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Ming Y, Abdullah Al M, Zhang D, Zhu W, Liu H, Cai L, Yu X, Wu K, Niu M, Zeng Q, He Z, Yan Q. Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities. Mol Ecol 2024:e17507. [PMID: 39158107 DOI: 10.1111/mec.17507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/19/2024] [Accepted: 08/07/2024] [Indexed: 08/20/2024]
Abstract
Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.
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Affiliation(s)
- Yuzhen Ming
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Mamun Abdullah Al
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Dandan Zhang
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Wengen Zhu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Huanping Liu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaoli Yu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Kun Wu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
| | - Mingyang Niu
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
| | - Qingyun Yan
- Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Zhuhai, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, China
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Yin M, Gao X, Kuang W, Zhang Y. Meta-analysis of the effect of nitrification inhibitors on the abundance and community structure of N 2O-related functional genes in agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161215. [PMID: 36584958 DOI: 10.1016/j.scitotenv.2022.161215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Application of nitrification inhibitors (NIs) in agricultural systems is an important strategy to enhance fertilizer nitrogen use efficiency and mitigate soil nitrous oxide (N2O) emissions. Here, we conducted a global meta-analysis of 88 published studies to assess the response of N2O-related functional gene and transcript abundances, and community structure to NIs application. Application of NIs significantly reduced the abundance of ammonia-oxidizing bacteria ammonia monooxygenase (AOB amoA) genes, AOB amoA transcript and nitrite reductase (nirS and nirK) genes. The effectiveness of NIs on reducing the AOB amoA abundance was influenced by N form, soil texture, soil pH and the experimental type (field vs. laboratory). Specifically, NIs were more effective when a mixed inorganic and organic N source was applied to a medium-textured soils. The NIs effectiveness increased with increasing soil pH. The response of AOB amoA abundance to NIs application was not affected by NI type, N rate, soil moisture, soil temperature and soil organic carbon (SOC). The inhibitory effect of NIs on nirS abundance increased with increasing soil temperature. NIs decreased soil nitrifying enzyme activity (NEA) and denitrifying enzyme activity (DEA) by 34.5 % and 27.0 %, respectively, leading to an overall 63.6 % reduction of N2O emissions. Soil NEA correlated positively with the abundance and community structure of AOB amoA but not with AOA amoA. Decrease in DEA with NIs application coincided with the decreasing nirS and nirK abundances. This global-scale assessment demonstrates that the effectiveness of NIs in reducing N2O emissions was attributed to the inhibiting effects on AOB amoA, nirS and nirK genes. Our findings highlight that NIs' inhibition effects on bacterial ammonia-oxidizing community and the encode enzymes in transformation of nitrite to nitric oxide are the main mechanisms for mitigation of N fertilizer-induced N2O emissions.
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Affiliation(s)
- Mingyuan Yin
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Shenyang 110044, China
| | - Xiaopeng Gao
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| | - Wennong Kuang
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| | - Yaohong Zhang
- School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, PR China
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3
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Zhu L, Zhang X, Zhang J, Liu T, Qiu Y. Saltwater intrusion weakens Fe-(oxyhydr)oxide-mediated (im)mobilization of Ni and Zn in redox-fluctuating soil-groundwater system. WATER RESEARCH 2022; 221:118799. [PMID: 35780765 DOI: 10.1016/j.watres.2022.118799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/03/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Iron in the form of (oxyhydr)oxides plays a profound role in the (im)mobilization of heavy metals in environmental geochemical processes occurring in the soil-groundwater system. Here, the influence of saltwater intrusion on Fe-(oxyhydr)oxide-mediated (im)mobilization of Ni(II) and Zn(II) in redox-fluctuating shallow aquifers was evaluated by chemical extraction, μ-XRF-XANES analysis, and 16S rRNA high-throughput sequencing. In phreatic water, the ferrihydrite-bound Ni/Zn (Fh-Ni/Zn) in soils contributed to a 12%-17% increase in carbonate-bound Ni/Zn (Cb-Ni/Zn) due to its own reductive dissolution, whereas the illite-adsorbed Ni/Zn (illite-Ni/Zn) only contributed 6%, 7%. The relative abundance of non-salt tolerant anaerobic Herbaspirillum and iron-reducing associated Ralstonia in soils accounted for nearly 50%. During the oxidation stage, the dissolved ferrihydrite reprecipitated to bind free Ni/Zn. However, saltwater invasion strongly weakened the dissolution-precipitation of ferrihydrite by inhibiting the growth of non-salt tolerant anaerobes and iron-reducing bacteria, and highlighted the contribution of illite-Ni/Zn. Under brackish water intrusion, illite-Zn contributed to a 12% increase in Cb-Zn, thereby surpassing the contribution of Fh-Zn (8%). Under seawater invasion, the dissolution-precipitation of ferrihydrite hardly occurred and the anaerobic salt-tolerant Bacillus (> 95%) prevailed. Therefore, the increase of Cb-Ni/Zn (7%-15%) in the reduction stages was contributed by illite-Ni/Zn. However, in the oxidation stages, the carbonate replaced the original role of reprecipitated ferrihydrite to bind the free Ni/Zn in solutions. These newly recognized mechanisms may be the key to predicting the mobility of toxic elements and developing appropriate remediation techniques of permeable reactive barriers under salinity stress.
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Affiliation(s)
- Ling Zhu
- Department of Environmental Science, College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaoxian Zhang
- Department of Environmental Science, College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Jichen Zhang
- Department of Environmental Science, College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Tingran Liu
- Department of Environmental Science, College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Yuping Qiu
- Department of Environmental Science, College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
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Li Z, Cupples AM. Diversity of nitrogen cycling genes at a Midwest long-term ecological research site with different management practices. Appl Microbiol Biotechnol 2021; 105:4309-4327. [PMID: 33944983 DOI: 10.1007/s00253-021-11303-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/12/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022]
Abstract
Nitrogen fertilizer results in the release of nitrous oxide (N2O), a concern because N2O is an ozone-depleting substance and a greenhouse gas. Although the reduction of N2O to nitrogen gas can control emissions, the factors impacting the enzymes involved have not been fully explored. The current study investigated the abundance and diversity of genes involved in nitrogen cycling (primarily denitrification) under four agricultural management practices (no tillage [NT], conventional tillage [CT], reduced input, biologically-based). The work involved examining soil shotgun sequencing data for nine genes (napA, narG, nirK, nirS, norB, nosZ, nirA, nirB, nifH). For each gene, relative abundance values, diversity and richness indices, and taxonomic classification were determined. Additionally, the genes associated with nitrogen metabolism (defined by the KEGG hierarchy) were examined. The data generated were statistically compared between the four management practices. The relative abundance of four genes (nifH, nirK, nirS, and norB) were significantly lower in the NT treatment compared to one or more of the other soils. The abundance values of napA, narG, nifH, nirA, and nirB were not significantly different between NT and CT. The relative abundance of nirS was significantly higher in the CT treatment compared to the others. Diversity and richness values were higher for four of the nine genes (napA, narG, nirA, nirB). Based on nirS/nirK ratios, CT represents the highest N2O consumption potential in four soils. In conclusion, the microbial communities involved in nitrogen metabolism were sensitive to different agricultural practices, which in turn, likely has implications for N2O emissions. KEY POINTS: • Four genes were less abundant in NT compared to one or more of the others soils (nifH, nirK, nirS, norB). • The most abundant sequences for many of the genes classified within the Proteobacteria. • Higher diversity and richness indices were observed for four genes (napA, narG, nirA, nirB). • Based on nirS/nirK ratios, CT represents the highest N2O consumption potential.
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Affiliation(s)
- Zheng Li
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.
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Goberna M, Donat S, Pérez-Valera E, Hallin S, Verdú M. nir gene-based co-occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire. Environ Microbiol 2020; 23:239-251. [PMID: 33118311 DOI: 10.1111/1462-2920.15298] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/25/2023]
Abstract
Denitrification causes nitrogen losses from terrestrial ecosystems. The magnitude of nitrogen loss depends on the prevalence of denitrifiers, which show ecological differences if they harbour nirS or nirK genes encoding nitrite reductases with the same biological function. Thus, it is relevant to understand the mechanisms of co-existence of denitrifiers, including their response to environmental filters and competition due to niche similarities. We propose a framework to analyse the co-existence of denitrifiers across multiple assemblages by using nir gene-based co-occurrence networks. We applied it in Mediterranean soils before and during 1 year after an experimental fire. Burning did not modify nir community structure, but significantly impacted co-occurrence patterns. Bacteria with the same nir co-occurred in space, and those with different nir excluded each other, reflecting niche requirements: nirS abundance responded to nitrate and salinity, whereas nirK to iron content. Prior to fire, mutual exclusion between bacteria with the same nir suggested competition due to niche similarities. Burning provoked an immediate rise in mineral nitrogen and erased the signals of competition, which emerged again within days as nir abundances peaked. nir co-occurrence patterns can help infer the assembly mechanisms of denitrifying communities, which control nitrogen losses in the face of ecological disturbance.
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Affiliation(s)
- Marta Goberna
- Department of Environment and Agronomy, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Santiago Donat
- Department of Ecology, Centro de Investigaciones sobre Desertificación (CIDE - CSIC), Valencia, Spain
| | - Eduardo Pérez-Valera
- Department of Ecology, Centro de Investigaciones sobre Desertificación (CIDE - CSIC), Valencia, Spain.,Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, České Budějovice, Czech Republic
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miguel Verdú
- Department of Ecology, Centro de Investigaciones sobre Desertificación (CIDE - CSIC), Valencia, Spain
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Huang R, Zeng J, Zhao D, Yong B, Yu Z. Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes. MICROBIAL ECOLOGY 2020; 80:809-821. [PMID: 32577778 DOI: 10.1007/s00248-020-01545-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH4+-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.
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Affiliation(s)
- Rui Huang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, School of Earth Sciences and Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Dayong Zhao
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, School of Earth Sciences and Engineering, Hohai University, Nanjing, 210098, China
| | - Bin Yong
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, School of Earth Sciences and Engineering, Hohai University, Nanjing, 210098, China
| | - Zhongbo Yu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, School of Earth Sciences and Engineering, Hohai University, Nanjing, 210098, China
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Liu RR, Tian Y, Zhou EM, Xiong MJ, Xiao M, Li WJ. Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462 T Improved Environmental Adaptability. MICROBIAL ECOLOGY 2020; 80:614-626. [PMID: 32474659 DOI: 10.1007/s00248-020-01528-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/14/2020] [Indexed: 05/21/2023]
Abstract
Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.
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Affiliation(s)
- Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - En-Min Zhou
- School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Jie Xiong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Han X, Huang C, Khan S, Zhang Y, Chen Y, Guo J. nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:28899-28911. [PMID: 32418104 DOI: 10.1007/s11356-020-09171-8] [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: 08/24/2019] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Mountain riparian zones are excellent buffers for protecting aquatic ecosystems from nutrient runoff in nitrogen deposition processes due to fertilization and manure. Denitrification is a critical process for transferring soil N to the atmosphere. Denitrifying bacterial communities in soil are indicative of the soil quality of a functional ecosystem. We investigated the effects of physicochemical properties of soil on the diversity and activity of denitrifiers in the top-soil and sub-soil of two typical montane riparian meadows: a multi-colored and a flood-plain meadow. Illumina MiSeq 2500 sequencing of nirS showed that the multi-colored meadow had greater diversity and abundance of nirS-type denitrifiers than the flood-plain meadow and that the total N content, ammonium content, and denitrification enzyme activity (DEA) in soil differed significantly between the two types of meadows. The abundances of dominant denitrifiers at phylum and genus levels showed different responses to the two soil layers of the two meadow types. In top-soils, the highest abundance of Firmicutes was recorded in the multi-colored meadow, while in the flood-plain meadow, there was the highest abundance of Proteobacteria. The Actinobacteria abundance was the highest in top-soil and sub-soil of the flood-plain meadow. The abundance of Chloroflexi was the highest in top-soil of the flood-plain meadow and in sub-soil of the multi-colored meadow. The diversity of denitrifying bacteria was strongly influenced by variations of soil properties down the soil profile. Spearman's rank correlation analyses showed that the diversity and community composition of denitrifying bacteria were strongly associated with most of the soil properties. Therefore, physicochemical soil properties, and particularly the organic carbon, nitrate, and ammonium contents, influence the diversity and abundance of denitrifiers in soil.
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Affiliation(s)
- Xiaoli Han
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, 030801, China
| | - Chunguo Huang
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Shahbaz Khan
- College of Agriculture, Shanxi Agricultural University, Taigu, 030801, China
| | - Yunxiang Zhang
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, 030801, China
| | - Yinglong Chen
- Institute of Agriculture, UWA School of Agriculture and Environment, The University of Western Australia, Perth, 6009, Australia
- Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, 712100, China
| | - Jinping Guo
- College of Forestry, Shanxi Agricultural University, Taigu, 030801, China.
- Shanxi Key Laboratory of Functional Oil Tree Cultivation and Research, Taigu, 030801, China.
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Wang S, Liu W, Zhao S, Wang C, Zhuang L, Liu L, Wang W, Lu Y, Li F, Zhu G. Denitrification is the main microbial N loss pathway on the Qinghai-Tibet Plateau above an elevation of 5000 m. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 696:133852. [PMID: 31442722 DOI: 10.1016/j.scitotenv.2019.133852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
Soil nitrogen (N) deficiency is the major factor contributing to low primary productivity on the Qinghai-Tibet Plateau. However, most of our understanding of N cycling is still based on human disturbed environments, and the microbial mechanisms governing N loss in low primary productivity environment remain unclear. This study explores three microbial N loss pathways in eight wetland and dryland soil profiles from the Qinghai-Tibet Plateau, at an elevation of above 5000 m with little human activity, using 15N isotopic tracing slurry technology, quantitative PCR, and high-throughput sequencing. No denitrifying anaerobic methane oxidation was detected. Anammox occurred in two of the wetland (n = 4) and dryland (n = 4) soil profiles, while denitrification widely occurred and was the dominant N loss pathway in all samples. Where denitrification and anammox co-occurred, both abundance and activity were higher in wetland than in dryland soils and higher in surface than in subsurface soils. In comparison with non-anammox sites, nitrate levels initiate anammox-related N cycling. High-throughput sequencing and network analysis of nirK, nirS, nosZ, and hzsB gene communities showed that Bradyrhizobiaceae (a family of rhizobia) may play a dominant role in N loss pathways in this region. Given the geological evolution and relatively undisturbed habitat, these findings strongly suggest that denitrification is the dominant N loss pathway in terrestrial habitats of the Qing-Tibet Plateau with minimal anthropogenic activity.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weiyue Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Cheng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Linjie Zhuang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lu Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weidong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yonglong Lu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Sciences and Technology, Guangzhou 510650, China
| | - Guibing Zhu
- 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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10
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Wang C, Li J, Wu Y, Song Y, Liu R, Cao Z, Cui Y. Shifts of the nirS and nirK denitrifiers in different land use types and seasons in the Sanjiang Plain, China. J Basic Microbiol 2019; 59:1040-1048. [PMID: 31469176 DOI: 10.1002/jobm.201900192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 08/10/2019] [Indexed: 11/12/2022]
Abstract
Denitrification is a key nitrogen removal process that involves many denitrifying bacteria. In this study, the denitrification performance was estimated for soil samples from different land use types including farmland soil, restored wetland soil, and wetland soil. The quantitative real-time polymerase chain reaction results showed that the average abundance of nirS and nirK genes was notably affected by seasonal changes, increasing from 2.34 × 10 6 and 2.81 × 10 6 to 1.97 × 10 6 and 4.55 × 10 6 gene copies/g of dry soil, respectively, from autumn to spring. This suggests that the abundance of nirS and nirK denitrifiers in spring is higher than those in autumn. Furthermore, the abundance of nirS and nirK genes was higher in the farmland soil than in restored wetland soil and wetland soil in both seasons. According to the analyses of MiSeq sequencing of nirS and nirK genes, Halobacteriaceae could be used as a special strain to distinguish wetland soil from farmland soil and restored wetland soil. Furthermore, redundancy analysis indicated that the soil environmental variables of total carbon, total nitrogen, moisture content, and organic matter were the main factors affecting the community structures of nirS and nirK denitrifiers existing in wetland soil. These findings could contribute to understanding the differences in nirS and nirK denitrifiers between different land use types during seasonal changes.
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Affiliation(s)
- Chunyong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Juan Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuntao Wu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yi Song
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zicheng Cao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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11
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Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16132298. [PMID: 31261730 PMCID: PMC6651097 DOI: 10.3390/ijerph16132298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/27/2022]
Abstract
Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NOx--N in the sediment, NH4+-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.
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12
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Nadeau SA, Roco CA, Debenport SJ, Anderson TR, Hofmeister KL, Walter MT, Shapleigh JP. Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients. Environ Microbiol 2019; 21:1255-1266. [DOI: 10.1111/1462-2920.14587] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Sarah A. Nadeau
- Department of Biological & Environmental Engineering Cornell University Ithaca NY USA
| | | | - Spencer J. Debenport
- Soil and Crop Sciences Section, School of Integrative Plant Science Cornell University Ithaca NY USA
| | - Todd R. Anderson
- Division of Natural Sciences and Mathematics Keuka College Keuka Park NY USA
| | | | - M. Todd Walter
- Department of Biological & Environmental Engineering Cornell University Ithaca NY USA
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13
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Li J, Wang JT, Hu HW, Cai ZJ, Lei YR, Li W, Zhang MY, Li ZM, Zhu YN, Cui LJ. Changes of the denitrifying communities in a multi-stage free water surface constructed wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:1419-1425. [PMID: 30308829 DOI: 10.1016/j.scitotenv.2018.09.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/09/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
Microorganisms play crucial roles in the nitrogen removal processes of wetlands. However, the key functional genes and microbes related to the nitrogen removal remain largely unknown in the free water surface constructed wetland (FWS CW). Here we studied the abundances of denitrifiers by targeting the key functional genes (nirS, nirK and nosZ) and investigated the community compositions of denitrifiers and their correlations with the abiotic variables in a FWS CW. The increase of nosZ/(nirS + nirK) and nirS/nirK ratios in the outlet indicated a shift of denitrifiers' communities which tended to release less nitrous oxide at the genetic potential level. The denitrifiers dominated the bacterial community which also remarkably changed from the inlet to the outlet. PICRUSt analysis revealed that the denitrifiers contributed to 39.1% of the nitrogen metabolism, 38.9% of the amino acid metabolism and 25.6% of the amino acid related enzymes. Four bacterial genera including Hydrogenophaga, Hylemonella, Aquabacterium and Cellvibrio were detected as the putative keystone denitrifiers. The abundance (nirS, nirK and nosZ) and the relative abundance of putative keystone denitrifiers were significantly correlated with total organic carbon, oxidation-reduction potential and C/N ratio, which could be regarded as the determinants for the denitrification process in the free water.
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Affiliation(s)
- Jing Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Zhang-Jie Cai
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Yin-Ru Lei
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Wei Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Man-Yin Zhang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Zong-Ming Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yi-Nuo Zhu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China
| | - Li-Juan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing 100091, China; Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing 101399, China.
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14
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Wittorf L, Jones CM, Bonilla-Rosso G, Hallin S. Expression of nirK and nirS genes in two strains of Pseudomonas stutzeri harbouring both types of NO-forming nitrite reductases. Res Microbiol 2018; 169:343-347. [PMID: 29752987 DOI: 10.1016/j.resmic.2018.04.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 12/01/2022]
Abstract
Reduction of nitrite to nitric oxide in denitrification is catalysed by two different nitrite reductases, encoded by nirS or nirK. Long considered mutually exclusive and functionally redundant in denitrifying bacteria, we show expression of both genes co-occurring in Pseudomonas stutzeri. The differential expression patterns between strain AN10 and JM300 in relation to oxygen and nitrate and their different denitrification phenotypes, with AN10 reducing nitrate more rapidly and accumulating nitrite, suggest that nirS and nirK can have different roles. Dissimilar gene arrangements and transcription factors in the nir gene neighbourhoods could explain the observed differences in gene expression and denitrification activity.
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Affiliation(s)
- Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden.
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden.
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden.
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden.
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15
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Lee SH, Megonigal PJ, Kang H. How do Elevated CO 2 and Nitrogen Addition Affect Functional Microbial Community Involved in Greenhouse Gas Flux in Salt Marsh System. MICROBIAL ECOLOGY 2017; 74:670-680. [PMID: 28331950 DOI: 10.1007/s00248-017-0960-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
Salt marshes are unique ecosystem of which a microbial community is expected to be affected by global climate change. In this study, by using T-RFLP analysis, quantitative PCR, and pyrosequencing, we comprehensively analyzed the microbial community structure responding to elevated CO2 (eCO2) and N addition in a salt marsh ecosystem subjected to CO2 manipulation and N addition for about 3 years. We focused on the genes of microbes relevant to N-cycling (denitrification and nitrification), CH4-flux (methanogens and methanotrophs), and S-cycling (sulfate reduction) considering that they are key functional groups involved in the nutrient cycle of salt marsh system. Overall, this study suggests that (1) eCO2 and N addition affect functional microbial community involved in greenhouse gas flux in salt marsh system. Specifically, the denitrification process may be facilitated, while the methanogenesis may be impeded due to the outcompeting of sulfate reduction by eCO2 and N. This implies that future global change may cause a probable change in GHGs flux and positive feedback to global climate change in salt marsh; (2) the effect of eCO2 and N on functional group seems specific and to contrast with each other, but the effect of single factor would not be compromised but complemented by combination of two factors. (3) The response of functional groups to eCO2 and/or N may be directly or indirectly related to the plant community and its response to eCO2 and/or N. This study provides new insights into our understanding of functional microbial community responses to eCO2 and/or N addition in a C3/C4 plant mixed salt marsh system.
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Affiliation(s)
- Seung-Hoon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea
| | | | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea.
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16
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Meng H, Wu R, Wang YF, Gu JD. A comparison of denitrifying bacterial community structures and abundance in acidic soils between natural forest and re-vegetated forest of Nanling Nature Reserve in southern China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 198:41-49. [PMID: 28500915 DOI: 10.1016/j.jenvman.2017.04.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/02/2017] [Accepted: 04/22/2017] [Indexed: 06/07/2023]
Abstract
Denitrification plays a key role in converting reactive nitrogen species to dinitrogen gas back into the atmosphere to maintain the equilibrium of nitrogen cycling in ecosystems. In this study, functional genes of nirK and nosZ were used to detect the community structure and abundance of denitrifying microorganisms in acidic forest soils in southern China. Three sets of factors were considered for a comparison among 5 forests, including forest types (natural vs. re-vegetated), depths (surface layer vs. lower layer) and seasons (winter vs. summer). The community of nirK gene detected from these acidic forest soils was closely related to Proteobacteria especially α-Proteobacteria and uncultured soil sequences, while that of nosZ gene was affiliated with the α-, β- and γ-Proteobacteria. Higher diversity of denitrifiers was observed in re-vegetated forest soils than natural ones. Not only the community but also the abundance showed significant differences between forest types as well as depths. The abundance of denitrifiers ranged from 105 to 107 gene copies g-1 dry soil in this study. For nirK gene, the abundance was much higher in the lower layer than surface layer in both forest types, and the differences between winter and summer in natural forest soils were higher than those in re-vegetated forest soils. The abundance of nosZ and nirK genes showed a similar trend in natural forest, but the former was higher in matured forest than re-vegetated forest. This study provided a direct comparison on community composition and abundance of denitrifying bacteria in natural and re-vegetated acidic forest soils to allow further assessment of the nitrogen cycling.
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Affiliation(s)
- Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, No. 233, Guangshan 1st Road, Guangzhou, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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17
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Fang L, Wang M, Cai L, Cang L. Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:14627-14636. [PMID: 28452034 DOI: 10.1007/s11356-017-9029-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.
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Affiliation(s)
- Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Mengke Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Lin Cai
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Long Cang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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18
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Paranychianakis NV, Tsiknia M, Kalogerakis N. Pathways regulating the removal of nitrogen in planted and unplanted subsurface flow constructed wetlands. WATER RESEARCH 2016; 102:321-329. [PMID: 27379728 DOI: 10.1016/j.watres.2016.06.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Single-stage constructed wetlands (CWs) are characterized by a low potential for N removal. Understanding the pathways regulating N cycling as well as their dependence on environmental variables might improve the potential of CWs for N removal and results in more accurate simulation tools. In this study we employed qPCR targeting marker functional genes (amoA, nirK, nirS, clade I and II nosZ) or microorganisms (anammox) regulating key pathways of N cycling to unravel their relative importance. Furthermore, the influence of plant species on treatment performance was studied. Our findings indicated nitrification-denitrification as the principal route of N removal in CWs, while anammox did not have a strong contribution. Evidence was also arisen that ammonia oxidizing archaea (AOA) contributed on NH3 oxidation. Overall, plant species had a weak effect on the abundance of N functional genes (amoA of AOA), but it strongly affected the performance of CWs in terms of N removal in the following order: unplanted < Phragmites communis < Typha latifolia. These findings suggest that plant species stimulate N removal by upregulating the rates that the responsible biochemical pathways operate, probably by increasing O2 supply. In addition, our study revealed differences in indicators linked to N2O emissions. The abundance of clade II nosZ genes remained low across the season scaling down a strong contribution in the reduction of the emitted N2O. The increasing ratios of nosZ/Σnir and nirS/nirK with the progress of season indicate a shift in the composition of denitrifiers towards strains with a lower genetic potential for N2O release. Similar trends were observed among the treatments but the mechanisms differed. The planted treatments stimulated an increase in the ΣnosZ/Σnir ratio, while the unplanted an increase in the nirS/nirK ratio.
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Affiliation(s)
- Nikolaos V Paranychianakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece.
| | - Myrto Tsiknia
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
| | - Nicolas Kalogerakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis, 73100, Chania, Greece
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19
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Wittorf L, Bonilla-Rosso G, Jones CM, Bäckman O, Hulth S, Hallin S. Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:486-492. [PMID: 26929183 DOI: 10.1111/1758-2229.12393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/27/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
Denitrification is of global significance for the marine nitrogen budget and the main process for nitrogen loss in coastal sediments. This facultative anaerobic respiratory pathway is modular in nature and the final step, the reduction of nitrous oxide (N2 O), is performed by microorganisms with a complete denitrification pathway as well as those only capable of N2 O reduction. Fluctuating oxygen availability is a significant driver of denitrification in sediments, but the effects on the overall N2 O-reducing community that ultimately controls the emission of N2 O from marine sediments is not well known. To investigate the effects of different oxygen regimes on N2 O reducing communities, coastal marine surface sediment was incubated in microcosms under oxic, anoxic or oscillating oxygen conditions in the overlying water for 137 days. Quantification of the genetic potential for denitrification, anammox and respiratory ammonification indicated that denitrification supported nitrogen removal in these sediments. Furthermore, denitrifiers with a complete pathway were identified as the dominant community involved in N2 O reduction, rather than organisms that are only N2 O reducers. Specific lineages within each group were associated with different oxygen regimes suggesting that oxygen availability in the overlying water is associated with habitat partitioning of N2 O reducers in coastal marine surface sediments.
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Affiliation(s)
- Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ola Bäckman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Hulth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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20
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Fan Z, Han RM, Ma J, Wang GX. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14102-14114. [PMID: 27048324 DOI: 10.1007/s11356-016-6390-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.
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Affiliation(s)
- Zhou Fan
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Rui-Ming Han
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ma
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Guo-Xiang Wang
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China.
- Nanjing Normal University, School of Geography Science, Wenyuan Road 1, Nanjing, 210023, China.
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Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers. BMC Genomics 2016; 17:155. [PMID: 26923558 PMCID: PMC4770552 DOI: 10.1186/s12864-016-2465-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/12/2016] [Indexed: 01/09/2023] Open
Abstract
Background Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset. Results Division of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3′ site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers. Conclusion The previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2465-0) contains supplementary material, which is available to authorized users.
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Powell JR, Welsh A, Hallin S. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties. Ecology 2015; 96:1985-93. [PMID: 26378320 DOI: 10.1890/14-1127.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAIC(c) = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAIC(c) = 12.02], and the abundance of one denitrifier genotype [ΔAIC(c) = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). This approach provides a valuable tool for explicitly linking microbial communities to ecosystem functioning. By making this link, we have demonstrated that including aspects of microbial community structure and diversity in biogeochemical models can improve predictions of nutrient cycling in ecosystems and enhance our understanding of ecosystem functionality.
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Tsiknia M, Paranychianakis NV, Varouchakis EA, Nikolaidis NP. Environmental drivers of the distribution of nitrogen functional genes at a watershed scale. FEMS Microbiol Ecol 2015; 91:fiv052. [PMID: 25962763 DOI: 10.1093/femsec/fiv052] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 11/14/2022] Open
Abstract
To date only few studies have dealt with the biogeography of microbial communities at large spatial scales, despite the importance of such information to understand and simulate ecosystem functioning. Herein, we describe the biogeographic patterns of microorganisms involved in nitrogen (N)-cycling (diazotrophs, ammonia oxidizers, denitrifiers) as well as the environmental factors shaping these patterns across the Koiliaris Critical Zone Observatory, a typical Mediterranean watershed. Our findings revealed that a proportion of variance ranging from 40 to 80% of functional genes abundance could be explained by the environmental variables monitored, with pH, soil texture, total organic carbon and potential nitrification rate being identified as the most important drivers. The spatial autocorrelation of N-functional genes ranged from 0.2 to 6.2 km and prediction maps, generated by cokriging, revealed distinct patterns of functional genes. The inclusion of functional genes in statistical modeling substantially improved the proportion of variance explained by the models, a result possibly due to the strong relationships that were identified among microbial groups. Significant relationships were set between functional groups, which were further mediated by land use (natural versus agricultural lands). These relationships, in combination with the environmental variables, allow us to provide insights regarding the ecological preferences of N-functional groups and among them the recently identified clade II of nitrous oxide reducers.
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Affiliation(s)
- Myrto Tsiknia
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Nikolaos V Paranychianakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Emmanouil A Varouchakis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
| | - Nikolaos P Nikolaidis
- School of Environmental Engineering, Technical University of Crete, Polytechnioupolis 73100 Chania, Greece
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Herbert RB, Winbjörk H, Hellman M, Hallin S. Nitrogen removal and spatial distribution of denitrifier and anammox communities in a bioreactor for mine drainage treatment. WATER RESEARCH 2014; 66:350-360. [PMID: 25233117 DOI: 10.1016/j.watres.2014.08.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/15/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
Mine drainage water may contain high levels of nitrate (NO3(-)) due to undetonated nitrogen-based explosives. The removal of NO3(-) and nitrite (NO2(-)) in cold climates through the microbial process of denitrification was evaluated using a pilot-scale fixed-bed bioreactor (27 m(3)). Surface water was diverted into the above-ground bioreactor filled with sawdust, crushed rock, and sewage sludge. At hydraulic residence times of ca.15 h and with the addition of acetate, NO3(-) and NO2(-) were removed to below detection levels at a NO3(-) removal rate of 5-10 g N m(-3) (bioreactor material) d(-1). The functional groups contributing to nitrogen removal in the bioreactor were studied by quantifying nirS and nirK present in denitrifying bacteria, nosZI and nosZII genes from the nitrous oxide - reducing community, and a taxa-specific part of the16S rRNA gene for the anammox community. The abundances of nirS and nirK were almost 2 orders of magnitude greater than the anammox specific 16S rRNA gene, indicating that denitrification was the main process involved in nitrogen removal. The spatial distribution of the quantified genes was heterogeneous in the bioreactor, with trends observed in gene abundance as a function of depth, distance from the bioreactor inlet, and along specific flowpaths. There was a significant relationship between the abundance of nirS, nirK, and nosZI genes and depth in the bioreactor, such that the abundance of organisms containing these genes may be controlled by oxygen diffusion and substrate supply in the partially or completely water-saturated material. Among the investigated microbial functional groups, nirS and anammox bacterial 16S rRNA genes exhibited a systematic trend of decreasing and increasing abundance, respectively, with distance from the inlet, which suggested that the functional groups respond differently to changing environmental conditions. The greater abundance of nirK along central flowpaths may indicate that the bioreactor design favored preferential flow along these flowpaths, away from the sides of the bioreactor. An improved bioreactor design should consider the role of preferential flowpaths and the heterogeneous distribution of the genetic potential for denitrification, nitrous oxide reduction and anammox on bioreactor function.
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Affiliation(s)
- Roger B Herbert
- Uppsala University, Department of Earth Sciences, Villavägen 16, SE-752 36 Uppsala, Sweden.
| | | | - Maria Hellman
- Swedish University of Agricultural Sciences, Department of Microbiology, Box 7025, SE-750 07 Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Microbiology, Box 7025, SE-750 07 Uppsala, Sweden
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Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 2014; 9:e114118. [PMID: 25436772 PMCID: PMC4250227 DOI: 10.1371/journal.pone.0114118] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/05/2014] [Indexed: 11/19/2022] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N2O emissions.
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Morrissey EM, Franklin RB. Resource effects on denitrification are mediated by community composition in tidal freshwater wetlands soils. Environ Microbiol 2014; 17:1520-32. [DOI: 10.1111/1462-2920.12575] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/16/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Ember M. Morrissey
- Department of Biology; Virginia Commonwealth University; 1000 W Cary Street Richmond VA 23284 USA
| | - Rima B. Franklin
- Department of Biology; Virginia Commonwealth University; 1000 W Cary Street Richmond VA 23284 USA
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Uchida Y, Wang Y, Akiyama H, Nakajima Y, Hayatsu M. Expression of denitrification genes in response to a waterlogging event in a Fluvisol and its relationship with large nitrous oxide pulses. FEMS Microbiol Ecol 2014; 88:407-23. [PMID: 24592962 DOI: 10.1111/1574-6941.12309] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/11/2014] [Accepted: 02/18/2014] [Indexed: 11/30/2022] Open
Abstract
The contributions of large N2 O pulses following waterlogging to the annual cumulative N2 O productions were significant in a Fluvisol. To uncover the mechanisms underlying these large N2 O pulses, a Fluvisol sampled from an agricultural field in Japan was subjected to waterlogging during incubation. Larger N2 O emissions were observed in intact soil cores when compared to emissions from sieved soils, indicating the importance of soil properties. The most important factor controlling the magnitude of the N2 O pulses after waterlogging was the soil moisture prior to waterlogging. The major pathway for N2 O production was denitrification. Quantitative PCR and quantitative RT-PCR analyses showed that the denitrification genes (nirS, nirK, and nosZ) correlated with N2 O emissions at the mRNA level but not at the DNA level. The change in denitrification gene mRNA levels was more prominent in the 0- to 1-cm soil compared with the 1- to 3-cm soil. Water-soluble and hot-water-soluble carbon contents also showed the highest amount in the 0- to 1-cm soil. These indicate that there was a strong variation in soil microbial properties over very small changes in soil depth, and this variation is important in determining the magnitude of N2 O emissions.
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Affiliation(s)
- Yoshitaka Uchida
- Task Force for Innovation in Life, Resources and Environment Sciences, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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