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Zhang X, Song X, Wang T, Huang L, Ma H, Wang M, Tan D. The responses to long-term nitrogen addition of soil bacterial, fungal, and archaeal communities in a desert ecosystem. Front Microbiol 2022; 13:1015588. [PMID: 36312972 PMCID: PMC9606763 DOI: 10.3389/fmicb.2022.1015588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 10/29/2023] Open
Abstract
Nitrogen (N) deposition is a worldwide issue caused by human activity. Long-term deposition of N strongly influences plant productivity and community composition. However, it is still unclear how the microbial community responds to long-term N addition in a desert ecosystem. Therefore, a long-term experiment was conducted in the Gurbantonggut Desert in northwestern China in 2015. Four N addition rates, 0 (CK), 5 (N1), 20 (N2), and 80 (N3) kg N ha-1 yr.-1, were tested and the soil was sampled after 6 years of N addition. High-throughput sequencing (HTS) was used to analyze the soil microbial composition. The HTS results showed that N addition had no significant effect on the bacterial α-diversity and β-diversity (p > 0.05) but significantly reduced the archaeal β-diversity (p < 0.05). The fungal Chao1 and ACE indexes in the N2 treatment increased by 24.10 and 26.07%, respectively. In addition, N addition affected the bacterial and fungal community structures. For example, compared to CK, the relative abundance of Actinobacteria increased by 17.80%, and the relative abundance of Bacteroidetes was reduced by 44.46% under N3 treatment. Additionally, N addition also changed the bacterial and fungal community functions. The N3 treatment showed increased relative abundance of nitrate-reducing bacteria (27.06% higher than CK). The relative abundance of symbiotrophic fungi was increased in the N1 treatment (253.11% higher than CK). SOC and NH4 +-N could explain 62% of the changes in the fungal community function. N addition can directly affect the bacterial community function or indirectly through NO3 --N. These results suggest that different microbial groups may have various responses to N addition. Compared with bacteria and fungi, the effect of N addition was less on the archaeal community. Meanwhile, N-mediated changes of the soil properties play an essential role in changes in the microbial community. The results in the present study provided a reliable basis for an understanding of how the microbial community in a desert ecosystem adapts to long-term N deposition.
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Affiliation(s)
- Xuan Zhang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Xin Song
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, College of Ecology, Lanzhou University, Lanzhou, China
| | - Taotao Wang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Lei Huang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Haiyang Ma
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Mao Wang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Dunyan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
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Chen W, Su F, Nie Y, Zhong B, Zheng Y, Mo J, Xiong B, Lu X. Divergent responses of soil microbial functional groups to long-term high nitrogen presence in the tropical forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153251. [PMID: 35051470 DOI: 10.1016/j.scitotenv.2022.153251] [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: 08/31/2021] [Revised: 01/04/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
A massive rise in atmospheric nitrogen deposition (ND) has threatened ecosystem health through accelerating soil nitrogen (N) cycling rates. While soil microbes serve a crucial function in soil N transformation, it remains poorly understood on how excess ND affects microbial functional populations regulating soil N transformation in tropical forests. To address this gap, we conducted 13-year N (as NH4NO3) addition experiments in one N-rich tropical primary forest (PF) and two N-poor tropical reforested forests (rehabilitated and disturbed) in South China. Based on our data, 13-year N introduction markedly enhanced soil N2O generation in all forests, regardless of soil N status, but microbial functional groups showed divergent responses to excess N addition among the studied forests. In the PF, long-term N introduction markedly decreased presence of bacterial 16S rRNA gene, nitrifier (amoA) and denitrifier genes (nirK, nirS and nosZ) and bacteria/fungi ratio, which could be attributed to the decreases in soil pH, dissolved organic carbon to N ratio and understory plant richness. In the two reforested forests, however, long-term N introduction generally did neither alter soil properties nor the abundance of most microbial groups. We further found that the elevated N2O generation was related to the increased soil N availability and decreased nosZ abundance, and the PF has the highest N2O generation than the other two forests. Overall, our data indicates that the baseline soil N status may dominate response of microbial functional groups to ND in tropical forests, and N-rich forests are more responsive to excess N inputs, compared to those with low-N status. Forests with high soil N status can produce more N2O than those with low-N status. With the spread of elevated ND from temperate to tropical zones, tropical forests should merit more attention because ecosystem N saturation may be common and high N2O emission will occur.
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Affiliation(s)
- Weibin Chen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fanglong Su
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yanxia Nie
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Buqing Zhong
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yong Zheng
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Jiangming Mo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Binghong Xiong
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiankai Lu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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3
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Ding L, Zhou J, Li Q, Tang J, Chen X. Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones. MICROBIAL ECOLOGY 2022; 83:393-407. [PMID: 33893533 DOI: 10.1007/s00248-021-01746-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.
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Affiliation(s)
- Lilian Ding
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jingyi Zhou
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Qiyao Li
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jianjun Tang
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
| | - Xin Chen
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
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Changes in soil ammonia oxidizers and potential nitrification after clear-cutting of boreal forests in China. World J Microbiol Biotechnol 2021; 37:126. [PMID: 34180026 DOI: 10.1007/s11274-021-03087-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
The Korean pine and broad-leaved mixed forests are the most typical and complete ecosystem among the global boreal forests, with extremely important ecological functions. However, few studies on the changes of soil ammonia oxidizers and potential nitrification after clear-cutting of forests are reported. In this study, in contrast to primary Korean pine forests, nitrate (NO3-) was significantly higher in secondary broad-leaved forests, while ammonium (NH4+) was on the contrary. The abundance of ammonia-oxidizing bacteria (AOB) was greatly higher in secondary broad-leaved forests, while levels of ammonia-oxidizing archaea (AOA) were not significantly different between them. The significant differences of community structure of AOA and AOB were observed in different forest types and soil layers. Compared with AOA, community compositions of AOB was more sensitive to forest type. The dominant groups of AOA were Nitrososphaera and Nitrosotalea, and the dominant group of AOB was Nitrosospira, of which Nitrosospira cluster 2 and 4 were functional groups with highly activity. Soil potential nitrification rate (PNR) was higher in secondary broad-leaved forests. Furthermore, PNR and AOB abundance had a significant positive correlation, but no significant correlation with AOA abundance. These results provide insights into the soil nitrogen balance and effects on forest restoration after clear-cutting.
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Gao GF, Peng D, Wu D, Zhang Y, Chu H. Increasing Inundation Frequencies Enhance the Stochastic Process and Network Complexity of the Soil Archaeal Community in Coastal Wetlands. Appl Environ Microbiol 2021; 87:e02560-20. [PMID: 33741614 PMCID: PMC8208137 DOI: 10.1128/aem.02560-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/07/2021] [Indexed: 01/03/2023] Open
Abstract
Coastal wetlands are experiencing frequent flooding because of global climate changes, such as the rising sea level. Despite the key role of archaea in soil biogeochemical cycles, the assembly processes and co-occurrence patterns of archaeal communities in coastal wetlands in response to increasing inundation frequencies remain elusive. In this study, we established an in situ mesocosm with an inundation frequency gradient to investigate the response of soil archaeal community toward increasing inundation frequencies in monocultures of Spartina alterniflora and a mangrove species, Kandelia obovata Both neutral community model and null model analyses suggested that stochastic processes are dominant in governing the archaeal community assembly and that the stochastic processes are enhanced with increasing inundation frequencies. Increasing inundation frequencies significantly increased the community niche width. Moreover, archaeal community in S. alterniflora soil displayed lower niche overlap and higher stochasticity than in K. obovata soil. Co-occurrence network analysis revealed that the network complexity increases with increase in the inundation frequencies. Soil water content is the most decisive factor influencing the archaeal communities. Overall, we found that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community in coastal wetlands. This study could enhance our understanding on the response of soil archaeal communities in coastal wetlands toward global change.IMPORTANCE Coastal wetlands, subjected to regular disturbances by periodic tides, are highly productive and important in the regulation of climate change. However, the assembly mechanisms and co-occurrence patterns of soil archaeal communities in coastal areas remain poorly known, especially for their responses to increasing inundation frequencies. In this study, we aimed at unraveling these uncertainties by studying typical estuarine ecosystems in southern China. We show that increasing inundation frequencies enhance the stochastic processes and network complexity of the soil archaeal community. This study offers a new path for an improved understanding of archaeal community assembly and species coexistence in coastal environments, with a special focus on the role of inundation frequency.
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Affiliation(s)
- Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Dan Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Di Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yihui Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
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6
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Liu J, Liu W, Zhang Y, Chen C, Wu W, Zhang TC. Microbial communities in rare earth mining soil after in-situ leaching mining. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142521. [PMID: 33035989 DOI: 10.1016/j.scitotenv.2020.142521] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/19/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China.
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding, China
| | - Yingbin Zhang
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang, China
| | - Chongjun Chen
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Tian C Zhang
- Department of Civil & Environmental Engineering, University of Nebraska-Lincoln, Omaha, USA
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7
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Netherway T, Bengtsson J, Krab EJ, Bahram M. Biotic interactions with mycorrhizal systems as extended nutrient acquisition strategies shaping forest soil communities and functions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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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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Zou Y, Ning D, Huang Y, Liang Y, Wang H, Duan L, Yuan T, He Z, Yang Y, Xue K, Van Nostrand JD, Zhou J. Functional structures of soil microbial community relate to contrasting N 2O emission patterns from a highly acidified forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138504. [PMID: 32302850 DOI: 10.1016/j.scitotenv.2020.138504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 05/23/2023]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas contributing to global climate change. Emissions of N2O from acidic forests are increasing rapidly; however, little is known about the mechanisms driving these emissions. We analyzed soil samples from a high N2O emission area (HEA, 224-601 μg N m-2 h-1) and an adjacent low emission area (LEA, 20-30 μg N m-2 h-1) of a highly acidified forest. HEA showed similar carbon and nitrogen (N) pools and microbial biomass to LEA, but significantly higher moisture and extractable nutrients than LEA did. GeoChip 4 detected 298 gene families (unadjusted P < 0.05; 94, adjusted P < 0.05) showing significantly different structures between HEA and LEA. Both areas had highly diverse N cycling functional genes. However, HEA had higher relative abundances of nor, P450nor, and archaeal nitrifier nirK, which provided evidence for the importance of denitrifiers in N2O emission. HEA also showed significantly higher relative abundances of lignin- and cellulose-degrading genes, oxygen-limitation-response genes and denitrifier ppk, but lower abundances of N- and phosphorus (P) -limitation-response genes especially denitrifier pstS, corresponding to the higher moisture and extractable nutrients conducive to denitrification. The moisture, extractable nutrients and pH explained over 50% variation in microbial communities, and extractable P appeared as the key factor driving community variation and consequently regulated N2O production. CAPSULE ABSTRACT: N2O emission in highly acidified forest soils was related to the diverse N functional genes, especially denitrification genes, and was affected by soil properties.
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Affiliation(s)
- Yina Zou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Yong Huang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yuting Liang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hui Wang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
| | - Lei Duan
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Yunfeng Yang
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Kai Xue
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory on Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK, USA; Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Yang X, Ni K, Shi Y, Yi X, Ji L, Ma L, Ruan J. Heavy nitrogen application increases soil nitrification through ammonia-oxidizing bacteria rather than archaea in acidic tea (Camellia sinensis L.) plantation soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137248. [PMID: 32084690 DOI: 10.1016/j.scitotenv.2020.137248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/09/2020] [Accepted: 02/09/2020] [Indexed: 05/20/2023]
Abstract
Nitrogen (N) fertilizer is widely used in agricultural ecosystems and influences N transformation processes in the soil such as nitrification. However, whether nitrification is primarily dominated by ammonia-oxidizing bacteria (AOB) or archaea (AOA) under heavy N application is still under debate. In the present work, the effect of long-term (12 years) N fertilization on soil nitrification and the key influencing factors were investigated in acidic tea plantation soil that received four different rates of N application (0, 119, 285, and 569 kg N ha-1 yr-1). Nitrification potential was measured and partitioned using chemical inhibitors. The abundance of functional genes involved in ammonia oxidation was quantified using quantitative polymerase chain reaction (qPCR). Ammonia-oxidizing communities were identified by shotgun metagenome sequencing. Potential nitrification rate in tea plantation soil was mainly dominated by autotrophic nitrification (PNRA) (71-79%). PNRA and heterotrophic nitrification (PNRH) were both significantly increased by heavy N (569 kg ha-1) application. Moreover, PNRA was mainly due to the contribution of AOB (52-66%) in N-treated soils, and N569 significantly increased the AOB contribution without affecting the AOA contribution. N569 increased the functional gene abundance of AOB and TAO100 (a non-halophilic γ-AOB) but decreased that of AOA. The dominant AOB (Nitrosomonas, Nitrosospira, and Nitrosococcus), AOA (Nitrososphaera and Nitrosopumilus) and commamox (Nitrospira) groups were profoundly altered by long-term N application rates. Partial least squares regression showed that total nitrification (PNRT), PNRA, and PNRAOB were primarily explained by the functional gene abundance of nitrifiers whereas PNRH and PNRAOA were closely associated with soil and pruned litter properties. Moreover, structural equation modeling (SEM) revealed that long-term N application significantly and indirectly affected nitrification potential by directly influencing soil properties, pruned litter properties, and functional gene abundance. Understanding the relative contribution of AOA and AOB to nitrification may help to better regulate N fertilizer use in agricultural ecosystems.
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Affiliation(s)
- Xiangde Yang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China
| | - Kang Ni
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Yuanzhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Xioayun Yi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Lingfei Ji
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lifeng Ma
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, the Ministry of Agriculture, Hangzhou 310008, China.
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11
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Zhang Y, Ma M, Fang H, Qin D, Cheng S, Yuan W. Impacts of nitrogen addition on nitrous oxide emission: Comparison of five nitrous oxide modules or algorithms. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.108963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields. SUSTAINABILITY 2020. [DOI: 10.3390/su12030953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.
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Isobe K, Ise Y, Kato H, Oda T, Vincenot CE, Koba K, Tateno R, Senoo K, Ohte N. Consequences of microbial diversity in forest nitrogen cycling: diverse ammonifiers and specialized ammonia oxidizers. THE ISME JOURNAL 2020; 14:12-25. [PMID: 31481743 PMCID: PMC6908637 DOI: 10.1038/s41396-019-0500-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 11/09/2022]
Abstract
We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.
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Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yuta Ise
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyu Kato
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tomoki Oda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Ryunosuke Tateno
- Field Science Education and Research Center, Kyoto University, Kyoto, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Nobuhito Ohte
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
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14
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Zhang H, Sun H, Zhou S, Bai N, Zheng X, Li S, Zhang J, Lv W. Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems. Sci Rep 2019; 9:9367. [PMID: 31249385 PMCID: PMC6597706 DOI: 10.1038/s41598-019-45877-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/11/2019] [Indexed: 01/27/2023] Open
Abstract
Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.
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Affiliation(s)
- Hanlin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China.,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Huifeng Sun
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Sheng Zhou
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China
| | - Naling Bai
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Xianqing Zheng
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Shuangxi Li
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China.,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China
| | - Weiguang Lv
- Eco-environmental Protection Institute, Shanghai Academy of Agricultural Science, Shanghai, 201403, China. .,Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai, 201403, China. .,Shanghai Key Laboratory of Horticultural Technology, Shanghai, 201403, China. .,Shanghai Engineering Research Center of Low-carbon Agriculture, Shanghai, 201415, China.
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Mohanty SR, Nagarjuna M, Parmar R, Ahirwar U, Patra A, Dubey G, Kollah B. Nitrification Rates Are Affected by Biogenic Nitrate and Volatile Organic Compounds in Agricultural Soils. Front Microbiol 2019; 10:772. [PMID: 31139154 PMCID: PMC6527594 DOI: 10.3389/fmicb.2019.00772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 03/26/2019] [Indexed: 11/18/2022] Open
Abstract
The processes regulating nitrification in soils are not entirely understood. Here we provide evidence that nitrification rates in soil may be affected by complexed nitrate molecules and microbial volatile organic compounds (mVOCs) produced during nitrification. Experiments were carried out to elucidate the overall nature of mVOCs and biogenic nitrates produced by nitrifiers, and their effects on nitrification and redox metabolism. Soils were incubated at three levels of biogenic nitrate. Soils containing biogenic nitrate were compared with soils containing inorganic fertilizer nitrate (KNO3) in terms of redox metabolism potential. Repeated NH4–N addition increased nitrification rates (mM NO31- produced g-1 soil d-1) from 0.49 to 0.65. Soils with higher nitrification rates stimulated (p < 0.01) abundances of 16S rRNA genes by about eight times, amoA genes of nitrifying bacteria by about 25 times, and amoA genes of nitrifying archaea by about 15 times. Soils with biogenic nitrate and KNO3 were incubated under anoxic conditions to undergo anaerobic respiration. The maximum rates of different redox metabolisms (mM electron acceptors reduced g-1 soil d-1) in soil containing biogenic nitrate followed as: NO31- reduction 4.01 ± 0.22, Fe3+ reduction 5.37 ± 0.12, SO42- reduction 9.56 ± 0.16, and CH4 production (μg g-1 soil) 0.46 ± 0.05. Biogenic nitrate inhibited denitrificaton 1.4 times more strongly compared to mineral KNO3. Raman spectra indicated that aliphatic hydrocarbons increased in soil during nitrification, and these compounds probably bind to NO3 to form biogenic nitrate. The mVOCs produced by nitrifiers enhanced (p < 0.05) nitrification rates and abundances of nitrifying bacteria. Experiments suggest that biogenic nitrate and mVOCs affect nitrification and redox metabolism in soil.
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Affiliation(s)
| | | | - Rakesh Parmar
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Usha Ahirwar
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Ashok Patra
- ICAR Indian Institute of Soil Science, Bhopal, India
| | - Garima Dubey
- ICAR Indian Institute of Soil Science, Bhopal, India
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Gai X, Liu H, Liu J, Zhai L, Wang H, Yang B, Ren T, Wu S, Lei Q. Contrasting impacts of long-term application of manure and crop straw on residual nitrate-N along the soil profile in the North China Plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:2251-2259. [PMID: 30292118 DOI: 10.1016/j.scitotenv.2018.09.275] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/20/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
The effects of long-term animal manure application and crop straw incorporation on the migration of carbon (C) and nitrogen (N) deep into the soil profile and the associated N leaching risk in particular have not been thoroughly elucidated to date. Soil profile samples were collected from depths of up to 200 cm from the following four treatments in a 27-year field experiment on the North China Plain: N + phosphorus (P) + potassium (K) fertilizers (NPK), NPK + 22.5 t ha-1 swine manure (NPKM), NPK + 33.7 t ha-1 swine manure (NPKM+) and NPK + straw incorporation (NPKS). The results revealed that long-term manure application and straw incorporation significantly enhanced the soil organic C (SOC) and total N (TN) contents in the upper 20 cm and that this effect was weaker in the deeper soil layers (P < 0.05). Residual nitrate-N (NO3--N) contents at 0 to 40 cm and 120 to 200 cm in the NPKM and NPKM+ were 4-16 and 2-9 times higher than those in the NPK and NPKS, respectively. These results indicated a greater potential for N leaching from manure addition and a higher propensity for NO3--N leaching out of the 40-100 cm soil layer. Pearson relationship analysis demonstrated that NO3--N content was clearly affected by SOC and dissolved organic N (DON) contents along the soil profile (20-200 cm), implying that the higher residual NO3--N contents in the deeper soil from manure addition were partially attributable to the mineralization and nitrification of the downward SOC and DON. Interestingly, a low level of residual NO3--N combined with negative mineralization in the 120-200 cm soil layers of the NPKS treatment was observed, suggesting that straw incorporation promotes soil NO3--N retention. Thus, we concluded that long-term manure application is beneficial for soil NO3--N content retention, whereas long-term straw incorporation benefits NO3--N retention.
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Affiliation(s)
- Xiapu Gai
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongbin Liu
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Liu
- School of Environment and Sustainability and Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK S7N 3H5, Canada
| | - Limei Zhai
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongyuan Wang
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Bo Yang
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianzhi Ren
- Department of Science and Technique Management, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuxia Wu
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuliang Lei
- Key Laboratory of Nonpoint Source Pollution Control, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Tang Y, Yu G, Zhang X, Wang Q, Tian D, Tian J, Niu S, Ge J. Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:653-662. [PMID: 30092521 DOI: 10.1016/j.scitotenv.2018.07.437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 05/02/2023]
Abstract
Because of increases in atmospheric nitrogen (N) deposition worldwide, nutrient imbalances and phosphorus (P) limitations in soil are aggravated, with the result that P fertilizer applications to terrestrial ecosystems worldwide may increase. Nitrification and denitrification in soil are major sources of nitrous oxide emissions, especially in soils treated with fertilizers. However, few researchers have studied how forest soils respond to nutrient additions, so we are not sure how the potential nitrification and denitrification activities (PNA and PDA, respectively) and microbial communities involved in these processes might respond when N and P are added to temperate and subtropical forest soils. We investigated how the PNA, PDA, the abundances and community compositions of nitrifiers and denitrifiers, and environmental properties, including soil pH, soil total and dissolved organic carbon, total and available N and phosphorus P, changed when N and/or P were added to subtropical and temperate forest soils. We quantified the abundance, and analyzed the composition, of functional marker genes of nitrifiers (ammonia-oxidizing bacteria and archaea amoA) and denitrifiers (nirK and nirS) using quantitative PCR and sequencing, respectively. We found that the PNA and PDA in the subtropical soil increased when P was added and PNA in the temperate forest soil increased when either N or P was added. The PNA and PDA were positively correlated with the abundance of ammonia-oxidizing bacteria and nirK-denitrifiers, respectively, in the subtropical forest soil but were not correlated with changes in corresponding community compositions in either of the forest soils. The soil total N to total P ratio explained most of the variabilities in the PNA and PDA in the subtropical forest soils, and the soil exchangeable ammonium concentrations and pH were the main controls on the PNA and PDA, respectively, in the temperate forest soils. Our results indicate that soil environmental conditions have more influence on variations in the PNA and PDA in forest soils fertilized with N and P than the corresponding microbial properties.
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Affiliation(s)
- Yuqian Tang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, Beijing Normal University, Beijing 100875, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Xinyu Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Qiufeng Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Dashuan Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jianping Ge
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, Beijing Normal University, Beijing 100875, China
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18
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Berkelmann D, Schneider D, Engelhaupt M, Heinemann M, Christel S, Wijayanti M, Meryandini A, Daniel R. How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities. Front Microbiol 2018; 9:2381. [PMID: 30364106 PMCID: PMC6191527 DOI: 10.3389/fmicb.2018.02381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Palm oil production in Indonesia increased constantly over the last decades, which led to massive deforestation, especially on Sumatra island. The ongoing conversion of rainforest to agricultural systems results in high biodiversity loss. Here, we present the first RNA-based study on the effects of rainforest transformation to rubber and oil palm plantations in Indonesia for the active soil bacterial communities. For this purpose, bacterial communities of three different converted systems (jungle rubber, rubber plantation, and oil palm plantation) were studied in two landscapes with rainforest as reference by RT-PCR amplicon-based analysis of 16S rRNA gene transcripts. Active soil bacterial communities were dominated by Frankiales (Actinobacteria), subgroup 2 of the Acidobacteria and Alphaproteobacteria (mainly Rhizobiales and Rhodospirillales). Community composition differed significantly between the converted land use systems and rainforest reference sites. Alphaproteobacteria decreased significantly in oil palm samples compared to rainforest samples. In contrast, relative abundances of taxa within the Acidobacteria increased. Most important abiotic drivers for shaping soil bacterial communities were pH, calcium concentration, base saturation and C:N ratio. Indicator species analysis showed distinct association patterns for the analyzed land use systems. Nitrogen-fixing taxa including members of Rhizobiales and Rhodospirillales were associated with rainforest soils while nitrifiers and heat-resistant taxa including members of Actinobacteria were associated with oil palm soils. Predicted metabolic profiles revealed that the relative abundances of genes associated with fixation of nitrogen significantly decreased in plantation soils. Furthermore, predicted gene abundances regarding motility, competition or gene transfer ability indicated rainforest conversion-induced changes as well.
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Affiliation(s)
- Dirk Berkelmann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Martin Engelhaupt
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Melanie Heinemann
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Stephan Christel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Marini Wijayanti
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Meryandini
- Department of Biology, Faculty of Mathematics and Natural Sciences IPB, Bogor Agricultural University, Bogor, Indonesia
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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Environmental Controls on Soil Microbial Communities in a Seasonally Dry Tropical Forest. Appl Environ Microbiol 2018; 84:AEM.00342-18. [PMID: 29959251 DOI: 10.1128/aem.00342-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Several studies have shown that rainfall seasonality, soil heterogeneity, and increased nitrogen (N) deposition may have important effects on tropical forest function. However, the effects of these environmental controls on soil microbial communities in seasonally dry tropical forests are poorly understood. In a seasonally dry tropical forest in the Yucatan Peninsula (Mexico), we investigated the influence of soil heterogeneity (which results in two different soil types, black and red soils), rainfall seasonality (in two successive seasons, wet and dry), and 3 years of repeated N enrichment on soil chemical and microbiological properties, including bacterial gene content and community structure. The soil properties varied with the soil type and the sampling season but did not respond to N enrichment. Greater organic matter content in the black soils was associated with higher microbial biomass, enzyme activities, and abundances of genes related to nitrification (amoA) and denitrification (nirK and nirS) than were observed in the red soils. Rainfall seasonality was also associated with changes in soil microbial biomass and activity levels and N gene abundances. Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria were the most abundant phyla. Differences in bacterial community composition were associated with soil type and season and were primarily detected at higher taxonomic resolution, where specific taxa drive the separation of communities between soils. We observed that soil heterogeneity and rainfall seasonality were the main correlates of soil bacterial community structure and function in this tropical forest, likely acting through their effects on soil attributes, especially those related to soil organic matter and moisture content.IMPORTANCE Understanding the response of soil microbial communities to environmental factors is important for predicting the contribution of forest ecosystems to global environmental change. Seasonally dry tropical forests are characterized by receiving less than 1,800 mm of rain per year in alternating wet and dry seasons and by high heterogeneity in plant diversity and soil chemistry. For these reasons, N deposition may affect their soils differently than those in humid tropical forests. This study documents the influence of rainfall seasonality, soil heterogeneity, and N deposition on soil chemical and microbiological properties in a seasonally dry tropical forest. Our findings suggest that soil heterogeneity and rainfall seasonality are likely the main factors controlling soil bacterial community structure and function in this tropical forest. Nitrogen enrichment was likely too low to induce significant short-term effects on soil properties, because this tropical forest is not N limited.
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Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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21
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Han X, Shen W, Zhang J, Müller C. Microbial adaptation to long-term N supply prevents large responses in N dynamics and N losses of a subtropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:1175-1187. [PMID: 29898524 DOI: 10.1016/j.scitotenv.2018.01.132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/13/2018] [Accepted: 01/14/2018] [Indexed: 06/08/2023]
Abstract
Atmospherically-deposited nitrogen (N) can stimulate complex soil N metabolisms and accumulations over time. Whether long-term (decadal) N deposition effects on soil N transformations and functional microbes differ from the short-term (annual) effects has rarely been assessed. Here we conducted a laboratory 15N tracing study with soil samples from a short-term (one year) N addition site and a long-term (12 years) site in a subtropical forest. The effects of simulated N deposition on soil N2O emissions, N transformation rates and microbial nitrifying and denitrifying genes were determined. Our results showed that: (1) long-term N addition did not change soil N2O fluxes significantly in comparison to the short-term N addition. Denitrification, heterotrophic nitrification and autotrophic nitrification contributed 53%, 28% and 18% to total N2O emissions, respectively. (2) Autotrophic nitrification was the dominant N transformation process, except for the high-N treatment at the long-term site. The magnitude of soil N transformation rates was significantly different among N addition treatments but not between short- and long-term N addition sites. However, long-term N addition changed the responses of specific N transformation rates to N addition markedly, especially for the rates of nitrification, organic N mineralization to NH4+, NO3- immobilization and dissimilatory NO3- reduction to NH4+ (DNRA). (3) Responses of ammonia oxidizing archaea and bacteria (AOA and AOB) were more variable than those of denitrifying N2O-producers (nirK) and denitrifying N2O-reducers (nosZ), particularly at the long-term site. (4) The close correlations among N2O flux, functional genes and soil properties observed at the short-term site were weakened at the long-term site, posing a decreased risk for N losses in the acid subtropical forest soil. There is evidence for an adaptation of functional microbial communities to the prevailing soil conditions and in response to long-term natural and anthropogenic N depositions.
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Affiliation(s)
- Xiaoge Han
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou 510650, China.
| | - Jinbo Zhang
- School of Geography Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Christoph Müller
- Department of Plant Ecology, Justus Liebig University Giessen, Heinrich-Buff Ring 26, 35392 Giessen, Germany; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Isoda R, Hara S, Tahvanainen T, Hashidoko Y. Comparison of Archaeal Communities in Mineral Soils at a Boreal Forest in Finland and a Cold-Temperate Forest in Japan. Microbes Environ 2017; 32:390-393. [PMID: 29109334 PMCID: PMC5745025 DOI: 10.1264/jsme2.me17100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Archaeal communities in mineral soils were compared between a boreal forest in Finland and cold-temperate forest in Japan using 16S rRNA gene-targeted high-throughput sequencing. In boreal soils, Thaumarchaeota Group 1.1c archaea predominated and Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were also detected. In temperate soils, Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea were dominant members at the subsurface, whereas their dominancy was replaced by Thermoplasmata archaea at the subsoil. An analysis of the ammonia monooxygenase subunit A gene of Archaea also indicated the distribution of Thaumarchaeota Group 1.1a-associated and Group 1.1b archaea in these soils.
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Affiliation(s)
- Reika Isoda
- Research Faculty of Agriculture, Hokkaido University
| | - Shintaro Hara
- Research Faculty of Agriculture, Hokkaido University
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Chen J, Nie Y, Liu W, Wang Z, Shen W. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil. Front Microbiol 2017; 8:1384. [PMID: 28790990 PMCID: PMC5522861 DOI: 10.3389/fmicb.2017.01384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+) and dissolved organic carbon concentrations] during the experiment.
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Affiliation(s)
- Jie Chen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China.,College of Life Science, University of Chinese Academy of SciencesBeijing, China.,Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Wei Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Zhengfeng Wang
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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24
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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25
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Xue C, Zhang X, Zhu C, Zhao J, Zhu P, Peng C, Ling N, Shen Q. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization. Sci Rep 2016; 6:28981. [PMID: 27356769 PMCID: PMC4928058 DOI: 10.1038/srep28981] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/13/2016] [Indexed: 12/04/2022] Open
Abstract
Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
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Affiliation(s)
- Chao Xue
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xu Zhang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chen Zhu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jun Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ping Zhu
- Agriculture Environment and Resources Center, Jilin Academy of Agricultural Sciences, Jilin 130033, China
| | - Chang Peng
- Agriculture Environment and Resources Center, Jilin Academy of Agricultural Sciences, Jilin 130033, China
| | - Ning Ling
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization and National Engineering Research Center for Organic-based Fertilizers, Department of Plant Nutrition, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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26
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Nagymáté Z, Homonnay ZG, Márialigeti K. Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms. Microbiol Res 2016; 188-189:80-89. [PMID: 27296965 DOI: 10.1016/j.micres.2016.04.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/24/2016] [Accepted: 04/30/2016] [Indexed: 10/21/2022]
Abstract
Total microbial community structure, and particularly nitrifying communities inhabiting five different small drinking water networks characterized with different water physical and chemical parameters was investigated, using cultivation-based methods and sequence aided Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis. Ammonium ion, originated from well water, was only partially oxidized via nitrite to nitrate in the drinking water distribution systems. Nitrification occurred at low ammonium ion concentration (27-46μM), relatively high pH (7.6-8.2) and over a wide range of dissolved oxygen concentrations (0.4-9.0mgL(-1)). The nitrifying communities of the distribution systems were characterized by variable most probable numbers (2×10(2)-7.1×10(4) MPN L(-1)) and probably originated from the non-treated well water. The sequence aided T-RFLP method revealed that ammonia-oxidizing microorganisms and nitrite-oxidizing Bacteria (Nitrosomonas oligotropha, Nitrosopumilus maritimus, and Nitrospira moscoviensis, 'Candidatus Nitrospira defluvii') were present in different ratios in the total microbial communities of the distinct parts of the water network systems. The nitrate generated by nitrification was partly utilized by nitrate-reducing (and denitrifying) Bacteria, present in low MPN and characterized by sequence aided T-RFLP as Comamonas sp. and Pseudomonas spp. Different environmental factors, like pH, chemical oxygen demand, calculated total inorganic nitrogen content (moreover nitrite and nitrate concentration), temperature had important effect on the total bacterial and archaeal community distribution.
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Affiliation(s)
- Zsuzsanna Nagymáté
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary.
| | - Zalán G Homonnay
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány P. sétány 1/C, 1117 Budapest, Hungary
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27
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Zhang FQ, Pan W, Gu JD, Xu B, Zhang WH, Zhu BZ, Wang YX, Wang YF. Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China. Appl Microbiol Biotechnol 2016; 100:6859-6869. [DOI: 10.1007/s00253-016-7506-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
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28
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Grunert O, Reheul D, Van Labeke MC, Perneel M, Hernandez-Sanabria E, Vlaeminck SE, Boon N. Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture. Microb Biotechnol 2016; 9:389-99. [PMID: 27005434 PMCID: PMC4835575 DOI: 10.1111/1751-7915.12354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 11/27/2022] Open
Abstract
Vegetables and fruits are an important part of a healthy food diet, however, the eco‐sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N‐fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.
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Affiliation(s)
- Oliver Grunert
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium.,Peltracom, Skaldenstraat 7a, Desteldonk, 9042, Belgium
| | - Dirk Reheul
- Department of Plant Production, Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | | | | | - Emma Hernandez-Sanabria
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Siegfried E Vlaeminck
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium.,Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
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29
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Gan XH, Zhang FQ, Gu JD, Guo YD, Li ZQ, Zhang WQ, Xu XY, Zhou Y, Wen XY, Xie GG, Wang YF. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China. Antonie van Leeuwenhoek 2015; 109:237-51. [DOI: 10.1007/s10482-015-0627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
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30
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Sterngren AE, Hallin S, Bengtson P. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil. Front Microbiol 2015; 6:1350. [PMID: 26648926 PMCID: PMC4663241 DOI: 10.3389/fmicb.2015.01350] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.
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Affiliation(s)
- Anna E Sterngren
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
| | - Sara Hallin
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Per Bengtson
- Microbial Ecology, Department of Biology, Lund University Lund, Sweden
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31
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Spatial distribution patterns of ammonia-oxidizing archaea abundance in subtropical forests at early and late successional stages. Sci Rep 2015; 5:16587. [PMID: 26565069 PMCID: PMC4643239 DOI: 10.1038/srep16587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/15/2015] [Indexed: 11/17/2022] Open
Abstract
Characterizing the spatial distribution patterns of soil microorganisms is helpful in understanding the biogeochemical processes they perform, but has been less studied relative to those of macroorganisms. In this study, we investigated and compared the spatially explicit distribution patterns of ammonia-oxidizing archaea (AOA) abundance and the influential factors between an early (ES) and a late successional (LS) subtropical forest stand. The average AOA abundance, vegetational attributes, and soil nutrient contents were mostly greater in the LS than the ES stand (P = 0.085 or smaller), but their spatial variations were more pronounced in the ES than the LS stand. The spatial distribution patches of AOA abundance were smaller and more irregular in the ES stand (patch size <50 m) than in the LS stand (patch size about 120 m). Edaphic and vegetational variables contributed more to the spatial variations of AOA abundance for the ES (9.3%) stand than for LS stand, whereas spatial variables (MEMs) were the main contributors (62%) for the LS stand. These results suggest that environmental filtering likely influence the spatial distribution of AOA abundance at early successional stage more than that at late successional stage, while spatial dispersal is dominant at late successional stage.
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32
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A comparative study of ammonia-oxidizing archaea and bacteria in acidic and alkaline purple soils. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1143-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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33
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Hong JK, Cho JC. Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects. PLoS One 2015; 10:e0133763. [PMID: 26241328 PMCID: PMC4524719 DOI: 10.1371/journal.pone.0133763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/01/2015] [Indexed: 11/18/2022] Open
Abstract
To find environmental variables (EVs) shaping the ecological niche of the archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting thaumarchaeotal 16S rRNA gene sequences. We employed our previously developed primer, THAUM-494, which had greater coverage for Thaumarchaeota and lower tolerance to nonthaumarchaeotal taxa than previous Thaumarchaeota-directed primers. The relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to a series of statistical analyses. Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs. Negative causal relationships between RTHAUM and nutrient level-related EVs were observed in an RDA biplot. These negative relationships were further confirmed by correlation and regression analyses. Total nitrogen content (TN) appeared to be the EV that affected RTHAUM most strongly, and total carbon content (TC), which reflected the content of organic matter (OM), appeared to be the EV that affected it least. However, in the path analysis, a path model indicated that TN might be a mediator EV that could be controlled directly by the OM. Additionally, another path model implied that water content (WC) might also indirectly affect RTHAUM by controlling ammonium nitrogen (NH4+-N) level through ammonification. Thus, although most directly affected by NH4+-N, RTHAUM could be ultimately determined by OM content, suggesting that Thaumarchaeota could prefer low-OM or low-WC conditions, because either of these EVs could subsequently result in low levels of NH4+-N in soil.
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Affiliation(s)
- Jin-Kyung Hong
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Jae-Chang Cho
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
- * E-mail:
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34
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Marusenko Y, Garcia-Pichel F, Hall SJ. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils. FEMS Microbiol Ecol 2014; 91:1-11. [PMID: 25764551 DOI: 10.1093/femsec/fiu023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability.
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Affiliation(s)
| | | | - Sharon J Hall
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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35
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Hanada A, Kurogi T, Giang NM, Yamada T, Kamimoto Y, Kiso Y, Hiraishi A. Bacteria of the candidate phylum TM7 are prevalent in acidophilic nitrifying sequencing-batch reactors. Microbes Environ 2014; 29:353-62. [PMID: 25241805 PMCID: PMC4262358 DOI: 10.1264/jsme2.me14052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Laboratory-scale acidophilic nitrifying sequencing-batch reactors (ANSBRs) were constructed by seeding with sewage-activated sludge and cultivating with ammonium-containing acidic mineral medium (pH 4.0) with or without a trace amount of yeast extract. In every batch cycle, the pH varied between 2.7 and 4.0, and ammonium was completely converted to nitrate. Attempts to detect nitrifying functional genes in the fully acclimated ANSBRs by PCR with previously designed primers mostly gave negative results. 16S rRNA gene-targeted PCR and a subsequent denaturating gradient gel electrophoresis analysis revealed that a marked change occurred in the bacterial community during the overall period of operation, in which members of the candidate phylum TM7 and the class Gammaproteobacteria became predominant at the fully acclimated stage. This result was fully supported by a 16S rRNA gene clone library analysis, as the major phylogenetic groups of clones detected (>5% of the total) were TM7 (33%), Gammaproteobacteria (37%), Actinobacteria (10%), and Alphaproteobacteria (8%). Fluorescence in situ hybridization with specific probes also demonstrated the prevalence of TM7 bacteria and Gammaproteobacteria. These results suggest that previously unknown nitrifying microorganisms may play a major role in ANSBRs; however, the ecophysiological significance of the TM7 bacteria predominating in this process remains unclear.
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Affiliation(s)
- Akiko Hanada
- Department of Environmental and Life Sciences, Toyohashi University of Technology
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Isobe K, Ohte N. Ecological perspectives on microbes involved in N-cycling. Microbes Environ 2014; 29:4-16. [PMID: 24621510 PMCID: PMC4041230 DOI: 10.1264/jsme2.me13159] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/09/2014] [Indexed: 11/12/2022] Open
Abstract
Nitrogen (N) cycles have been directly linked to the functional stability of ecosystems because N is an essential element for life. Furthermore, the supply of N to organisms regulates primary productivity in many natural ecosystems. Microbial communities have been shown to significantly contribute to N cycles because many N-cycling processes are microbially mediated. Only particular groups of microbes were implicated in N-cycling processes, such as nitrogen fixation, nitrification, and denitrification, until a few decades ago. However, recent advances in high-throughput sequencing technologies and sophisticated isolation techniques have enabled microbiologists to discover that N-cycling microbes are unexpectedly diverse in their functions and phylogenies. Therefore, elucidating the link between biogeochemical N-cycling processes and microbial community dynamics can provide a more mechanistic understanding of N cycles than the direct observation of N dynamics. In this review, we summarized recent findings that characterized the microbes governing novel N-cycling processes. We also discussed the ecological role of N-cycling microbial community dynamics, which is essential for advancing our understanding of the functional stability of ecosystems.
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Affiliation(s)
- Kazuo Isobe
- 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
| | - Nobuhito Ohte
- Department of Forest Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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Wang YF, Gu JD. Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms. Appl Microbiol Biotechnol 2013; 98:3257-74. [DOI: 10.1007/s00253-013-5399-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/02/2013] [Accepted: 11/09/2013] [Indexed: 10/26/2022]
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Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China. Appl Environ Microbiol 2013; 79:4065-71. [PMID: 23624482 DOI: 10.1128/aem.00543-13] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH4(+)-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH4(+)-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present.
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Pett-Ridge J, Petersen DG, Nuccio E, Firestone MK. Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil. FEMS Microbiol Ecol 2013; 85:179-94. [PMID: 23556538 DOI: 10.1111/1574-6941.12111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/29/2022] Open
Abstract
Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α-subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.
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Sims A, Gajaraj S, Hu Z. Nutrient removal and greenhouse gas emissions in duckweed treatment ponds. WATER RESEARCH 2013; 47:1390-8. [PMID: 23276427 DOI: 10.1016/j.watres.2012.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/10/2012] [Accepted: 12/06/2012] [Indexed: 05/24/2023]
Abstract
Stormwater treatment ponds provide a variety of functions including sediment retention, organic and nutrient removal, and habitat restoration. The treatment ponds are, however, also a source of greenhouse gases. The objectives of this study were to assess greenhouse gas (CH(4), CO(2) and N(2)O) emissions in duckweed treatment ponds (DWPs) treating simulated stormwater and to determine the role of ammonia-oxidizing organisms in nutrient removal and methanogens in greenhouse gas emissions. Two replicated DWPs operated at a hydraulic retention time (HRT) of 10 days were able to remove 84% (± 4% [standard deviation]) chemical oxygen demand (COD), 79% (± 3%) NH(4)(+)-N, 86% (± 2%) NO(3)(-)-N and 56% (± 7%) orthophosphate. CH(4) emission rates in the DWPs ranged from 502 to 1900 mg CH(4) m(-2) d(-1) while those of nitrous oxide (N(2)O) ranged from 0.63 to 4 mg N(2)O m(-2) d(-1). The CO(2) emission rates ranged from 1700 to 3300 mg CO(2) m(-2) day(-1). Duckweed coverage on water surface along with the continued deposit of duckweed debris in the DWPs and low-nutrient influent water created a low dissolved oxygen environment for the growth of unique ammonia-oxidizing organisms and methanogens. Archaeal and bacterial amoA abundance in the DWPs ranged from (1.5 ± 0.2) × 10(7) to (1.7 ± 0.2) × 10(8) copies/g dry soil and from (1.0 ± 0.3) × 10(3) to (1.5 ± 0.4) × 10(6) copies/g dry soil, respectively. The 16S rRNA acetoclastic and hydrogenotrophic methanogens ranged from (5.2 ± 0.2) × 10(5) to (9.0 ± 0.3) × 10(6) copies/g dry soil and from (1.0 ± 0.1) × 10(2) to (5.5 ± 0.4) × 10(3) copies/g dry soil, respectively. Ammonia-oxidizing archaea (AOA) appeared to be the dominant nitrifiers and acetoclastic Methanosaeta was the major methanogenic genus. The results suggest that methane is the predominant (>90%) greenhouse gas in the DWPs, where the relatively low stormwater nutrient inputs facilitate the growth of K-strategists such as AOA and Methanosaeta that may be responsible for ammonia removal and greenhouse gas emissions, respectively.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol 2012; 20:523-31. [PMID: 22959489 DOI: 10.1016/j.tim.2012.08.001] [Citation(s) in RCA: 412] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/28/2012] [Accepted: 08/01/2012] [Indexed: 11/27/2022]
Abstract
Autotrophic archaeal and bacterial ammonia-oxidisers (AOA and AOB) drive soil nitrification. Ammonia limitation, mixotrophy, and pH have been suggested as factors providing niche specialisation and differentiation between soil AOA and AOB. However, current data from genomes, cultures, field studies, and microcosms suggest that no single factor discriminates between AOA and AOB. In addition, there appears to be sufficient physiological diversity within each group for growth and activity in all soils investigated, with the exception of acidic soils (pH <5.5), which are dominated by AOA. Future investigation of niche specialisation in ammonia-oxidisers, and other microbial communities, requires characterisation of a wider range of environmentally representative cultures, emphasis on experimental studies rather than surveys, and greater consideration of small-scale soil heterogeneity.
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Sims A, Horton J, Gajaraj S, McIntosh S, Miles RJ, Mueller R, Reed R, Hu Z. Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands. WATER RESEARCH 2012; 46:4121-4129. [PMID: 22673339 DOI: 10.1016/j.watres.2012.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 03/18/2012] [Accepted: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Ammonia-oxidizing organisms play an important role in wetland water purification and nitrogen cycling. We determined soil nitrification rates and investigated the seasonal and spatial distributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in three freshwater wetlands by using specific primers targeting the amoA genes of AOA and AOB and real-time quantitative polymerase chain reaction (qPCR). The nitrifying potentials of wetland soils ranged from 1.4 to 4.0 μg g(-1) day(-1). The specific rates of ammonia oxidation activity by AOA and AOB at the Bee Hollow wetlands were 1.9 fmol NH(3) cell(-1) day(-1) and 36.8 fmol NH(3) cell(-1) day(-1), respectively. Soil nitrification potential was positively correlated with both archaeal and bacterial amoA abundance. However, the gene copies of AOA amoA were higher than those of AOB amoA by at least an order of magnitude in wetland soils and water in both summer and winter over a three year study period. AOB were more sensitive to low temperature than AOA. The amoA gene copy ratios of AOA to AOB in top soils (0-10 cm) ranged from 19 ± 4 to 100 ± 11 among the wetland sites. In contrast, the ratio of the wetland boundary soil was 10 ± 2, which was significantly lower than that of the wetland soils (P < 0.001). The NH(4)(+)-N concentrations in wetland water were lower than 2 mg/L throughout the study. The results suggest that ammonium concentration is a major factor influencing AOA and AOB population in wetlands, although other factors such as temperature, dissolved oxygen, and soil organic matter are involved. AOA are more persistent and more abundant than AOB in the nutrient-depleted oligotrophic wetlands. Therefore, ratio of AOA amoA gene copies to AOB amoA gene copies may serve as a new biological indicator for wetland condition assessment and wetland restoration applications.
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Affiliation(s)
- Atreyee Sims
- Department of Civil and Environmental Engineering, University of Missouri, E2509 Lafferre Hall, Columbia, MO 65211, USA
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Zhalnina K, de Quadros PD, Camargo FAO, Triplett EW. Drivers of archaeal ammonia-oxidizing communities in soil. Front Microbiol 2012; 3:210. [PMID: 22715335 PMCID: PMC3375578 DOI: 10.3389/fmicb.2012.00210] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/22/2012] [Indexed: 01/24/2023] Open
Abstract
Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.
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Affiliation(s)
- Kateryna Zhalnina
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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Koba K, Fang Y, Mo J, Zhang W, Lu X, Liu L, Zhang T, Takebayashi Y, Toyoda S, Yoshida N, Suzuki K, Yoh M, Senoo K. The15N natural abundance of the N lost from an N-saturated subtropical forest in southern China. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/2010jg001615] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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