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Wu Z, Jiang X, Chen J, Wang S, Yao C. Geochemistry and release risk for nutrients in lake sediments based on diffusive gradients in thin films. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:40588-40607. [PMID: 36622617 DOI: 10.1007/s11356-022-24961-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
A comprehensive understanding of the mobility of both nitrogen (N) and phosphorus (P) and the inter-relationships between P, N, and iron (Fe) in sediments is important for controlling the "internal loadings" of nutrients in lakes. In this research, diffusive gradients in thin film (DGT) assemblies with binding layers (ZrO-AT, chelex, and ZrO) were designed for PO4-P, Fe, ammonium (NH4-N), and nitrate (NO3-N) at sediment/water interface (SWI) in Western Lake Taihu (China). The biogeochemical processes of N and P related to the physicochemical properties, the dynamic P transfer, the distribution characteristics of P microniches, and the estimation of the release risks in sediments in Western Lake Taihu were simultaneously revealed by the passive sampling technique-DGT with the high spatial resolutions (millimeter and sub-millimeter). Based on DGT concentration (CDGT) related to physicochemical properties in sediments, (1) P biogeochemical reactions included P release from Fe-bound P during Fe reduction, algae biomass decomposition, and phosphatase enzyme activity increased by NH4-N; (2) denitrification and dissimilatory nitrate reduction to ammonium (DNRA) led to exchangeable ammonium (NH4ex) enrichment and NH4-N release; anammox depleted NH4-N transfer; organic matter (OM) mineralization favored NH4-N release; and (3) aerobic nitrification led to NO3-N remobilization; denitrification and DNRA reduced NO3-N release. Redox status, OM, Fe, aluminum, or calcium influenced mobilization of nutrients. The numerical model of DGT-induced fluxes in sediments was used for dynamic P transfers with resupply types ("slow" ~ "fast") controlled by labile P pool, resupply constant, response time, and Dspt rate. The formation of P microniches in two dimensions was revealed. Sediment P release risk index (0.49 ~ 36.85 [lg (nmol cm-3 d-1)]) with "light" ~ "high" risks and diffusive fluxes across SWI (µg m-2 d-1) of 15.0 ~ 639 (PO4-P), - 1403 ~ 5010 (NH4-N), and - 1395 ~ 149 (NO3-N) were derived and lake management strategies were provided. The DGT technique provides the characterization of the mobilization of nutrients and evidence for biogeochemical processes at the fine spatial scales for control of internal loadings in sediments.
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Affiliation(s)
- Zhihao Wu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China.,State Environmental Protection Key Laboratory for Lake Pollution Control, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China
| | - Xia Jiang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China.,State Environmental Protection Key Laboratory for Lake Pollution Control, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China
| | - Junyi Chen
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China.,State Environmental Protection Key Laboratory for Lake Pollution Control, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China
| | - Shuhang Wang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China. .,State Environmental Protection Key Laboratory for Lake Pollution Control, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China.
| | - Cheng Yao
- State Environmental Protection Key Laboratory for Lake Pollution Control, Institute of Lake Environment, Chinese Research Academy of Environmental Sciences (CRAES), Beijing, 100012, China.,College of Water Science, Beijing Normal University, Beijing, 100875, China
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Nojiri Y, Kaneko Y, Azegami Y, Shiratori Y, Ohte N, Senoo K, Otsuka S, Isobe K. Dissimilatory Nitrate Reduction to Ammonium and Responsible Microbes in Japanese Rice Paddy Soil. Microbes Environ 2020; 35. [PMID: 33028782 PMCID: PMC7734399 DOI: 10.1264/jsme2.me20069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nitrification–denitrification processes in the nitrogen cycle have been extensively examined in rice paddy soils. Nitrate is generally depleted in the reduced soil layer below the thin oxidized layer at the surface, and this may be attributed to high denitrification activity. In the present study, we investigated dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate, in order to challenge the conventional view of nitrogen cycling in paddy soils. We performed paddy soil microcosm experiments using 15N tracer analyses to assess DNRA and denitrification rates and conducted clone library analyses of transcripts of nitrite reductase genes (nrfA, nirS, and nirK) in order to identify the microbial populations carrying out these processes. The results obtained showed that DNRA occurred to a similar extent to denitrification and appeared to be enhanced by a nitrate limitation relative to organic carbon. We also demonstrated that different microbial taxa were responsible for these distinct processes. Based on these results and previous field observations, nitrate produced by nitrification within the surface oxidized layer may be reduced not only to gaseous N2 via denitrification, but also to NH4+ via DNRA, within the reduced layer. The present results also indicate that DNRA reduces N loss through denitrification and nitrate leaching and provides ammonium to rice roots in rice paddy fields.
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Affiliation(s)
- Yosuke Nojiri
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Yuka Kaneko
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Yoichi Azegami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | | | | | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Shigeto Otsuka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Huang X, Weisener CG, Ni J, He B, Xie D, Li Z. Nitrate assimilation, dissimilatory nitrate reduction to ammonium, and denitrification coexist in Pseudomonas putida Y-9 under aerobic conditions. BIORESOURCE TECHNOLOGY 2020; 312:123597. [PMID: 32506044 DOI: 10.1016/j.biortech.2020.123597] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
The specific nitrate reduction pathway in Pseudomonas putida Y-9 under aerobic conditions was studied. Strain Y-9 removed 82% of the nitrate accompanied by an accumulation of ammonium and a decrease of total nitrogen. Ammonium inhibited nitrate transformation (removal efficiency was 22.65%), illustrating that nitrate assimilation exists in strain Y-9. The detectable ammonium in the supernatant during the nitrate reduction process came from intracellular locations in strain Y-9. The nirBD that encodes nitrite reductase had an important role in strain growth and ammonium production. A 15N isotope experiment demonstrated that strain Y-9 can conduct dissimilatory nitrate reduction to ammonium (DNRA) and nirBD controls this process. This further indicated that the loss of total nitrogen is due to denitrification. All results highlighted that strain Y-9 performs simultaneous nitrate assimilation, DNRA, and denitrification under aerobic conditions, and nirBD controls the assimilation and DNRA process. Thereinto, nitrate assimilation dominates the removal of nitrate.
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Affiliation(s)
- Xuejiao Huang
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Christopher G Weisener
- Great Lakes Institute of Environmental Research, University of Windsor, Ontario N9B3P4, Canada
| | - Jiupai Ni
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Binghui He
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Deti Xie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, Southwest University, Chongqing 400716, China.
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Anderson E, Jang J, Venterea R, Feyereisen G, Ishii S. Isolation and characterization of denitrifiers from woodchip bioreactors for bioaugmentation application. J Appl Microbiol 2020; 129:590-600. [DOI: 10.1111/jam.14655] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/28/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022]
Affiliation(s)
- E.L. Anderson
- Department of Soil, Water, and Climate University of Minnesota St. Paul MN USA
| | - J. Jang
- BioTechnology Institute University of Minnesota St. Paul MN USA
| | - R.T. Venterea
- Department of Soil, Water, and Climate University of Minnesota St. Paul MN USA
- USDA‐ARS Soil and Water Management Research Unit St. Paul MN USA
| | - G.W. Feyereisen
- USDA‐ARS Soil and Water Management Research Unit St. Paul MN USA
| | - S. Ishii
- Department of Soil, Water, and Climate University of Minnesota St. Paul MN USA
- BioTechnology Institute University of Minnesota St. Paul MN USA
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Ishii S, Ikeda S, Minamisawa K, Senoo K. Nitrogen cycling in rice paddy environments: past achievements and future challenges. Microbes Environ 2011; 26:282-92. [PMID: 22008507 DOI: 10.1264/jsme2.me11293] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nitrogen is generally the most limiting nutrient for rice production. In rice paddy soils, various biochemical processes can occur regarding N cycling, including nitrification, denitrification, and nitrogen fixation. Since its discovery in the 1930s, the nitrification-denitrification process has been extensively studied in Japan. It may cause N loss from rice paddy soils, while it can also reduce environmental pollutions such as nitrate leaching and emission of nitrous oxide (N(2)O). In this review article, we first summarize the early and important findings regarding nitrification-denitrification in rice paddy soils, and then update recent findings regarding key players in denitrification and N(2)O reduction. In addition, we also discuss the potential occurrence of other newly found reactions in the N cycle, such as archaeal ammonia oxidization, fungal denitrification, anaerobic methane oxidation coupled with denitrification, and anaerobic ammonium oxidation.
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Affiliation(s)
- Satoshi Ishii
- Division of Environmental Engineering, Hokkaido University, Sapporo, Japan.
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Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields. Microbes Environ 2011; 26:30-5. [PMID: 21487200 DOI: 10.1264/jsme2.me10167] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Denitrifiers can produce and consume nitrous oxide (N(2)O). While little N(2)O is emitted from rice paddy soil, the same soil produces N(2)O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N(2) in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N(2)-producing denitrifiers.
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Affiliation(s)
- Kanako Tago
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan.
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Use of a microchip electrophoresis system for estimation of bacterial phylogeny and analysis of NO3- reducing bacterial flora in field soils. Biosci Biotechnol Biochem 2009; 73:479-88. [PMID: 19270404 DOI: 10.1271/bbb.70712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Phylogenetic estimation method without determination of DNA sequence was developed. By this method, fragment length polymorphism separately digested with multiple restriction enzymes was measured using microchip electrophoresis and affiliated with those calculated from corresponding DNA sequence in the theoretical database. The phylogenies of 129 NO(3)(-) reducing bacteria newly isolated from field soils were estimated by this method, and were compared to those by carbon source utilization profiles and by comparative sequence analysis of 16S rDNA. Various bacteria such as Micrococcus sp. (one isolate), Acidovorax delofieldii (one isolate), Cupriavidus necator (one isolate), Burkholderia sp., (seven isolates), Commamonas acidovorans (two isolates), Herbaspirillum seropedicae (two isolates), Ralstonia sp. (six isolates), Pseudomonas spp. (14 isolates), and Acinetobacter spp. (one isolate), were affiliated as similar to those by sequence analysis of 16S rDNA, while exact affiliation of genus was difficult for those belonging to Enterobacteriaceae.
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Saito T, Ishii S, Otsuka S, Nishiyama M, Senoo K. Identification of Novel Betaproteobacteria in a Succinate-Assimilating Population in Denitrifying Rice Paddy Soil by Using Stable Isotope Probing. Microbes Environ 2008; 23:192-200. [DOI: 10.1264/jsme2.23.192] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Takayuki Saito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Satoshi Ishii
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | | | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Katsuyama C, Kondo N, Suwa Y, Yamagishi T, Itoh M, Ohte N, Kimura H, Nagaosa K, Kato K. Denitrification Activity and Relevant Bacteria Revealed by Nitrite Reductase Gene Fragments in Soil of Temperate Mixed Forest. Microbes Environ 2008; 23:337-45. [DOI: 10.1264/jsme2.me08541] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chie Katsuyama
- Graducate School of Science and Technology, Shizuoka University
| | - Naho Kondo
- Graduate School of Science, Shizuoka University
| | - Yuichi Suwa
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology
- Department of Biological Sciences, Faculty of Science and Technology, Chuo University
| | - Takao Yamagishi
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology
| | | | - Nobuhito Ohte
- Graduate School of Agriculture, Kyoto University
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Hiroyuki Kimura
- Graduate School of Science, Shizuoka University
- Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kazuyo Nagaosa
- Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kenji Kato
- Graducate School of Science and Technology, Shizuoka University
- Graduate School of Science, Shizuoka University
- Department of Geosciences, Faculty of Science, Shizuoka University
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Sameshima-Saito R, Chiba K, Minamisawa K. Correlation of Denitrifying Capability with the Existence of nap, nir, nor and nos Genes in Diverse Strains of Soybean Bradyrhizobia. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.174] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Kaori Chiba
- Graduate School of Life Sciences, Tohoku University
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Rich JJ, Heichen RS, Bottomley PJ, Cromack K, Myrold DD. Community composition and functioning of denitrifying bacteria from adjacent meadow and forest soils. Appl Environ Microbiol 2004; 69:5974-82. [PMID: 14532052 PMCID: PMC201216 DOI: 10.1128/aem.69.10.5974-5982.2003] [Citation(s) in RCA: 212] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in alpha-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.
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Affiliation(s)
- J J Rich
- Departments of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, USA
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Ihssen J, Horn MA, Matthies C, Gössner A, Schramm A, Drake HL. N2O-producing microorganisms in the gut of the earthworm Aporrectodea caliginosa are indicative of ingested soil bacteria. Appl Environ Microbiol 2003; 69:1655-61. [PMID: 12620856 PMCID: PMC150113 DOI: 10.1128/aem.69.3.1655-1661.2003] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main objectives of this study were (i) to determine if gut wall-associated microorganisms are responsible for the capacity of earthworms to emit nitrous oxide (N(2)O) and (ii) to characterize the N(2)O-producing bacteria of the earthworm gut. The production of N(2)O in the gut of garden soil earthworms (Aporrectodea caliginosa) was mostly associated with the gut contents rather than the gut wall. Under anoxic conditions, nitrite and N(2)O were transient products when supplemental nitrate was reduced to N(2) by gut content homogenates. In contrast, nitrite and N(2)O were essentially not produced by nitrate-supplemented soil homogenates. The most probable numbers of fermentative anaerobes and microbes that used nitrate as a terminal electron acceptor were approximately 2 orders of magnitude higher in the earthworm gut than in the soil from which the earthworms originated. The fermentative anaerobes in the gut and soil displayed similar physiological functionalities. A total of 136 N(2)O-producing isolates that reduced either nitrate or nitrite were obtained from high serial dilutions of gut homogenates. Of the 25 representative N(2)O-producing isolates that were chosen for characterization, 22 isolates exhibited >99% 16S rRNA gene sequence similarity with their closest cultured relatives, which in most cases was a soil bacterium, most isolates were affiliated with the gamma subclass of the class Proteobacteria or with the gram-positive bacteria with low DNA G+C contents, and 5 isolates were denitrifiers and reduced nitrate to N(2)O or N(2). The initial N(2)O production rates of denitrifiers were 1 to 2 orders of magnitude greater than those of the nondenitrifying isolates. However, most nondenitrifying nitrate dissimilators produced nitrite and might therefore indirectly stimulate the production of N(2)O via nitrite-utilizing denitrifiers in the gut. The results of this study suggest that most of the N(2)O emitted by earthworms is due to the activation of ingested denitrifiers and other nitrate-dissimilating bacteria in the gut lumen.
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Affiliation(s)
- Julian Ihssen
- Department of Ecological Microbiology, BITOEK, University of Bayreuth, 95440 Bayreuth, Germany
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