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Liu H, Li Y, Pan B, Zheng X, Yu J, Ding H, Zhang Y. Pathways of soil N 2O uptake, consumption, and its driving factors: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:30850-30864. [PMID: 35092587 DOI: 10.1007/s11356-022-18619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas that plays a significant role in atmospheric photochemical reactions and contributes to stratospheric ozone depletion. Soils are the main sources of N2O emissions. In recent years, it has been demonstrated that soil is not only a source but also a sink of N2O uptake and consumption. N2O emissions at the soil surface are the result of gross N2O production, uptake, and consumption, which are co-occurring processes. Soil N2O uptake and consumption are complex biological processes, and their mechanisms are still worth an in-depth systematic study. This paper aimed to systematically address the current research progress on soil N2O uptake and consumption. Based on a bibliometric perspective, this study has highlighted the pathways of soil N2O uptake and consumption and their driving factors and measurement techniques. This systematic review of N2O uptake and consumption will help to further understand N transformations and soil N2O emissions.
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Affiliation(s)
- Hongshan Liu
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yuefen Li
- College of Earth Sciences, Jilin University, Chao'yang, Changchun, 130061, Jilin, People's Republic of China.
| | - Baobao Pan
- School of Agriculture and Food, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences/ Fujian Key Laboratory of Plant Nutrition and Fertilizer, Jin'an, Fuzhou, 350013, Fujian, People's Republic of China.
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Hall NC, Sikaroodi M, Hogan D, Jones RC, Gillevet PM. The Presence of Denitrifiers In Bacterial Communities of Urban Stormwater Best Management Practices (BMPs). ENVIRONMENTAL MANAGEMENT 2022; 69:89-110. [PMID: 34860281 PMCID: PMC8758610 DOI: 10.1007/s00267-021-01529-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Stormwater best management practices (BMPs) are engineered structures that attempt to mitigate the impacts of stormwater, which can include nitrogen inputs from the surrounding drainage area. The goal of this study was to assess bacterial community composition in different types of stormwater BMP soils to establish whether a particular BMP type harbors more denitrification potential. Soil sampling took place over the summer of 2015 following precipitation events. Soils were sampled from four bioretention facilities, four dry ponds, four surface sand filters, and one dry swale. 16S rRNA gene analysis of extracted DNA and RNA amplicons indicated high bacterial diversity in the soils of all BMP types sampled. An abundance of denitrifiers was also indicated in the extracted DNA using presence/absence of nirS, nirK, and nosZ denitrification genes. BMP soil bacterial communities were impacted by the surrounding soil physiochemistry. Based on the identification of a metabolically-active community of denitrifiers, this study has indicated that denitrification could potentially occur under appropriate conditions in all types of BMP sampled, including surface sand filters that are often viewed as providing low potential for denitrification. The carbon content of incoming stormwater could be providing bacterial communities with denitrification conditions. The findings of this study are especially relevant for land managers in watersheds with legacy nitrogen from former agricultural land use.
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Affiliation(s)
- Natalie C Hall
- U.S. Geological Survey, Florence Bascom Geoscience Center, Reston, VA, USA.
| | - Masoumeh Sikaroodi
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
| | - Dianna Hogan
- U.S. Geological Survey, Deputy Regional Director for Science, Southeast Region, Reston, VA, USA
| | - R Christian Jones
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
- Potomac Environmental Research and Education Center (PEREC), George Mason University, Woodbridge, VA, USA
| | - Patrick M Gillevet
- Department of Biology, George Mason University, Manassas, VA, USA
- Microbiome Analysis Center (MBAC), Manassas, VA, USA
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Guo B, Zheng X, Yu J, Ding H, Pan B, Luo S, Zhang Y. Dissolved organic carbon enhances both soil N2O production and uptake. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Wang Y, Qi L, Huang R, Wang F, Wang Z, Gao M. Characterization of Denitrifying Community for Application in Reducing Nitrogen: a Comparison of nirK and nirS Gene Diversity and Abundance. Appl Biochem Biotechnol 2020; 192:22-41. [PMID: 32212109 DOI: 10.1007/s12010-020-03250-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/08/2020] [Indexed: 01/03/2023]
Abstract
Studies have shown that the addition of biochar to agricultural soils has the potential to mitigate climate change by decreasing nitrous oxide (N2O) emissions resulting from denitrification. Rice paddy field soils have been known to have strong denitrifying activity, but the response of microbes to biochar for weakening denitrification in rice paddy field soils is not well known. In this work, compared with the chemical fertilizer alone, the chemical fertilizer + 20 t hm-2 biochar fertilizer slightly decreased denitrifying the nitrite reductase activity (S-NiR) and N2O emission without statistic difference, whereas the chemical fertilizer + 40 t hm-2 biochar significantly boosted them. The abundance of nir-denitrifiers contributed to S-NiR and N2O emission, especially nirS-denitrifiers, rather than the variation of community structure. Pearson correlation analysis showed that NO2--N was a key factor for controlling the abundance of nir-denitrifiers, S-NiR and N2O emission. The biochar addition fertilization treatments strongly shaped the community structure of nirK-denitrifiers, while the community structure of nirS-denitrifiers remained relatively stable. In addition, Paracoccus and Sinorhizobium were revealed to be as the predominant lineage of nirS- and nirK-containing denitrifiers, respectively. Distance-based redundancy analysis (db-RDA) showed that changes in the nir-denitrifier community structure were significantly related to soil organic carbon, NO3--N, and total phosphorus. Our findings suggest that, although the nirS- and nirK-denitrifiers are both controlling nitrite reductase, their responses to biochar addition fertilization treatments showed significant discrepancies of diversity, abundance, and contribution to N2O and S-NiR in a paddy soil.
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Affiliation(s)
- Yingyan Wang
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China
| | - Le Qi
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China
| | - Rong Huang
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China.,College of Resource, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fuhua Wang
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China
| | - Zifang Wang
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China.
| | - Ming Gao
- College of Resources and Environment, Southwest University, No. 2, Tiansheng Street, Beibei, Chongqing, 400716, People's Republic of China.
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Xie D, Si G, Zhang T, Mulder J, Duan L. Nitrogen deposition increases N 2O emission from an N-saturated subtropical forest in southwest China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:1818-1824. [PMID: 30408869 DOI: 10.1016/j.envpol.2018.09.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Nitrous oxide (N2O) is a major greenhouse gas, with elevated emission being reported from subtropical forests that receive high nitrogen (N) deposition. After 10 years of monthly addition of ammonium nitrate (NH4NO3) or sodium nitrate (NaNO3) to a Mason pine forest at Tieshanping, near Chongqing city in Southwest China, the simulated N deposition was stopped in October 2014. The results of soil N2O emissions monitoring in different seasons during the nitrogen application period showed that nitrogen addition significantly increased soil N2O emission. In general, the N2O emission fluxes were positively correlated to nitrate (NO3-) concentrations in soil solution, supporting the important role of denitrification in N2O production, which was also modified by environmental factors such as soil temperature and moisture. After stopping the application of nitrogen, the soil N2O emissions from the treatment plots were no longer significantly higher than those from the reference plots, implying that a decrease in nitrogen deposition in the future would cause a decrease in N2O emission. Although the major forms of N deposition, NH4+ and NO3-, had not shown significantly different effects on soil N2O emission, the reduction in NH4+ deposition may decrease the NO3- concentrations in soil solution faster than the reduction in NO3- deposition, and thus be more effective in reducing N2O emission from N-saturated forest soil in the future.
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Affiliation(s)
- Danni Xie
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Gaoyue Si
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Ting Zhang
- Shenzhen Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, PR China
| | - Jan Mulder
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Box 5003, NO-1432, Ås, Norway
| | - Lei Duan
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China; Collaborative Innovation Centre for Regional Environmental Quality, Tsinghua University, Beijing, 100084, PR China.
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6
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Cui J, Zhu J, Wang Z, Mulder J, Wang B, Zhang X. The regional variation of denitrification phenotypes under anoxic incubation with soils from eight forested catchments in different climate zones of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:319-329. [PMID: 28982081 DOI: 10.1016/j.scitotenv.2017.09.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/23/2017] [Accepted: 09/23/2017] [Indexed: 06/07/2023]
Abstract
Denitrification characteristics of forest soils from eight headwater catchments in China were investigated in this study, along a climatic gradient from the tropics in the South to the temperate zones. Within each catchment, different landscape positions along hydrological flow paths were also considered, including well-drained soils on hill slopes and poorly drained soils in groundwater discharge zones. The results showed that instantaneous denitrification rates were much greater in soils from the northern sites than those from the southern sites (with the average of 110.0 and 25.4nmolNg-1drysoilh.-1, respectively). Large potentials for nitrous oxide (N2O) loss (evaluated as maximum N2O accumulation before it was reduced to dinitrogen (N2)) were observed in the six tropical and subtropical catchments, particularly in soils with high carbon (C) and nitrogen (N). Meanwhile high N2O/(N2O+N2) stoichiometries were displayed in soils from these southern sites. Within catchments, soils from the groundwater discharge zones showed greater potential denitrification rates but smaller N2O/(N2O+N2) ratios in comparison with those on the hill slopes, implying large N removal potentials of soils from the groundwater discharge zones. Furthermore, our findings suggest soil pH is the key controller for the potential denitrification rates and the N2O/(N2O+N2) stoichiometries. Soil pH, C and N availability affect the potential for N2O loss synergistically. Our findings not only pinpoint the denitrification phenotypes of soils along the climatic gradient, but also confirm the small-scale variations within catchments which reflect the in situ habitat of the denitrifiers. These indicate the importance of discrimination related to different landscape positions when modeling N2O emissions and N removals from regional N loading.
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Affiliation(s)
- Juan Cui
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Zhu
- Norwegian University of Life Sciences, Postbox 5003, Ås 1430, Norway; College of Environment and resources, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Zhangwei Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jan Mulder
- Norwegian University of Life Sciences, Postbox 5003, Ås 1430, Norway
| | - Bing Wang
- Institute of Ecological and Environmental Research, Chinese Academy of Forestry Science, Beijing 100080, China
| | - Xiaoshan Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K, Matsumoto T, Uenishi H. Community structure of denitrifying and total bacteria during nitrogen accumulation in an ammonia‐loaded biofilter. J Appl Microbiol 2017; 123:1498-1511. [DOI: 10.1111/jam.13603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 09/26/2017] [Accepted: 09/30/2017] [Indexed: 11/29/2022]
Affiliation(s)
- T. Yasuda
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - M. Waki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - Y. Fukumoto
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - D. Hanajima
- Hokkaido Agricultural Research Center National Agriculture and Food Research Organization Sapporo Hokkaido Japan
| | - K. Kuroda
- Kyushu Okinawa Agricultural Research Center National Agriculture and Food Research Organization Koshi Kumamoto Japan
| | - K. Suzuki
- Institute of Livestock and Grassland Science National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
| | - T. Matsumoto
- Institute of Crop Science National Agricultural and Food Research Organization Tsukuba Ibaraki Japan
| | - H. Uenishi
- Institute of Agrobiological Sciences National Agriculture and Food Research Organization Tsukuba Ibaraki Japan
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8
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Genomics and Ecology of Novel N 2O-Reducing Microorganisms. Trends Microbiol 2017; 26:43-55. [PMID: 28803698 DOI: 10.1016/j.tim.2017.07.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/29/2017] [Accepted: 07/14/2017] [Indexed: 11/22/2022]
Abstract
Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N2O) to harmless dinitrogen gas are receiving increased attention due to increasing N2O emissions (and our need to mitigate climate change) and to recent discoveries of novel N2O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N2O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N2O reducers, which could be N2O sinks without major contribution to N2O formation. We review the recent advances about fundamental understanding of the genomics, physiology, and ecology of N2O reducers and the importance of these findings for curbing N2O emissions.
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Herrmann M, Opitz S, Harzer R, Totsche KU, Küsel K. Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. MICROBIAL ECOLOGY 2017; 74:264-277. [PMID: 28214969 DOI: 10.1007/s00248-017-0950-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Oxygen and nitrate availability as well as the presence of suitable organic or inorganic electron donors are strong drivers of denitrification; however, the factors influencing denitrifier abundance and community composition in pristine aquifers are not well understood. We explored the denitrifier community structure of suspended and attached groundwater microorganisms in two superimposed limestone aquifer assemblages with contrasting oxygen regime in the Hainich Critical Zone Exploratory (Germany). Attached communities were retrieved from freshly crushed parent rock material which had been exposed for colonization in two groundwater wells (12.7 and 48 m depth). Quantitative PCR and amplicon pyrosequencing of nirK and nirS genes encoding copper-containing or cytochrome cd1 heme-type nitrite reductase, respectively, and of bacterial 16S ribosomal RNA genes showed a numerical predominance of nirS-type denitrifiers in both attached and suspended groundwater communities and a dominance of nirS-type denitrifiers closely related to the autotrophic thiosulfate- and hydrogen-oxidizing Sulfuritalea hydrogenivorans and the iron- and sulfide-oxidizing Sideroxydans lithotrophicus ES-1. Potential rates of nitrate reduction in association with exposed crushed rock material were higher with an inorganic electron donor (thiosulfate) compared to an organic electron donor (fumarate/acetate) in the upper aquifer assemblage but similar in the lower, oxic aquifer. Our results have clearly demonstrated that groundwater from pristine limestone aquifers harbors diverse denitrifier communities which appear to selectively attach to rock surfaces and harbor a high potential for nitrate reduction. Our findings suggest that the availability of suitable inorganic versus organic electron donors rather than oxygen availability shapes denitrifier communities and their potential activity in these limestone aquifers.
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Affiliation(s)
- M Herrmann
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - S Opitz
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - R Harzer
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - K U Totsche
- Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - K Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K. Characterization of the denitrifying bacterial community in a full-scale rockwool biofilter for compost waste-gas treatment. Appl Microbiol Biotechnol 2017; 101:6779-6792. [DOI: 10.1007/s00253-017-8398-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/22/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022]
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Das S, Chou ML, Jean JS, Yang HJ, Kim PJ. Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata. JOURNAL OF HAZARDOUS MATERIALS 2017; 325:279-287. [PMID: 27940117 DOI: 10.1016/j.jhazmat.2016.12.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
Phytoremediation of arsenic (As)-contaminated soil by hyperaccumulator Pteris vittata is promising. A better understanding of the rhizosphere microbial dynamics that regulate As availability and plant growth is important to optimize the phytoremediation process. In this study, Illumina sequencing of 16S rRNA genes was applied to assess the rhizosphere microbial community structure of P. vittata. Microbial functionality was monitored by soil enzyme activities and MPN-PCR targeting genes of interest. Arsenic (100mgkg-1 AsV) addition to soil significantly increased DOC, root exudates, As and P uptake and the frond biomass of P. vittata. Moreover, As-enrichment significantly increased soil enzyme activities involved in N, P and S cycling and the gene abundance of As transforming bacteria, Fe- and S-reducing bacteria and N and C fixing bacteria in the rhizosphere of P. vittata. Together, the results revealed that the combined selective pressure of As and rhizosphere resulted in stimulation of microbial community, which most likely has a role in reductive dissolution of Fe and S, As and P mobilization, C degradation and fixation, and N fixation. These changes appeared to have a role in mitigation of As toxicity and to promote growth and the As uptake ability of P. vittata under As-enriched conditions.
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Affiliation(s)
- Suvendu Das
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan; Institute of Agricultural Science and Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Mon-Lin Chou
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jiin-Shuh Jean
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Huai-Jen Yang
- Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Pil Joo Kim
- Institute of Agricultural Science and Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
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12
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Capturing Compositional Variation in Denitrifying Communities: a Multiple-Primer Approach That Includes Epsilonproteobacteria. Appl Environ Microbiol 2017; 83:AEM.02753-16. [PMID: 28087525 DOI: 10.1128/aem.02753-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/03/2017] [Indexed: 11/20/2022] Open
Abstract
Denitrifying Epsilonproteobacteria may dominate nitrogen loss processes in marine habitats with intense redox gradients, but assessment of their importance is limited by the currently available primers for nitrite reductase genes. Nine new primers targeting the nirS gene of denitrifying Epsilonproteobacteria were designed and tested for use in sequencing and quantitative PCR on two microbial mat samples (vent 2 and vent 4) from the Calypso hydrothermal vent field, Bay of Plenty, New Zealand. Commonly used nirS and nirK primer sets nirS1F/nirS6R, cd3aF/R3cd, nirK1F/nirK5R, and F1aCu/R3Cu were also tested to determine what may be missed by the common single-primer approach to assessing denitrifier diversity. The relative importance of Epsilonproteobacteria in these samples was evaluated by 16S rRNA gene sequencing. Epsilonproteobacteria represented up to 75.6% of 16S rRNA libraries, but nirS genes from this group were not found with commonly used primers. Pairing of the new primer EPSnirS511F with either EPSnirS1100R or EPSnirS1105R recovered nirS sequences from members of the genera Sulfurimonas, Sulfurovum, and Nitratifractor. The new quantitative PCR primers EPSnirS103F/EPSnirS530R showed dominance of denitrifying Epsilonproteobacteria in vent 4 compared to vent 2, which had greater representation by "standard" denitrifiers measured with the cd3aF/R3cd primers. Limited results from commonly used nirK primers suggest biased amplification between primers. Future application of multiple nirS and nirK primers, including the new epsilonproteobacterial nirS primers, will improve the detection of denitrifier diversity and the capability to identify changes in dominant denitrifying communities.IMPORTANCE Estimating the potential for increasing nitrogen limitation in the changing global ocean is reliant on understanding the microbial community that removes nitrogen through the process of denitrification. This process is favored under oxygen limitation, which is a growing global-ocean phenomenon. Current methods use the nitrite reductase genes nirS and nirK to assess denitrifier diversity and abundance using primers that target only a few known denitrifiers and systematically exclude denitrifying Epsilonproteobacteria, a group known to dominate in reducing environments, such as hydrothermal vents and anoxic basins. As oxygen depletion expands in the oceans, it is important to study denitrifier community dynamics within those areas to predict future global ocean changes. This study explores the design and testing of new primers that target epsilonproteobacterial nirS and reveals the varied success of existing primers, leading to the recommendation of a multiple-primer approach to assessing denitrifier diversity.
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Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219. [PMID: 27774985 PMCID: PMC5079060 DOI: 10.1038/ncomms13219] [Citation(s) in RCA: 594] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Christopher T. Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Alexander J. Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Michael J. Wilkins
- School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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Srivastava M, Kaushik MS, Singh A, Singh D, Mishra AK. Molecular phylogeny of heterotrophic nitrifiers and aerobic denitrifiers and their potential role in ammonium removal. J Basic Microbiol 2016; 56:907-21. [PMID: 27037833 DOI: 10.1002/jobm.201500689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/09/2016] [Indexed: 11/06/2022]
Abstract
To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (>98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.
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Affiliation(s)
- Meenakshi Srivastava
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Manish Singh Kaushik
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Anumeha Singh
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Deepti Singh
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, India
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Braker G, Matthies D, Hannig M, Brandt FB, Brenzinger K, Gröngröft A. Impact of Land Use Management and Soil Properties on Denitrifier Communities of Namibian Savannas. MICROBIAL ECOLOGY 2015; 70:981-992. [PMID: 25977143 DOI: 10.1007/s00248-015-0623-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
We studied potential denitrification activity and the underlying denitrifier communities in soils from a semiarid savanna ecosystem of the Kavango region in NE Namibia to help in predicting future changes in N(2)O emissions due to continuing changes of land use in this region. Soil type and land use (pristine, fallow, and cultivated soils) influenced physicochemical characteristics of the soils that are relevant to denitrification activity and N(2)O fluxes from soils and affected potential denitrification activity. Potential denitrification activity was assessed by using the denitrifier enzyme activity (DEA) assay as a proxy for denitrification activity in the soil. Soil type and land use influenced C and N contents of the soils. Pristine soils that had never been cultivated had a particularly high C content. Cultivation reduced soil C content and the abundance of denitrifiers and changed the composition of the denitrifier communities. DEA was strongly and positively correlated with soil C content and was higher in pristine than in fallow or recently cultivated soils. Soil type and the composition of both the nirK- and nirS-type denitrifier communities also influenced DEA. In contrast, other soil characteristics like N content, C:N ratio, and pH did not predict DEA. These findings suggest that due to greater availability of soil organic matter, and hence a more effective N cycling, the natural semiarid grasslands emit more N(2)O than managed lands in Namibia.
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Affiliation(s)
- Gesche Braker
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Kiel University, Kiel, Germany.
| | | | - Michael Hannig
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LGC Genomics, Berlin, Germany
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Brenzinger K, Dörsch P, Braker G. pH-driven shifts in overall and transcriptionally active denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil. Front Microbiol 2015; 6:961. [PMID: 26441895 PMCID: PMC4585170 DOI: 10.3389/fmicb.2015.00961] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/31/2015] [Indexed: 01/27/2023] Open
Abstract
Soil pH is a strong regulator for activity as well as for size and composition of denitrifier communities. Low pH not only lowers overall denitrification rates but also influences denitrification kinetics and gaseous product stoichiometry. N2O reductase is particularly sensitive to low pH which seems to impair its activity post-transcriptionally, leading to higher net N2O production. Little is known about how complex soil denitrifier communities respond to pH change and whether their ability to maintain denitrification over a wider pH range relies on phenotypic redundancy. In the present study, we followed the abundance and composition of an overall and transcriptionally active denitrifier community extracted from a farmed organic soil in Sweden (pHH2O = 7.1) when exposed to pH 5.4 and drifting back to pH 6.6. The soil was previously shown to retain much of its functioning (low N2O/N2 ratios) over a wide pH range, suggesting a high functional versatility of the underlying community. We found that denitrifier community composition, abundance and transcription changed throughout incubation concomitant with pH change in the medium, allowing for complete reduction of nitrate to N2 with little accumulation of intermediates. When exposed to pH 5.4, the denitrifier community was able to grow but reduced N2O to N2 only when near-neutral pH was reestablished by the alkalizing metabolic activity of an acid-tolerant part of the community. The genotypes proliferating under these conditions differed from those dominant in the control experiment run at neutral pH. Denitrifiers of the nirS-type appeared to be severely suppressed by low pH and nirK-type and nosZ-containing denitrifiers showed strongly reduced transcriptional activity and growth, even after restoration of neutral pH. Our study suggests that low pH episodes alter transcriptionally active populations which shape denitrifier communities and determine their gas kinetics.
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Affiliation(s)
- Kristof Brenzinger
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Peter Dörsch
- Department of Environmental Sciences, Norwegian University of Life Sciences Ås, Norway
| | - Gesche Braker
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany ; University of Kiel Kiel, Germany
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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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Yin C, Fan F, Song A, Cui P, Li T, Liang Y. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil. Appl Microbiol Biotechnol 2015; 99:5719-29. [DOI: 10.1007/s00253-015-6461-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/02/2015] [Accepted: 02/04/2015] [Indexed: 10/23/2022]
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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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Köster JR, Well R, Dittert K, Giesemann A, Lewicka-Szczebak D, Mühling KH, Herrmann A, Lammel J, Senbayram M. Soil denitrification potential and its influence on N2O reduction and N2O isotopomer ratios. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2363-2373. [PMID: 24097392 DOI: 10.1002/rcm.6699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/27/2013] [Accepted: 07/29/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE N2O isotopomer ratios may provide a useful tool for studying N2O source processes in soils and may also help estimating N2O reduction to N2. However, remaining uncertainties about different processes and their characteristic isotope effects still hamper its application. We conducted two laboratory incubation experiments (i) to compare the denitrification potential and N2O/(N2O+N2) product ratio of denitrification of various soil types from Northern Germany, and (ii) to investigate the effect of N2O reduction on the intramolecular (15)N distribution of emitted N2O. METHODS Three contrasting soils (clay, loamy, and sandy soil) were amended with nitrate solution and incubated under N2 -free He atmosphere in a fully automated incubation system over 9 or 28 days in two experiments. N2O, N2, and CO2 release was quantified by online gas chromatography. In addition, the N2O isotopomer ratios were determined by isotope-ratio mass spectrometry (IRMS) and the net enrichment factors of the (15)N site preference (SP) of the N2O-to-N2 reduction step (η(SP)) were estimated using a Rayleigh model. RESULTS The total denitrification rate was highest in clay soil and lowest in sandy soil. Surprisingly, the N2O/(N2O+N2) product ratio in clay and loam soil was identical; however, it was significantly lower in sandy soil. The IRMS measurements revealed highest N2O SP values in clay soil and lowest SP values in sandy soil. The η(SP) values of N2O reduction were between -8.2 and -6.1‰, and a significant relationship between δ(18)O and SP values was found. CONCLUSIONS Both experiments showed that the N2O/(N2O+N2) product ratio of denitrification is not solely controlled by the available carbon content of the soil or by the denitrification rate. Differences in N2O SP values could not be explained by variations in N2O reduction between soils, but rather originate from other processes involved in denitrification. The linear δ(18)O vs SP relationship may be indicative for N2O reduction; however, it deviates significantly from the findings of previous studies.
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Affiliation(s)
- Jan Reent Köster
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Str. 2, D-24118, Kiel, Germany
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Poulsen M, Kofoed MVW, Larsen LH, Schramm A, Stief P. Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment. Syst Appl Microbiol 2013; 37:51-9. [PMID: 24054696 DOI: 10.1016/j.syapm.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 11/27/2022]
Abstract
Benthic invertebrates affect microbial processes and communities in freshwater sediment by enhancing sediment-water solute fluxes and by grazing on bacteria. Using microcosms, the effects of larvae of the widespread midge Chironomus plumosus on the efflux of denitrification products (N2O and N2+N2O) and the diversity and abundance of nitrate- and nitrous-oxide-reducing bacteria were investigated. Additionally, the diversity of actively nitrate- and nitrous-oxide-reducing bacteria was analyzed in the larval gut. The presence of larvae increased the total effluxes of N2O and N2+N2O up to 8.6- and 4.2-fold, respectively, which was mostly due to stimulation of sedimentary denitrification; incomplete denitrification in the guts accounted for up to 20% of the N2O efflux. Phylotype richness of the nitrate reductase gene narG was significantly higher in sediment with than without larvae. In the gut, 47 narG phylotypes were found expressed, which may contribute to higher phylotype richness in colonized sediment. In contrast, phylotype richness of the nitrous oxide reductase gene nosZ was unaffected by the presence of larvae and very few nosZ phylotypes were expressed in the gut. Gene abundance of neither narG, nor nosZ was different in sediments with and without larvae. Hence, C. plumosus increases activity and diversity, but not overall abundance of nitrate-reducing bacteria, probably by providing additional ecological niches in its burrow and gut.
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Affiliation(s)
- Morten Poulsen
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Michael V W Kofoed
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Lone H Larsen
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Andreas Schramm
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Peter Stief
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark; Max-Planck-Institute for Marine Microbiology, Microsensor Group, Celsiusstraße 1, 28359 Bremen, Germany.
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Schreiber F, Wunderlin P, Udert KM, Wells GF. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies. Front Microbiol 2012; 3:372. [PMID: 23109930 PMCID: PMC3478589 DOI: 10.3389/fmicb.2012.00372] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022] Open
Abstract
Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.
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Affiliation(s)
- Frank Schreiber
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland ; Department of Environmental Systems Sciences, Eidgenössische Technische Hochschule Zurich, Switzerland
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Actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in N2O-metabolizing palsa peat. Appl Environ Microbiol 2012; 78:5584-96. [PMID: 22660709 DOI: 10.1128/aem.00810-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (N(2)O). Palsa peats are predicted to react sensitively to global warming. The acidic palsa peat Skalluvaara (approximate pH 4.4) is located in the discontinuous permafrost zone in northwestern Finnish Lapland. In situ N(2)O fluxes were spatially variable, ranging from 0.01 to -0.02 μmol of N(2)O m(-2) h(-1). Fertilization with nitrate stimulated in situ N(2)O emissions and N(2)O production in anoxic microcosms without apparent delay. N(2)O was subsequently consumed in microcosms. Maximal reaction velocities (v(max)) of nitrate-dependent denitrification approximated 3 and 1 nmol of N(2)O per h per gram (dry weight [g(DW)]) in soil from 0 to 20 cm and below 20 cm of depth, respectively. v(max) values of nitrite-dependent denitrification were 2- to 5-fold higher than the v(max) nitrate-dependent denitrification, and v(max) of N(2)O consumption was 1- to 6-fold higher than that of nitrite-dependent denitrification, highlighting a high N(2)O consumption potential. Up to 12 species-level operational taxonomic units (OTUs) of narG, nirK and nirS, and nosZ were retrieved. Detected OTUs suggested the presence of diverse uncultured soil denitrifiers and dissimilatory nitrate reducers, hitherto undetected species, as well as Actino-, Alpha-, and Betaproteobacteria. Copy numbers of nirS always outnumbered those of nirK by 2 orders of magnitude. Copy numbers of nirS tended to be higher, while copy numbers of narG and nosZ tended to be lower in 0- to 20-cm soil than in soil below 20 cm. The collective data suggest that (i) the source and sink functions of palsa peat soils for N(2)O are associated with denitrification, (ii) actinobacterial nitrate reducers and nirS-type and nosZ-harboring proteobacterial denitrifiers are important players, and (iii) acidic soils like palsa peats represent reservoirs of diverse acid-tolerant denitrifiers associated with N(2)O fluxes.
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Bakken LR, Bergaust L, Liu B, Frostegård A. Regulation of denitrification at the cellular level: a clue to the understanding of N2O emissions from soils. Philos Trans R Soc Lond B Biol Sci 2012; 367:1226-34. [PMID: 22451108 PMCID: PMC3306626 DOI: 10.1098/rstb.2011.0321] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Denitrifying prokaryotes use NO(x) as terminal electron acceptors in response to oxygen depletion. The process emits a mixture of NO, N(2)O and N(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of NO(3)(-) to N(2)O and finally to N(2). Cultured denitrifying prokaryotes show characteristic transient accumulation of NO(2)(-), NO and N(2)O during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears unrelated to phylogeny. Thus, although the denitrifying community of soils may differ in their propensity to emit N(2)O, it may be difficult to predict such characteristics by analysis of the community composition. A common feature of strains tested in our laboratory is that the relative amounts of N(2)O produced (N(2)O/(N(2)+N(2)O) product ratio) is correlated with acidity, apparently owing to interference with the assembly of the enzyme N(2)O reductase. The same phenomenon was demonstrated for soils and microbial communities extracted from soils. Liming could be a way to reduce N(2)O emissions, but needs verification by field experiments. More sophisticated ways to reduce emissions may emerge in the future as we learn more about the regulation of denitrification at the cellular level.
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Affiliation(s)
- Lars R Bakken
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Aas, Norway.
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Orlando J, Carú M, Pommerenke B, Braker G. Diversity and activity of denitrifiers of chilean arid soil ecosystems. Front Microbiol 2012; 3:101. [PMID: 22493591 PMCID: PMC3319911 DOI: 10.3389/fmicb.2012.00101] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility, and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of denitrifiers in particular.
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Affiliation(s)
- Julieta Orlando
- Department of Ecological Sciences, Faculty of Sciences, University of Chile Santiago, Chile
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Dörsch P, Braker G, Bakken LR. Community-specific pH response of denitrification: experiments with cells extracted from organic soils. FEMS Microbiol Ecol 2011; 79:530-41. [DOI: 10.1111/j.1574-6941.2011.01233.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 10/04/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022] Open
Affiliation(s)
- Peter Dörsch
- Department of Plant and Environmental Sciences; Norwegian University of Life Sciences; Ås; Norway
| | - Gesche Braker
- Max Planck Institute for Terrestrial Microbiology; Marburg; Germany
| | - Lars Reier Bakken
- Department of Plant and Environmental Sciences; Norwegian University of Life Sciences; Ås; Norway
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