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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Affiliation(s)
- Fuyun Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
| | - Haoxin Fan
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China
| | - Dan Luo
- College of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, People's Republic of China
| | | | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430073, People's Republic of China.
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Zhang Q, Chen M, Leng Y, Wang X, Fu Y, Wang D, Zhao X, Gao W, Li N, Chen X, Fan C, Li Q. Organic substitution stimulates ammonia oxidation-driven N 2O emissions by distinctively enriching keystone species of ammonia-oxidizing archaea and bacteria in tropical arable soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162183. [PMID: 36804975 DOI: 10.1016/j.scitotenv.2023.162183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/01/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Partial organic substitution (POS) is pivotal in enhancing soil productivity and changing nitrous oxide (N2O) emissions by profoundly altering soil nitrogen (N) cycling, where ammonia oxidation is a fundamental core process. However, the regulatory mechanisms of N2O production by ammonia oxidizers at the microbial community level under POS regimes remain unclear. This study explored soil ammonia oxidation and related N2O production, further building an understanding of the correlations between ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) activity and community structure in tropical arable soils under four-year field management regimes (CK, without fertilizer N; N, with only inorganic N; M1N1, with 1/2 organic N + 1/2 inorganic N; M1N2, with 1/3 organic N + 2/3 inorganic N). AOA contributed more to potential ammonia oxidation (PAO) than AOB across all treatments. In comparison with CK, N treatment had no obvious effects on PAO and lowered related N2O emissions by decreasing soil pH and downregulating the abundance of AOA- and AOB-amoA. POS regimes significantly enhanced PAO and N2O emissions relative to N treatment by promoting the abundances and contributions of AOA and AOB. The stimulated AOA-dominated N2O production under M1N1 was correlated with promoted development of Nitrososphaera. By contrast, the increased AOB-dominated N2O production under M1N2 was linked to the enhanced development of Nitrosospira multiformis. Our study suggests organic substitutions with different proportions of inorganic and organic N distinctively regulate the development of specific species of ammonia oxidizers to increase associated N2O emissions. Accordingly, appropriate options should be adopted to reduce environmental risks under POS regimes in tropical croplands.
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Affiliation(s)
- Qi Zhang
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miao Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Youfeng Leng
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; College of Eco-environment Engineering, Guizhou Minzu University, Guiyang 550025, China
| | - Xiaotong Wang
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yajun Fu
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Danfeng Wang
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiongwei Zhao
- College of Ecology and Environment, Hainan University, Haikou 570228, China; Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenlong Gao
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Ning Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Xin Chen
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Changhua Fan
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China.
| | - Qinfen Li
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China; Key Laboratory of Green and Low Carbon Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou 571101, China.
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Xing XY, Tang YF, Xu HF, Qin HL, Liu Y, Zhang WZ, Chen AL, Zhu BL. Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N 2O Emission in Acidic Paddy Soil. Appl Environ Microbiol 2021; 87:e0296520. [PMID: 33837014 PMCID: PMC8174758 DOI: 10.1128/aem.02965-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/13/2021] [Indexed: 11/20/2022] Open
Abstract
Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.
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Affiliation(s)
- Xiao-Yi Xing
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- Urban Construction College, Shaoyang University, Shaoyang, China
| | - Ya-Fang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Hui-Fang Xu
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, China
| | - Hong-Ling Qin
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yi Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Wen-Zhao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - An-Lei Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Bao-Li Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agroecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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4
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Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests. Appl Microbiol Biotechnol 2019; 103:4229-4240. [PMID: 30923872 DOI: 10.1007/s00253-019-09721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.
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Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:6957210. [PMID: 30833827 PMCID: PMC6369511 DOI: 10.1155/2019/6957210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 11/18/2018] [Indexed: 12/29/2022]
Abstract
The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado sensu stricto soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and amoA genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c Thaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher amoA diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.
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Liu H, Li J, Zhao Y, Xie K, Tang X, Wang S, Li Z, Liao Y, Xu J, Di H, Li Y. Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:641-648. [PMID: 29597161 DOI: 10.1016/j.scitotenv.2018.03.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers' abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO3--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers' abundance and communities with long-term manure addition.
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Affiliation(s)
- Haiyang Liu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Jia Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yan Zhao
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Kexin Xie
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Xianjin Tang
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Shaoxian Wang
- Institute of Soil & Fertilizer and Resource & Environment, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, PR China
| | - Zhongpei Li
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu, PR China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Changsha, Hunan, PR China
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Hongjie Di
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China
| | - Yong Li
- College of Environmental and Natural Resource Sciences, Zhejiang University, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Hangzhou, Zhejiang, PR China.
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Wu S, Zhuang G, Bai Z, Cen Y, Xu S, Sun H, Han X, Zhuang X. Mitigation of nitrous oxide emissions from acidic soils by Bacillus amyloliquefaciens, a plant growth-promoting bacterium. GLOBAL CHANGE BIOLOGY 2018; 24:2352-2365. [PMID: 29251817 DOI: 10.1111/gcb.14025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/30/2017] [Indexed: 06/07/2023]
Abstract
Nitrous oxide (N2 O) is a long-lived greenhouse gas that can result in the alteration of atmospheric chemistry and cause accompanying changes in global climate. To date, many techniques have been used to mitigate the emissions of N2 O from agricultural fields, which represent one of the most important sources of N2 O. In this study, we designed a greenhouse pot experiment and a microcosmic serum bottle incubation experiment using acidic soil from a vegetable farm to study the effects of Bacillus amyloliquefaciens (BA) on plant growth and N2 O emission rates. The addition of BA to the soil promoted plant growth enhanced the soil pH and increased the total nitrogen (TN) contents in the plants. At the same time, it decreased the concentrations of ammonium (NH4+ ), nitrate (NO3- ) and TN in the soil. Overall, the addition of BA resulted in a 50% net reduction of N2 O emissions compared with the control. Based on quantitative PCR and the network analysis of DNA sequencing, it was demonstrated that BA partially inhibited the nitrification process through the significant reduction of ammonia oxidizing bacteria. Meanwhile, it enhanced the denitrification process, mainly by increasing the abundance of N2 O-reducing bacteria in the treatment with BA. The results of our microcosm experiment provided evidence that strongly supported the above findings under more strictly controlled laboratory conditions. Taken together, the results of our study evidently demonstrated that BA has dual effects on the promotion of plant growth and the dramatic reduction of greenhouse emissions, thus suggesting the possibility of screening beneficial microbial organisms from the environment that can promote plant growth and mitigate greenhouse trace gases.
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Affiliation(s)
- Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Cen
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shengjun Xu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haishu Sun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Xingguo Han
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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Wu RN, Meng H, Wang YF, Lan W, Gu JD. A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils. MICROBIAL ECOLOGY 2017; 74:910-922. [PMID: 28808742 DOI: 10.1007/s00248-017-1045-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 05/20/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4+ equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.
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Affiliation(s)
- Ruo-Nan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yong-Feng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
- Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, Guangzhou, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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Jung MY, Kim JG, Sinninghe Damsté JS, Rijpstra WIC, Madsen EL, Kim SJ, Hong H, Si OJ, Kerou M, Schleper C, Rhee SK. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:983-992. [PMID: 27700018 DOI: 10.1111/1758-2229.12477] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 06/06/2023]
Abstract
A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of 13 C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.
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Affiliation(s)
- Man-Young Jung
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, Utrecht, 3508, TA, The Netherlands
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, P.O. Box 59, AB Den Burg, 1790, The Netherlands
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - So-Jeong Kim
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Heeji Hong
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Ok-Ja Si
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Melina Kerou
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Vienna, A-1090, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, South Korea
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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11
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Souza RC, Mendes IC, Reis-Junior FB, Carvalho FM, Nogueira MA, Vasconcelos ATR, Vicente VA, Hungria M. Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado? BMC Microbiol 2016; 16:42. [PMID: 26983403 PMCID: PMC4794851 DOI: 10.1186/s12866-016-0657-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/02/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. RESULTS Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. CONCLUSION High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.
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Affiliation(s)
- Renata Carolini Souza
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Iêda Carvalho Mendes
- />Embrapa Cerrado, Soil Microbiology, C.P. 08223, 73301-970 Planaltina, DF Brazil
| | | | | | | | | | - Vânia Aparecida Vicente
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Mariangela Hungria
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
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From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 2015; 72:4287-308. [PMID: 26254872 PMCID: PMC4611022 DOI: 10.1007/s00018-015-2004-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022]
Abstract
Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.
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