Nitrate (NO3-) pollution is a serious problem worldwide. Identification of NO3- sources and transformation processes in aquifers is a key step in effectively controlling and mitigating NO3- contamination. In this study, hydrochemical, microbial, and dual isotopic approaches were integrated to elucidate the sources and processes influencing NO3- contamination in the Pearl River Delta, China. The results showed a severe NO3- contamination, with 75% of the samples having NO3--N concentrations above the WHO standard of 10 mg L-1. The δ15NNO3- and δ18ONO3- values and a multivariate statistical analysis of hydrochemical data both revealed that manure and sewage were mainly responsible for NO3- contamination. Biological indicators further demonstrated that, manure and sewage had greater impacts on groundwater quality during the rainy season than during the dry season. Based on the significant relationships of δ15NNO3- and δ18ONO3- with the logarithmic NO3- concentration (Ln(NO3-)), denitrification was confirmed to occur in the discharge zone during the rainy season. Proteobacteria, Bacteroidetes, and Planctomycetes were identified as the dominant phyla, and Dechloromonas, Flavobacterium, and Nitrospira were dominant among the denitrifying bacteria in groundwater. The abundance of denitrifying bacteria had significant positive correlations with δ15NNO3- and NO2--N during the rainy season, further confirming the occurrence of denitrification during the rainy season. This study showed that dual isotope techniques combined with microbial data can be a powerful tool for identifying the sources and microbial processes affecting NO3- in groundwater. Moreover, the results can provide useful insights for environmental managers to verify groundwater pollution and better apply remediation solutions.
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Affiliation(s)
- Aiping Zhu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Urbanization and Geo‑simulation, School of Geography and Planning, Sun Yat-Sen University, Guangzhou 510275, PR China; Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jianyao Chen
- Guangdong Provincial Key Laboratory of Urbanization and Geo‑simulation, School of Geography and Planning, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Gao
- Guangdong Provincial Key Laboratory of Urbanization and Geo‑simulation, School of Geography and Planning, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Yuta Shimizu
- Office for Agricultural Artificial Intelligence Research, Research Center for Agricultural Information Technology, 3-5-1 Kasumigaseki, Chiyoda, Tokyo, Japan
| | - Dongmei Liang
- Bureau of Hydrology and Water Resources of Nanning City, Nanning, 530001, PR China
| | - Ming Yi
- Guangdong Provincial Key Laboratory of Urbanization and Geo‑simulation, School of Geography and Planning, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lixiang Cao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China.
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29
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Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
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Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
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30
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Xu S, Feng S, Sun H, Wu S, Zhuang G, Deng Y, Bai Z, Jing C, Zhuang X. Linking N 2O Emissions from Biofertilizer-Amended Soil of Tea Plantations to the Abundance and Structure of N 2O-Reducing Microbial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:11338-11345. [PMID: 30199630 DOI: 10.1021/acs.est.8b04935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nitrous oxide (N2O) contributes up to 8% of global greenhouse gas emissions, with approximately 70% from terrestrial sources; over one-third of this terrestrial emission has been linked to increased agricultural fertilizer use. Much of the nitrogen in fertilizers is converted to N2O by microbial processes in soil. However, the potential mechanism of biofertilizers and the role of microbial communities in mitigating soil N2O emissions are not fully understood. Here, we used a greenhouse-based pot experiment with tea plantation soil to investigate the effect of Trichoderma viride biofertilizer on N2O emission. The addition of biofertilizer reduced N2O emissions from fertilized soil by 67.6%. Quantitative PCR (qPCR) analysis of key functional genes involved in N2O generation and reduction ( amoA, nirK, nirS, and nosZ) showed an increased abundance of nirS and nosZ genes linked to the pronounced reduction in N2O emissions. High-throughput sequencing of nosZ showed enhanced relative abundance of nosZ-harboring denitrifiers in the T. viride biofertilizer treatments, thus linking greater N2O reduction capacity to the reduced emissions. Our findings showed that biofertilizers can affect the microbial nitrogen transformation process and reduce N2O emissions from agroecosystems.
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Affiliation(s)
- Shengjun Xu
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shugeng Feng
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Haishu Sun
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
- College of Resources and Environment , University of Chinese Academy of Sciences , Beijing 100049 , China
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Brenzinger K, Kujala K, Horn MA, Moser G, Guillet C, Kammann C, Müller C, Braker G. Soil Conditions Rather Than Long-Term Exposure to Elevated CO 2 Affect Soil Microbial Communities Associated with N-Cycling. Front Microbiol 2017; 8:1976. [PMID: 29093701 PMCID: PMC5651278 DOI: 10.3389/fmicb.2017.01976] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Continuously rising atmospheric CO2 concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO2 (eCO2) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N2O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO2 (aCO2). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO2 effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO2 on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO2 and aCO2, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO2 differed only slightly from soil under aCO2. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO2 level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO2 had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N2O emissions under eCO2 and future studies should aim at exploring the active members of the soil microbial community.
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Affiliation(s)
- Kristof Brenzinger
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Katharina Kujala
- Water Resources and Environmental Engineering Research Unit, University of Oulu, Oulu, Finland
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany.,Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Gerald Moser
- Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Cécile Guillet
- Department of Plant Ecology, University of Giessen, Giessen, Germany
| | - Claudia Kammann
- Department of Plant Ecology, University of Giessen, Giessen, Germany.,Climate Change Research for Special Crops, Department of Soil Science and Plant Nutrition, Geisenheim University, Geisenheim, Germany
| | - Christoph Müller
- Department of Plant Ecology, University of Giessen, Giessen, Germany.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gesche Braker
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,University of Kiel, Kiel, Germany
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32
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Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform. PLoS One 2017; 12:e0176716. [PMID: 28453559 PMCID: PMC5409056 DOI: 10.1371/journal.pone.0176716] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/15/2017] [Indexed: 12/12/2022] Open
Abstract
Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was observed when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the reproducibility was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.
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33
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Morgalev YN, Lushchaeva IV, Morgaleva TG, Kolesnichenko LG, Loiko SV, Krickov IV, Lim A, Raudina TV, Volkova II, Shirokova LS, Morgalev SY, Vorobyev SN, Kirpotin SN, Pokrovsky OS. Bacteria primarily metabolize at the active layer/permafrost border in the peat core from a permafrost region in western Siberia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2088-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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34
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Isotope signatures of N2O emitted from vegetable soil: Ammonia oxidation drives N2O production in NH4(+)-fertilized soil of North China. Sci Rep 2016; 6:29257. [PMID: 27387280 PMCID: PMC4937382 DOI: 10.1038/srep29257] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 11/10/2022] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas. In North China, vegetable fields are amended with high levels of N fertilizer and irrigation water, which causes massive N2O flux. The aim of this study was to determine the contribution of microbial processes to N2O production and characterize isotopic signature effects on N2O source partitioning. We conducted a microcosm study that combined naturally abundant isotopologues and gas inhibitor techniques to analyze N2O flux and its isotopomer signatures [δ15Nbulk, δ18O, and SP (intramolecular 15N site preference)] that emitted from vegetable soil after the addition of NH4+ fertilizers. The results show that ammonia oxidation is the predominant process under high water content (70% water-filled pore space), and nitrifier denitrification contribution increases with increasing N content. δ15Nbulk and δ18O of N2O may not provide information about microbial processes due to great shifts in precursor signatures and atom exchange, especially for soil treated with NH4+ fertilizer. SP and associated two end-member mixing model are useful to distinguish N2O source and contribution. Further work is needed to explore isotopomer signature stability to improve N2O microbial process identification.
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Palmer K, Köpp J, Gebauer G, Horn MA. Drying-Rewetting and Flooding Impact Denitrifier Activity Rather than Community Structure in a Moderately Acidic Fen. Front Microbiol 2016; 7:727. [PMID: 27313566 PMCID: PMC4887476 DOI: 10.3389/fmicb.2016.00727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
Wetlands represent sources or sinks of the greenhouse gas nitrous oxide (N2O). The acidic fen Schlöppnerbrunnen emits denitrification derived N2O and is also capable of N2O consumption. Global warming is predicted to cause more extreme weather events in future years, including prolonged drought periods as well as heavy rainfall events, which may result in flooding. Thus, the effects of prolonged drought and flooding events on the abundance, community composition, and activity of fen denitrifiers were investigated in manipulation experiments. The water table in the fen was experimentally lowered for 8 weeks in 2008 and raised for 5.5 months in 2009 on three treatment plots, while three plots were left untreated and served as controls. In situ N2O fluxes were rather unaffected by the drought treatment and were marginally increased by the flooding treatment. Samples were taken before and after treatment in both years. The structural gene markers narG and nosZ were used to assess possible changes in the nitrate reducer and denitrifier community in response to water table manipulations. Detected copy numbers of narG and nosZ were essentially unaffected by the experimental drought and flooding. Terminal restriction fragment length polymorphism (TRFLP) patterns of narG and nosZ were similar before and after experimental drought or experimental flooding, indicating a stable nitrate reducer and denitrifier community in the fen. However, certain TRFs of narG and nosZ transcripts responded to experimental drought or flooding. Nitrate-dependent Michaelis-Menten kinetics were assessed in anoxic microcosms with peat samples taken before and 6 months after the onset of experimental flooding. Maximal reaction velocities vmax were higher after than before flooding in samples from treament but not in those from control plots taken at the same time. The ratio of N2O to N2O + N2 was lower in soil from treatment plots after flooding than in soil from control plots, suggesting mitigation of N2O emissions by increased N2O-reduction rates after flooding. N2O was consumed to subatmospheric levels in all microcosms after flooding. The collective data indicate that water table manipulations had only minor effects on in situ N2O fluxes, denitrifier abundance, and denitrifier community composition of the acidic fen, while active subpopulations of denitrifiers changed in response to water table manipulations, suggesting functionally redundant subpopulations occupying distinct ecological niches in the fen.
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Affiliation(s)
- Katharina Palmer
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany; Water Resources and Environmental Engineering Research Group, University of OuluOulu, Finland
| | - Julia Köpp
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Gerhard Gebauer
- BayCEER-Laboratory of Isotope Biogeochemistry, University of Bayreuth Bayreuth, Germany
| | - Marcus A Horn
- Department of Ecological Microbiology, University of Bayreuth Bayreuth, Germany
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36
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Nikrad MP, Kerkhof LJ, Häggblom MM. The subzero microbiome: microbial activity in frozen and thawing soils. FEMS Microbiol Ecol 2016; 92:fiw081. [PMID: 27106051 DOI: 10.1093/femsec/fiw081] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2016] [Indexed: 01/15/2023] Open
Abstract
Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.
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Affiliation(s)
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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37
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Nie Y, Li L, Wang M, Tahvanainen T, Hashidoko Y. Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss Sphagnum fuscum*. Biosci Biotechnol Biochem 2015; 79:2086-95. [DOI: 10.1080/09168451.2015.1061420] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Using a culture-based nitrous oxide (N2O) emission assay, three active N2O emitters were isolated from Sphagnum fuscum leaves and all identified as members of Burkholderia. These isolates showed N2O emission in the medium supplemented with but not with , and Burkholderia sp. SF-E2 showed the most efficient N2O emission (0.20 μg·vial−1·day−1) at 1.0 mM KNO3. In Burkholderia sp. SF-E2, the optimum pH for N2O production was 5.0, close to that of the phyllosphere of Sphagnum mosses, while the optimum temperature was uniquely over 30 °C. The stimulating effect of additional 1.5 mM sucrose on N2O emission was ignorable, but Burkholderia sp. SF-E2 upon exposure to 100 mg·L−1 E-caffeic acid showed uniquely 67-fold higher N2O emission. All of the three N2O emitters were negative in both acetylene inhibition assay and PCR assay for nosZ-detection, suggesting that N2O reductase or the gene itself is missing in the N2O-emitting Burkholderia.
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Affiliation(s)
- Yanxia Nie
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Li Li
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Mengcen Wang
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Teemu Tahvanainen
- Department of Biology, University of Eastern Finland, Joensuu, Finland
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38
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Arctic soil microbial diversity in a changing world. Res Microbiol 2015; 166:796-813. [DOI: 10.1016/j.resmic.2015.07.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 01/23/2023]
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39
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Zhao L, Meng Q, Ren L, Liu W, Zhang X, Huo Y, Zhou Z. Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1433-41. [PMID: 26194220 PMCID: PMC4554850 DOI: 10.5713/ajas.15.0091] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/06/2015] [Accepted: 03/25/2015] [Indexed: 11/27/2022]
Abstract
This study examined changes of rumen fermentation, ruminal bacteria biodiversity and abundance caused by nitrate addition with Ion Torrent sequencing and real-time polymerase chain reaction. Three rumen-fistulated steers were fed diets supplemented with 0%, 1%, and 2% nitrate (dry matter %) in succession. Nitrate supplementation linearly increased total volatile fatty acids and acetate concentration obviously (p = 0.02; p = 0.02; p<0.01), butyrate and isovalerate concentration numerically (p = 0.07). The alpha (p>0.05) and beta biodiversity of ruminal bacteria were not affected by nitrate. Nitrate increased typical efficient cellulolytic bacteria species (Ruminococcus flavefaciens, Ruminococcus ablus, and Fibrobacter succinogenes) (p<0.01; p = 0.06; p = 0.02). Ruminobactr, Sphaerochaeta, CF231, and BF311 genus were increased by 1% nitrate. Campylobacter fetus, Selenomonas ruminantium, and Mannheimia succiniciproducens were core nitrate reducing bacteria in steers and their abundance increased linearly along with nitrate addition level (p<0.01; p = 0.02; p = 0.04). Potential nitrate reducers in the rumen, Campylobacter genus and Cyanobacteria phyla were significantly increased by nitrate (p<0.01; p = 0.01). To the best of our knowledge, this was the first detailed view of changes in ruminal microbiota by nitrate. This finding would provide useful information on nitrate utilization and nitrate reducer exploration in the rumen.
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Affiliation(s)
- Liping Zhao
- Beijing Computing Center, Beijing 100094, China
| | | | - Liping Ren
- Beijing Computing Center, Beijing 100094, China
| | - Wei Liu
- Beijing Computing Center, Beijing 100094, China
| | | | - Yunlong Huo
- Beijing Computing Center, Beijing 100094, China
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40
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Penton CR, St Louis D, Pham A, Cole JR, Wu L, Luo Y, Schuur EAG, Zhou J, Tiedje JM. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils. Front Microbiol 2015; 6:746. [PMID: 26284038 PMCID: PMC4523034 DOI: 10.3389/fmicb.2015.00746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 07/06/2015] [Indexed: 01/06/2023] Open
Abstract
Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.
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Affiliation(s)
- Christopher R Penton
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA ; College of Letters and Sciences, Arizona State University, Polytechnic Campus Mesa, AZ, USA
| | - Derek St Louis
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Amanda Pham
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - James R Cole
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
| | - E A G Schuur
- Department of Biological Sciences, Center for Ecosystem Science and Society, Northern Arizona University Flagstaff, AZ, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA ; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China ; Earth Science Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
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41
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Palmer K, Horn MA. Denitrification activity of a remarkably diverse fen denitrifier community in finnish lapland is N-oxide limited. PLoS One 2015; 10:e0123123. [PMID: 25860353 PMCID: PMC4393310 DOI: 10.1371/journal.pone.0123123] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/21/2015] [Indexed: 11/23/2022] Open
Abstract
Peatlands cover more than 30% of the Finnish land area and impact N2O fluxes. Denitrifiers release N2O as an intermediate or end product. In situ N2O emissions of a near pH neutral pristine fen soil in Finnish Lapland were marginal during gas chamber measurements. However, nitrate and ammonium fertilization significantly stimulated in situ N2O emissions. Stimulation with nitrate was stronger than with ammonium. N2O was produced and subsequently consumed in gas chambers. In unsupplemented anoxic microcosms, fen soil produced N2O only when acetylene was added to block nitrous oxide reductase, suggesting complete denitrification. Nitrate and nitrite stimulated denitrification in fen soil, and maximal reaction velocities (vmax) of nitrate or nitrite dependent denitrification where 18 and 52 nmol N2O h-1 gDW-1, respectively. N2O was below 30% of total produced N gases in fen soil when concentrations of nitrate and nitrite were <500 μM. vmax for N2O consumption was up to 36 nmol N2O h-1 gDW-1. Denitrifier diversity was assessed by analyses of narG, nirK/nirS, and nosZ (encoding nitrate-, nitrite-, and nitrous oxide reductases, respectively) by barcoded amplicon pyrosequencing. Analyses of ~14,000 quality filtered sequences indicated up to 25 species-level operational taxonomic units (OTUs), and up to 359 OTUs at 97% sequence similarity, suggesting diverse denitrifiers. Phylogenetic analyses revealed clusters distantly related to publicly available sequences, suggesting hitherto unknown denitrifiers. Representatives of species-level OTUs were affiliated with sequences of unknown soil bacteria and Actinobacterial, Alpha-, Beta-, Gamma-, and Delta-Proteobacterial sequences. Comparison of the 4 gene markers at 97% similarity indicated a higher diversity of narG than for the other gene markers based on Shannon indices and observed number of OTUs. The collective data indicate (i) a high denitrification and N2O consumption potential, and (ii) a highly diverse, nitrate limited denitrifier community associated with potential N2O fluxes in a pH-neutral fen soil.
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Affiliation(s)
- Katharina Palmer
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
- * E-mail:
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42
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Long A, Song B, Fridey K, Silva A. Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils. FEMS Microbiol Ecol 2014; 91:1-9. [PMID: 25764542 DOI: 10.1093/femsec/fiu004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of producing N2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils.
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Affiliation(s)
- Andrew Long
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Bongkeun Song
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403 Department of Biological Sciences, Virginia Institute of Marine Sciences, Gloucester Point, VA 23062, USA Department of Life Science, Dongguk University-Seoul, Seoul 100-715, South Korea
| | - Kelly Fridey
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
| | - Amy Silva
- Department of Biology and Marine Biology, University of North Carolina, Wilmington, NC 28403
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Impaired reduction of N2O to N2 in acid soils is due to a posttranscriptional interference with the expression of nosZ. mBio 2014; 5:e01383-14. [PMID: 24961695 PMCID: PMC4073493 DOI: 10.1128/mbio.01383-14] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accumulating empirical evidence over the last 60 years has shown that the reduction of N2O to N2 is impaired by low soil pH, suggesting that liming of acid soils may reduce N2O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N2O reductase. We hypothesized that the reason is that denitrifying organisms in soils are unable to assemble functional N2O reductase (N2OR) at low pH, as shown to be the case for the model strain Paracoccus denitrificans. We tested this by experiments with bacteria extracted from soils by density gradient centrifugation. The soils were sampled from a long-term liming experiment (soil pH 4.0, 6.1, and 8.0). The cells were incubated (stirred batches, He atmosphere) at pH levels ranging from 5.7 to 7.6, while gas kinetics (NO, N2O, and N2) and abundances of relevant denitrification genes (nirS, nirK, and nosZ) and their transcripts were monitored. Cells from the most acidic soil (pH 4.0) were unable to reduce N2O at any pH. These results warrant a closer inspection of denitrification communities of very acidic soils. Cells from the neutral soils were unable to produce functional N2OR at pH values of ≤6.1, despite significant transcription of the nosZ gene. The N2OR expressed successfully at pH 7.0, however, was functional over the entire pH range tested (5.7 to 7.6). These observations lend strong support to our hypothesis: low soil pH diminishes/prevents reduction of N2O, primarily by precluding a successful assembly of functional N2O reductase. Impaired N2O reduction in acid soils was first observed ~60 years ago, and the phenomenon has been rediscovered several times since then. The practical implication would be that the emissions of N2O from cropped soils could be controlled by soil pH management, but this option has largely been ignored till now. One reason for this could be that the mechanisms involved have remained obscure. Here, we provide compelling evidence that the primary reason is that low pH interferes with the making of the enzyme N2O reductase rather than the function of the enzyme if properly assembled. The implications are important for understanding how pH controls the kinetics of N2O and N2 production by denitrification. The improved understanding provides credibility for soil pH management as a way to mitigate N2O emissions.
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Penton CR, Johnson TA, Quensen JF, Iwai S, Cole JR, Tiedje JM. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter. Front Microbiol 2013; 4:279. [PMID: 24062736 PMCID: PMC3775264 DOI: 10.3389/fmicb.2013.00279] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/28/2013] [Indexed: 12/03/2022] Open
Abstract
Targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised) method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature's related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification.
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Affiliation(s)
- C Ryan Penton
- Department of Plant, Soil and Microbial Sciences, Center for Microbial Ecology, Michigan State University East Lansing, MI, USA
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Vilar-Sanz A, Puig S, García-Lledó A, Trias R, Balaguer MD, Colprim J, Bañeras L. Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell. PLoS One 2013; 8:e63460. [PMID: 23717427 PMCID: PMC3662693 DOI: 10.1371/journal.pone.0063460] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/03/2013] [Indexed: 11/22/2022] Open
Abstract
The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs) is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite) and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs) for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A·m−3 NCC (Net Cathodic Compartment), when nitrate was used as an electron acceptor, to 14.1 A·m−3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O) accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK)/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.
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Affiliation(s)
- Ariadna Vilar-Sanz
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
| | - Sebastià Puig
- LEQUIA, Institute of the Environment, Universitat de Girona, Girona, Spain
| | - Arantzazu García-Lledó
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
| | - Rosalia Trias
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
| | - M. Dolors Balaguer
- LEQUIA, Institute of the Environment, Universitat de Girona, Girona, Spain
| | - Jesús Colprim
- LEQUIA, Institute of the Environment, Universitat de Girona, Girona, Spain
| | - Lluís Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, Universitat de Girona, Girona, Spain
- * E-mail:
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