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Deng N, Gubry-Rangin C, Song XT, Ju XT, Liu SY, Shen JP, Di HJ, Han LL, Zhang LM. AOB Nitrosospira cluster 3a.2 (D11) dominates N 2O emissions in fertilised agricultural soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120504. [PMID: 38447513 DOI: 10.1016/j.jenvman.2024.120504] [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: 12/16/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024]
Abstract
Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.
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Affiliation(s)
- Na Deng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Xiao-Tong Song
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Xiao-Tang Ju
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Ju-Pei Shen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Hong-Jie Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhang K, Qiu Y, Zhao Y, Wang S, Deng J, Chen M, Xu X, Wang H, Bai T, He T, Zhang Y, Chen H, Wang Y, Hu S. Moderate precipitation reduction enhances nitrogen cycling and soil nitrous oxide emissions in a semi-arid grassland. GLOBAL CHANGE BIOLOGY 2023; 29:3114-3129. [PMID: 36892227 DOI: 10.1111/gcb.16672] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 05/03/2023]
Abstract
The ongoing climate change is predicted to induce more weather extremes such as frequent drought and high-intensity precipitation events, causing more severe drying-rewetting cycles in soil. However, it remains largely unknown how these changes will affect soil nitrogen (N)-cycling microbes and the emissions of potent greenhouse gas nitrous oxide (N2 O). Utilizing a field precipitation manipulation in a semi-arid grassland on the Loess Plateau, we examined how precipitation reduction (ca. -30%) influenced soil N2 O and carbon dioxide (CO2 ) emissions in field, and in a complementary lab-incubation with simulated drying-rewetting cycles. Results obtained showed that precipitation reduction stimulated plant root turnover and N-cycling processes, enhancing soil N2 O and CO2 emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N2 O emissions primarily originated from nitrification process. The incubation experiment further showed that in field soils under precipitation reduction, drying-rewetting stimulated N mineralization and ammonia-oxidizing bacteria in favor of genera Nitrosospira and Nitrosovibrio, increasing nitrification and N2 O emissions. These findings suggest that moderate precipitation reduction, accompanied with changes in drying-rewetting cycles under future precipitation scenarios, may enhance N cycling processes and soil N2 O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.
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Affiliation(s)
- Kangcheng Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunfeng Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuhong Wang
- Ningxia Yunwu Mountains Grassland Natural Reserve Administration, Guyuan, 756000, China
| | - Jun Deng
- Ningxia Yunwu Mountains Grassland Natural Reserve Administration, Guyuan, 756000, China
| | - Mengfei Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyu Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tongshuo Bai
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tangqing He
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huaihai Chen
- School of Ecology, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yi Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Shuijin Hu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27695, USA
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Zhang X, Liang Q, Wang G, Zhang H, Zhang A, Tan Y, Bol R. Incorporating straw into intensively farmed cropland soil can reduce N 2O emission via inhibition of nitrification and denitrification pathways. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118115. [PMID: 37196616 DOI: 10.1016/j.jenvman.2023.118115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
Straw incorporation (SI) combined with N fertilizer has been shown to affect soil N2O emission and N-related functional microbes in agriculture. However, the responses of N2O emission, community structure of nitrifiers and denitrifiers and related microbial functional genes to straw management strategies in the winter wheat season in China remain unclear. Here, we conducted a two-season experiment in a winter wheat field in Ningjing County, northern China, to examine four treatments: no fertilizer with (N0S1) and without maize straw (N0S0); N fertilizer with (N1S1) and without maize straw (N1S0), and their effects on N2O emissions, soil chemical parameters, crop yield, as well as the dynamics of nitrifying and denitrifying microbial communities. We found that seasonal N2O emissions decreased by 7.1-11.1% (p < 0.05) in N1S1 as compared to N1S0, without significant difference between N0S1 and N0S0. In combination with N fertilization, SI increased the yield by 2.6-4.3%, altered the microbial community composition, increased Shannon and ACE indexes, and decreased the abundance of AOA (9.2%), AOB (32.2%; p < 0.05), nirS (35.2%; p < 0.05), nirK (21.6%; p < 0.05) and nosZ (19.2%). However, in the absence of N fertilizer, SI promoted the major genera of Nitrosavbrio (AOB), unclassifiied_Gammaproteobacteria, Rhodanobacter (nirS), Sinorhizobium (nirK), which strongly correlated positively with N2O emissions. Thereby, a negative interaction effect between SI and N fertilizer on AOB and nirS emphasized that SI could offset the increase of N2O emission caused by fertilization. Soil moisture and NO3- concentration were the major factors affecting N-related microbial community structure. Our study reveals that SI suppressed N2O emission significantly and simultaneously decreased the abundance of N-related functional genes and altered denitrifying bacterial community composition. We conclude that SI helps to enhance yield and alleviate fertilizer-induced environmental costs in intensively farmed fields in northern China.
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Affiliation(s)
- Xin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China.
| | - Qing Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China
| | - Guiyan Wang
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, Hebei, 071001, China
| | - Haowen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Resources and Environmental Sciences, Hebei Agricultural University, Baoding, 071000, China
| | - Aijun Zhang
- Mountainous Area Research Institute of Hebei Province, Baoding, 071000, China
| | - Yuechen Tan
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, 100091, China
| | - Roland Bol
- Institute of Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany; School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, LL57 2UW, UK
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Kaushal R, Hsueh YH, Chen CL, Lan YP, Wu PY, Chen YC, Liang MC. Isotopic assessment of soil N 2O emission from a sub-tropical agricultural soil under varying N-inputs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154311. [PMID: 35257756 DOI: 10.1016/j.scitotenv.2022.154311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen fertilizers result in high crop productivity but also enhance the emission of N2O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N2O and N2 via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N2O production. Here, we report the results of N2O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N2O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N2O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N2O during the entire course of the incubation experiments. Peak N2O emissions of 122 ± 98 μg N2O-N m-2 h-1, 338 ± 49 μg N2O-N m-2 h-1 and 739 ± 296 μg N2O-N m-2 h-1 were observed for urea application rate of 40, 80, and 120 μg N g-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ15N, δ18O, and 15N site preference, we inferred co-occurrence of several microbial N2O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N2O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N2O emission pulse in intermediate urea-N levels. Signature of N2O consumption by reduction could be traced during declining emissions in treatment with high urea level.
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Affiliation(s)
- Ritika Kaushal
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsin Hsueh
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan; Taiwan International Graduate Program-Earth Systems Science, Academia Sinica, Taipei, Taiwan
| | - Chi-Ling Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Ping Lan
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan
| | - Ping-Yu Wu
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Yi-Chun Chen
- Agricultural Chemistry Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | - Mao-Chang Liang
- Institute of Earth Sciences, Academia Sinica, Taipei, Taiwan.
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Zhao Y, Yao Y, Xu H, Xie Z, Guo J, Qi Z, Jiang H. Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley. PeerJ 2022; 10:e13254. [PMID: 35415021 PMCID: PMC8995024 DOI: 10.7717/peerj.13254] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/22/2022] [Indexed: 01/13/2023] Open
Abstract
Continuous cropping often leads to an unbalanced soil microbial community, which in turn negatively affects soil functions. However, systematic research of how these effects impact the bacterial composition, microbial functional traits, and soil metabolites is lacking. In the present study, the rhizosphere soil samples of Tibetan barley continuously monocropped for 2 (CCY02), 5 (CCY05), and 10 (CCY10) years were collected. By utilizing 16S high-throughput sequencing, untargeted metabolomes, and quantitative microbial element cycling smart chips, we examined the bacterial community structure, soil metabolites, and bacterial functional gene abundances, respectively. We found that bacterial richness (based on Chao1 and Phylogenetic Diversity [PD] indices) was significantly higher in CCY02 and CCY10 than in CCY05. As per principal component analysis (PCA), samples from the continuous monocropping year tended to share more similar species compositions and soil metabolites, and exhibited distinct patterns over time. The results of the Procrustes analysis indicated that alterations in the soil metabolic profiles and bacterial functional genes after long-term continuous cropping were mainly mediated by soil microbial communities (P < 0.05). Moreover, 14 genera mainly contributed to the sample dissimilarities. Of these, five genera were identified as the dominant shared taxa, including Blastococcus, Nocardioides, Sphingomonas, Bacillus, and Solirubrobacter. The continuous cropping of Tibetan barley significantly increased the abundances of genes related to C-degradation (F = 9.25, P = 0.01) and P-cycling (F = 5.35, P = 0.03). N-cycling significantly negatively correlated with bacterial diversity (r = - 0.71, P = 0.01). The co-occurrence network analysis revealed that nine hub genera correlated with most of the functional genes and a hub taxon, Desulfuromonadales, mainly co-occurred with the metabolites via both negative and positive correlations. Collectively, our findings indicated that continuous cropping significantly altered the bacterial community structure, functioning of rhizosphere soils, and soil metabolites, thereby providing a comprehensive understanding of the effects of the long-term continuous cropping of Tibetan barley.
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Affiliation(s)
- Yuan Zhao
- Qinghai University, College of Eco-Environmental Engineering, Xining, Qinghai, China
| | - Youhua Yao
- Qinghai University, Academy of Agriculture and Forestry Sciences, Xining, Qinghai, China
| | - Hongyan Xu
- Qinghai University, College of Eco-Environmental Engineering, Xining, Qinghai, China,Qinghai University, Academy of Agriculture and Forestry Sciences, Xining, Qinghai, China
| | - Zhanling Xie
- Qinghai University, College of Eco-Environmental Engineering, Xining, Qinghai, China
| | - Jing Guo
- Qinghai University, College of Eco-Environmental Engineering, Xining, Qinghai, China
| | - Zhifan Qi
- Qinghai University, College of Eco-Environmental Engineering, Xining, Qinghai, China
| | - Hongchen Jiang
- China University of Geosciences, State Key Laboratory of Biogeology and Environmental Geology, Wuhan, Hubei, China
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Ashraf A, Akhtar M, Ashraf M, Hussain S. Controlled nitrogen transformation in chemo-amended urea improves nitrogen use efficiency and productivity of wheat grown on alkaline calcareous soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:28700-28713. [PMID: 34988797 DOI: 10.1007/s11356-021-17837-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Low wheat production is linked to soil degradation, low organic matter, temperature variation, and nutrient depletion in soils of semiarid regions. Nitrogen is mostly applied as urea to meet crop requirements; however, excessive N application may pollute the environment and contaminate groundwater. The current studies explored possible ways for decreasing N losses (NH3 volatilization and NO3 leaching) and improving N availability for wheat production in alkaline soil. The ZnO was coated on urea (1% Zn coating) to get zinc-coated urea (ZnU), and both urea and ZnU were incubated in laboratory at recommended rate (RR), i.e., 150 kg N ha-1 and 80% (N of RR), after further coating with inhibitors [N-(n-butyl) thiophosphoric triamide (NBPT) at 1% of urea and 4-amino-1,2,4-triazole (ATC) at 2% of urea], thus creating six treatments. The results showed higher NH3-N loss at day 4 and thereafter a decreasing trend reaching to minimum at day 14. The cumulative NH3-N volatilization from urea alone was found higher (28.99%), except ATC treatments producing statistically similar losses due to restriction in nitrification process. In greenhouse, the treatments were tested in wheat cultivars (Faisalabad 2008 and Lasani) for crop growth, nutrient (N, P, K, and Zn) uptake, and yield parameters, where 80% of RR treatment, i.e., NBPT + ZnU80, was found at par with full RR as commercial products, especially comparable to ZnU (at RR) that produced the highest chlorophyll (53.65unit value), net leaf photosynthetic rate (19.64 μmol CO2 m-2 s-1), plant biomass (208.13 g/pot), grain yield (63.65 g/pot), and nutrient (NPK and Zn) accumulation in grain of Fsd-2008 cultivar. In field trial, NBPT + ZnU80 also outperformed and produced the highest physiological efficiency (PE), agronomic efficiency (AE), and nitrogen recovery efficiency (REN); the treatment also found statistically similar with ZnU (at RR) that produced the maximum plant height (95.4 cm), plant biomass (11.58 t/ha), grain yield (4.69 t/ha), and 1000-grain weight (42.55 g). The relative NO3 leaching was found lower in 80% N treatments, yet leaching was not significant from either treatment at the three stages of crop growth. Overall, current studies revealed the effectiveness of NBPT-amended urea (followed by ZnU) with 20% saving of N inputs through higher N availability for plant uptake that could benefit growers as well as conserve environment.
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Affiliation(s)
- Arooba Ashraf
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Akhtar
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan.
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan.
| | - Muhammad Ashraf
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Crop Stress Physiology Lab, Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Saddam Hussain
- Crop Stress Physiology Lab, Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan.
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Ecological Role of Bacteria Involved in the Biogeochemical Cycles of Mangroves Based on Functional Genes Detected through GeoChip 5.0. mSphere 2022; 7:e0093621. [PMID: 35019668 PMCID: PMC8754168 DOI: 10.1128/msphere.00936-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mangroves provide a variety of ecosystem services and contribute greatly to the global biogeochemical cycle. Microorganisms play important roles in biogeochemical cycles and maintain the dynamic balance of mangroves. However, the roles of bacteria in the biogeochemical cycles of mangroves and their ecological distribution and functions remain largely uncharacterized. This study thus sought to analyze and compare the ecological distributions and potential roles of bacteria in typical mangroves using 16S rRNA gene amplicon sequencing and GeoChip. Interestingly, the bacterial community compositions were largely similar in the studied mangroves, including Shenzhen, Yunxiao, Zhanjiang, Hainan, Hongkong, Fangchenggang, and Beihai mangroves. Moreover, gamma-proteobacterium_uncultured and Woeseia were the most abundant microorganisms in the mangroves. Furthermore, most of the bacterial communities were significantly correlated with phosphorus levels (P < 0.05; −0.93 < R < 0.93), suggesting that this nutrient is a vital driver of bacterial community composition. Additionally, GeoChip analysis indicated that the functional genes amyA, narG, dsrA, and ppx were highly abundant in the studied mangroves, suggesting that carbon degradation, denitrification, sulfite reduction, and polyphosphate degradation are crucial processes in typical mangroves. Moreover, several genera were found to synergistically participate in biogeochemical cycles in mangroves. For instance, Neisseria, Ruegeria, Rhodococcus, Desulfotomaculum, and Gordonia were synergistically involved in the carbon, nitrogen, and sulfur cycles, whereas Neisseria and Treponema were synergistically involved in the nitrogen cycle and the sulfur cycle. Taken together, our findings provide novel insights into the ecological roles of bacteria in the biogeochemical cycles of mangroves. IMPORTANCE Bacteria have important functions in biogeochemical cycles, but studies on their function in an important ecosystem, mangroves, are still limited. Here, we investigated the ecological role of bacteria involved in biogeochemical cycles in seven representative mangroves of southern China. Furthermore, various functional genes from bacteria involved in biogeochemical cycles were identified by GeoChip 5.0. The functional genes associated with the carbon cycle (particularly carbon degradation) were the most abundant, suggesting that carbon degradation is the most active process in mangroves. Additionally, some high-abundance bacterial populations were found to synergistically mediate key biogeochemical cycles in the mangroves, including Neisseria, Pseudomonas, Treponema, Desulfotomaculum, and Nitrosospira. In a word, our study gives novel insights into the function of bacteria in biogeochemical cycles in mangroves.
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Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
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Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
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Tao R, Zhang H, Gu X, Hu B, Li J, Chu G. Di-(2-ethylhexyl) phthalate (DEHP) exposure suppressed the community diversity and abundance of ammonia-oxidizers and mitigated N 2O emissions in an alkaline soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112910. [PMID: 34678627 DOI: 10.1016/j.ecoenv.2021.112910] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Phthalic acid esters (PAEs) pollution has become an increasing issue worldwide, but little is known about its effects on ammonia-oxidizers and nitrous oxide (N2O) in the soil environment. Here, a 50-day soil microcosm experiment was conducted using low and high doses bis (2-Ethylhexyl) phthalate (DEHP) to estimate the effect of DEHP exposure on soil N2O emissions and the nitrifying community in calcareous soil. The results showed that DEHP exposure at 10 and 100 mg kg-1 doses significantly reduced N2O by 67.5% and 73.6%, respectively, relative to the DEHP absent treatment. The microbial biomass carbon and nitrogen (MBC and MBN) were consistently and significantly decreased with DEHP exposure at 5, 22, and 50 days after incubation, especially with high-dose. The bipartite association networks showed that DEHP exposure changed the compositions of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. Moreover, the AOA and AOB amoA gene abundances were significantly decreased by DEHP addition to the soil (P < 0.05). Random forest modeling showed that the AOB Shannon index and pH were the most important biotic and abiotic factors affecting N2O emissions in the soil with DEHP exposure, respectively. Partial least squares path modeling (PLS-PM) demonstrated that the reduction of N2O emissions due to DEHP exposure was mainly ascribed to the changes of the AOB community. The results from this study highlight the toxicity of DEHP on the ammonia oxidizers, and its mitigating effect on N2O emissions in the soil where ammonia-oxidation is largely driven by AOB.
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Affiliation(s)
- Rui Tao
- School of life science, Shaoxing University, Zhejiang 312000, PR China
| | - Hanjie Zhang
- School of life science, Shaoxing University, Zhejiang 312000, PR China
| | - Xiuping Gu
- Department of Resources and Environmental Science, Agronomy College, Shihezi University, 832000 Shihezi, Xinjiang, PR China
| | - Baowei Hu
- School of life science, Shaoxing University, Zhejiang 312000, PR China
| | - Jun Li
- School of life science, Shaoxing University, Zhejiang 312000, PR China
| | - Guixin Chu
- School of life science, Shaoxing University, Zhejiang 312000, PR China.
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Allegrini M, Morales ME, Villamil MB, Zabaloy MC. Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat's Rhizosphere. Front Microbiol 2021; 12:746524. [PMID: 34690996 PMCID: PMC8527175 DOI: 10.3389/fmicb.2021.746524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.
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Affiliation(s)
- Marco Allegrini
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Marianela E Morales
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Maria B Villamil
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - María Celina Zabaloy
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.,Departamento de Agronomía, Universidad Nacional del Sur, Bahía Blanca, Argentina
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11
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Canisares LP, Rosolem CA, Momesso L, Crusciol CAC, Villegas DM, Arango J, Ritz K, Cantarella H. Maize-Brachiaria intercropping: A strategy to supply recycled N to maize and reduce soil N 2O emissions? AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2021; 319:107491. [PMID: 34602686 PMCID: PMC8363933 DOI: 10.1016/j.agee.2021.107491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen use in agriculture directly impacts food security, global warming, and environmental degradation. Forage grasses intercropped with maize produce feed for animals and or mulch for no-till systems. Forage grasses may exude nitrification inhibitors. It was hypothesized that brachiaria intercropping increases N recycling and maize grain yield and reduces nitrous oxide (N2O) emissions from soil under maize cropping. A field experiment was set up in December 2016 to test three cropping system (maize monocropped, maize intercropped with Brachiaria brizantha or with B. humidicola) and two N rates (0 or 150 kg ha-1). The grasses were sown with maize, but B. humidicola did not germinate well in the first year. B. brizantha developed slowly during the maize cycle because of shading but expanded after maize was harvested. The experiment was repeated in 2017/2018 when B. humidicola was replanted. N2O and carbon dioxide (CO2) emissions, maize grain yield and N content were measured during the two seasons. After the first maize harvest, the above- and below-ground biomass, C and N content of B. brizantha grown during fall-winter, and the biological nitrification inhibition potential of B. brizantha were evaluated. Maize yield responded to N fertilization (5.1 vs. 9.8 t ha-1) but not to brachiaria intercropping. B. brizantha recycled approximately 140 kg N ha-1 and left 12 t dry matter ha-1 for the second maize crop. However, the 2017/18 maize yields were not affected by the N recycled by B. brizantha, whereas N2O emissions were higher in the plots with brachiaria, suggesting that part of the recycled N was released too early after desiccation. Brachiarias showed no evidence of causing nitrification inhibition. The strategy of intercropping brachiarias did not increase maize yield, although it added C and recycled N in the system.
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Affiliation(s)
| | - Ciro Antonio Rosolem
- São Paulo State University, College of Agricultural Sciences, Botucatu, São Paulo 18603-970, Brazil
| | - Letusa Momesso
- São Paulo State University, College of Agricultural Sciences, Botucatu, São Paulo 18603-970, Brazil
| | | | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Karl Ritz
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicester LE12 5RD, UK
| | - Heitor Cantarella
- Agronomic Institute of Campinas, Campinas, São Paulo 13012-970, Brazil
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12
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Ramírez-Fernández L, Orellana LH, Johnston ER, Konstantinidis KT, Orlando J. Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147693. [PMID: 34029816 DOI: 10.1016/j.scitotenv.2021.147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/02/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.
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Affiliation(s)
- Lia Ramírez-Fernández
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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13
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Yun J, Crombie AT, Ul Haque MF, Cai Y, Zheng X, Wang J, Jia Z, Murrell JC, Wang Y, Du W. Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau. Environ Microbiol 2021; 23:6520-6535. [PMID: 34390603 DOI: 10.1111/1462-2920.15697] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023]
Abstract
The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.
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Affiliation(s)
- Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 10049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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14
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Wang W, Han L, Zhang X, Wei K. Plastic film mulching affects N 2O emission and ammonia oxidizers in drip irrigated potato soil in northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142113. [PMID: 32920397 DOI: 10.1016/j.scitotenv.2020.142113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 08/29/2020] [Indexed: 06/11/2023]
Abstract
In soil, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are regarded as key factors mediating nitrous oxide (N2O) production and emission. However, there are scarce reports about the effect of film mulching on ammonia oxidizers, and the biological nitrification process of N2O emission is unclear. This study was based on potato field experiments under different mulching films, including polyethylene mulching film (PM), transparent degradable mulching film (TDM), black degradable mulching film (BDM), and bare land (CK). AOB and AOA abundances were estimated using real-time PCR, and their diversity and community structure were measured using high-throughput sequencing. Result revealed that the total N2O emission from CK was 12.32%-41.03% higher than that from film mulching soil. Under film mulching, according to total N2O emission from soil and N2O concentration in soil treatments were ordered as PM > BDM > TDM, and N2O production was closely correlated with copy numbers of the amoA gene. BDM significantly increased the number of amoA-AOB gene copies (P < 0.01), and PM significantly increased the those of amoA-AOA (P < 0.01). BDM and TDM increased AOB operational taxonomic units (OTUs), Chao1, Simpson, and Shannon indices, while PM increased the AOA OTUs and Chao1 index. Variations in AOA abundance and diversity were closely related to soil mineral N and temperature changes induced by polyethylene film mulching (P < 0.05), whereas AOB showed no significant association with soil properties. Meanwhile, we did not find a distinct treatment effect on AOB community structure. Our findings indicate that (i) degradable film mulching increased AOB abundance and diversity and N2O concentration, but obviously reduced N2O emissions, and (ii) AOA were more sensitive than AOB to polyethylene mulching film.
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Affiliation(s)
- Wen Wang
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China.
| | - Lu Han
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
| | - Xiong Zhang
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
| | - Ku Wei
- College of Life Science, Yulin University, Chongwen Road No.4, Yulin, 719000, Shaanxi, China
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15
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Navarrete AA, de Cássia Bonassi R, Américo-Pinheiro JHP, Vazquez GH, Mendes LW, de Souza Loureiro E, Kuramae EE, Tsai SM. Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops. Methods Mol Biol 2021; 2232:251-263. [PMID: 33161552 DOI: 10.1007/978-1-0716-1040-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.
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Affiliation(s)
- Acacio Aparecido Navarrete
- Graduate Program in Agronomy, Federal University of Mato Grosso do Sul, Chapadão do Sul, MS, Brazil.
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil.
| | - Rita de Cássia Bonassi
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil
| | | | - Gisele Herbst Vazquez
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil
| | - Lucas William Mendes
- Cell and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Siu Mui Tsai
- Cell and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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16
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Lv B, Cui Y, Wei H, Chen Q, Zhang D. Elucidating the role of earthworms in N 2O emission and production pathway during vermicomposting of sewage sludge and rice straw. JOURNAL OF HAZARDOUS MATERIALS 2020; 400:123215. [PMID: 32593023 DOI: 10.1016/j.jhazmat.2020.123215] [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: 04/23/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Vermicomposting is a sustainable option for the recycling of biodegradable organic waste. However, it also produces nitrous oxide (N2O), which is a highly potent greenhouse gas. In this study, the N2O stable isotope and functional genes for nitrogen cycling were determined to investigate the sources of N2O during vermicomposting. The results showed that vermicomposting promoted the organic degradation and nitrogen nitrification, and the presence of earthworms increased the emission of N2O during vermicomposting compared to that during the control treatment with no earthworms. The site preference analysis of N2O stable isotope showed that both nitrification and denitrification were present during the early stages of vermicomposting, while nitrification was the dominant contributor to N2O production in the later stages. Moreover, earthworms increased the gene copies of amoA, and stimulated the nitrifying bacteria, and hence, increased the N2O emission via nitrification. In addition, the activity of earthworms reduced the gene number of nosZ during vermicomposting, while the denitrification was the main source of N2O in the earthworm gut, as the conditions inside the gut inhibited nosZ. Overall, nitrification was the major pathway (55.8-88.7 %) for N2O production, which was promoted by the introduction of earthworms through nitrification.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China.
| | - Yuxue Cui
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China
| | - Huawei Wei
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, East China Normal University, Shanghai 200241, China
| | - Qihao Chen
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Di Zhang
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China; International Joint Research Center for Persistent Toxic Substances (IJRC-PTS), Shanghai Maritime University, Shanghai, 201306, China
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17
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Zhou Y, Lambrides CJ, Li J, Xu Q, Toh R, Tian S, Yang P, Yang H, Ryder M, Denton MD. Nitrifying Microbes in the Rhizosphere of Perennial Grasses are Modified by Biological Nitrification Inhibition. Microorganisms 2020; 8:microorganisms8111687. [PMID: 33138329 PMCID: PMC7693952 DOI: 10.3390/microorganisms8111687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Soil nitrification (microbial oxidation of ammonium to nitrate) can lead to nitrogen leaching and environmental pollution. A number of plant species are able to suppress soil nitrifiers by exuding inhibitors from roots, a process called biological nitrification inhibition (BNI). However, the BNI activity of perennial grasses in the nutrient-poor soils of Australia and the effects of BNI activity on nitrifying microbes in the rhizosphere microbiome have not been well studied. Here we evaluated the BNI capacity of bermudagrass (Cynodon dactylon L.), St. Augustinegrass (Stenotaphrum secundatum (Walt.) Kuntze), saltwater couch (Sporobolus virginicus), seashore paspalum (Paspalum vaginatum Swartz.), and kikuyu grass (Pennisetum clandestinum) compared with the known positive control, koronivia grass (Brachiaria humidicola). The microbial communities were analysed by sequencing 16S rRNA genes. St. Augustinegrass and bermudagrass showed high BNI activity, about 80 to 90% of koronivia grass. All the three grasses with stronger BNI capacities suppressed the populations of Nitrospira in the rhizosphere, a bacteria genus with a nitrite-oxidizing function, but not all of the potential ammonia-oxidizing archaea. The rhizosphere of saltwater couch and seashore paspalum exerted a weak recruitment effect on the soil microbiome. Our results demonstrate that BNI activity of perennial grasses played a vital role in modulating nitrification-associated microbial populations.
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Affiliation(s)
- Yi Zhou
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Christopher J. Lambrides
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Jishun Li
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
- Correspondence: ; Tel.: +86-531-8872-8276
| | - Qili Xu
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Ruey Toh
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Shenzhong Tian
- Institute of Agricultural Resources and Environment, Shandong Academy of Agricultural Sciences, Jinan 250013, China;
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Hetong Yang
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Maarten Ryder
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
| | - Matthew D. Denton
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (Y.Z.); (R.T.); (H.Y.); (M.R.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA 5064, Australia;
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18
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Villegas D, Arevalo A, Nuñez J, Mazabel J, Subbarao G, Rao I, De Vega J, Arango J. Biological Nitrification Inhibition (BNI): Phenotyping of a Core Germplasm Collection of the Tropical Forage Grass Megathyrsus maximus Under Greenhouse Conditions. FRONTIERS IN PLANT SCIENCE 2020; 11:820. [PMID: 32595688 PMCID: PMC7304326 DOI: 10.3389/fpls.2020.00820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/22/2020] [Indexed: 05/31/2023]
Abstract
Modern intensively managed pastures that receive large external nitrogen (N) inputs account for high N losses in form of nitrate (NO3 -) leaching and emissions of the potent greenhouse gas nitrous oxide (N2O). The natural plant capacity to shape the soil N cycle through exudation of organic compounds can be exploited to favor N retention without affecting productivity. In this study, we estimated the relationship between biological nitrification inhibition (BNI), N2O emissions and plant productivity for 119 germplasm accessions of Guineagrass (Megathyrsus maximus), an important tropical forage crop for livestock production. This relation was tested in a greenhouse experiment measuring BNI as (i) rates of soil nitrification; (ii) abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA); and (iii) the capacity of root tissue extracts to inhibit nitrification in vitro. We then measured N2O emissions, aboveground biomass and forage nutrition quality parameters. Reductions on nitrification activity ranging between 30 and 70% were found across the germplasm collection of M. maximus. Accessions with low nitrification rates showed a lower abundance of AOB as well as a reduction in N2O emissions compared to accessions of high nitrification rates. The BNI capacity was not correlated to N uptake of plants, suggesting that there may be intraspecific variation in the exploitation of different N sources in this grass species. A group of accessions (cluster) with the most desirable agronomic and environmental traits among the collection was identified for further field validation. These results provide evidence of the ability of M. maximus to suppress soil nitrification and N2O emissions and their relationship with productivity and forage quality, pointing a way to develop N conservative improved forage grasses for tropical livestock production.
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Affiliation(s)
- Daniel Villegas
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ashly Arevalo
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jonathan Nuñez
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Johanna Mazabel
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Guntur Subbarao
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Idupulapati Rao
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Jose De Vega
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
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19
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Li Y, Tremblay J, Bainard LD, Cade‐Menun B, Hamel C. Long‐term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production. Environ Microbiol 2019; 22:1066-1088. [DOI: 10.1111/1462-2920.14824] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Yunliang Li
- Quebec Research and Development CentreAgriculture and Agri‐Food Canada 2560 Hochelaga Boulevard Quebec City Quebec G1V 2J3 Canada
| | - Julien Tremblay
- Energy, Mining and EnvironmentNational Research Council Canada 6100 Royalmount Ave Montreal Quebec H4P 2R2 Canada
| | - Luke D. Bainard
- Swift Current Research and Development CentreAgriculture and Agri‐Food Canada 1 Airport Rd. Box 1030 Swift Current Saskatchewan S9H 3X2 Canada
| | - Barbara Cade‐Menun
- Swift Current Research and Development CentreAgriculture and Agri‐Food Canada 1 Airport Rd. Box 1030 Swift Current Saskatchewan S9H 3X2 Canada
| | - Chantal Hamel
- Quebec Research and Development CentreAgriculture and Agri‐Food Canada 2560 Hochelaga Boulevard Quebec City Quebec G1V 2J3 Canada
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De Tender C, Mesuere B, Van der Jeugt F, Haegeman A, Ruttink T, Vandecasteele B, Dawyndt P, Debode J, Kuramae EE. Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. Sci Rep 2019; 9:9890. [PMID: 31289280 PMCID: PMC6617458 DOI: 10.1038/s41598-019-46106-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 11/09/2022] Open
Abstract
Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.
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Affiliation(s)
- C De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium.
| | - B Mesuere
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000, Ghent, Belgium
| | - F Van der Jeugt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - A Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - T Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - B Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - P Dawyndt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - J Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - E E Kuramae
- Netherlands Institute of Ecology, department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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Cipriano MAP, Suleiman AKA, da Silveira APD, do Carmo JB, Kuramae EE. Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop. PeerJ 2019; 7:e6768. [PMID: 31024771 PMCID: PMC6475576 DOI: 10.7717/peerj.6768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/12/2019] [Indexed: 11/20/2022] Open
Abstract
The use of residue of sugarcane ethanol industry named vinasse in fertirrigation is an established and widespread practice in Brazil. Both non-concentrated vinasse (NCV) and concentrated vinasse (CV) are used in fertirrigation, particularly to replace the potassium fertilizer. Although studies on the chemical and organic composition of vinasse and their impact on nitrous oxide emissions when applied in soil have been carried out, no studies have evaluated the microbial community composition and diversity in different forms of vinasse. We assessed the bacterial community composition of NCV and CV by non-culturable and culturable approaches. The non-culturable bacterial community was assessed by next generation sequencing of the 16S rRNA gene and culturable community by isolation of bacterial strains and molecular and biochemical characterization. Additionally, we assessed in the bacterial strains the presence of genes of nitrogen cycle nitrification and denitrification pathways. The microbial community based on 16S rRNA sequences of NCV was overrepresented by Bacilli and Negativicutes while CV was mainly represented by Bacilli class. The isolated strains from the two types of vinasse belong to class Bacilli, similar to Lysinibacillus, encode for nirK gene related to denitrification pathway. This study highlights the bacterial microbial composition particularly in CV what residue is currently recycled and recommended as a sustainable practice in sugarcane cultivation in the tropics.
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Affiliation(s)
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | | | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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22
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Cassman NA, Soares JR, Pijl A, Lourenço KS, van Veen JA, Cantarella H, Kuramae EE. Nitrification inhibitors effectively target N 2 O-producing Nitrosospira spp. in tropical soil. Environ Microbiol 2019; 21:1241-1254. [PMID: 30735001 PMCID: PMC6850170 DOI: 10.1111/1462-2920.14557] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/09/2019] [Accepted: 02/04/2019] [Indexed: 01/01/2023]
Abstract
The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.
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Affiliation(s)
- Noriko A. Cassman
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Johnny R. Soares
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Agata Pijl
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Késia S. Lourenço
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Johannes A. van Veen
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
| | - Heitor Cantarella
- Soil Sciences and Fertility, Soil and Environmental Resources Center, Agronomic Institute of CampinasP.O. Box 28, 13012‐970, CampinasSPBrazil
| | - Eiko E. Kuramae
- Department of Microbial EcologyNetherlands Institute for Ecology NIOO‐KNAWWageningenNetherlands
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