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He T, Lin W, Yang S, Du J, Giri B, Feng C, Gilliam FS, Zhang F, Zhang X, Zhang X. Arbuscular mycorrhizal fungi reduce soil N 2O emissions by altering root traits and soil denitrifier community composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173065. [PMID: 38723969 DOI: 10.1016/j.scitotenv.2024.173065] [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: 02/29/2024] [Revised: 04/23/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) increase the ability of plants to obtain nitrogen (N) from the soil, and thus can affect emissions of nitrous oxide (N2O), a long-lived potent greenhouse gas. However, the mechanisms underlying the effects of AMF on N2O emissions are still poorly understood, particularly in agroecosystems with different forms of N fertilizer inputs. Utilizing a mesocosm experiment in field, we examined the effects of AMF on N2O emissions via their influence on maize root traits and denitrifying microorganisms under ammonia and nitrate fertilizer input using 15N isotope tracer. Here we show that the presence of AMF alone or both maize roots and AMF increased maize biomass and their 15N uptake, root length, root surface area, and root volume, but led to a reduction in N2O emissions under both N input forms. Random forest model showed that root length and surface area were the most important predictors of N2O emissions. Additionally, the presence of AMF reduced the (nirK + nirS)/nosZ ratio by increasing the relative abundance of nirS-Bradyrhizobium and Rubrivivax with ammonia input, but reducing nosZ-Azospirillum, Cupriavidus and Rhodopseudomonas under both fertilizer input. Further, N2O emissions were significantly and positively correlated with the nosZ-type Azospirillum, Cupriavidus and Rhodopseudomonas, but negatively correlated with the nirS-type Bradyrhizobium and Rubrivivax. These results indicate that AMF reduce N2O emissions by increasing root length to explore N nutrients and altering the community composition of denitrifiers, suggesting that effective management of N fertilizer forms interacting with the rhizosphere microbiome may help mitigate N2O emissions under future N input scenarios.
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Affiliation(s)
- Tangqing He
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China
| | - Wei Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Shuo Yang
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China
| | - Jiaqi Du
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China
| | - Bhoopander Giri
- Department of Botany, Swami Shraddhanand College, University of Delhi, Delhi, India
| | - Cheng Feng
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China
| | - Frank S Gilliam
- Department of Earth and Environmental Sciences, University of West Florida, Pensacola FL32514, USA
| | - Fuliang Zhang
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China
| | - Xiaoquan Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450046, PR China.
| | - Xuelin Zhang
- College of Agronomy, Henan Agricultural University, Co-construction State Key, Laboratory of Wheat and Maize Crop Science, Zhengzhou 450046, PR China.
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Ma B, Wang Y, Zhao K, Stirling E, Lv X, Yu Y, Hu L, Tang C, Wu C, Dong B, Xue R, Dahlgren RA, Tan X, Dai H, Zhu YG, Chu H, Xu J. Biogeographic patterns and drivers of soil viromes. Nat Ecol Evol 2024; 8:717-728. [PMID: 38383853 DOI: 10.1038/s41559-024-02347-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Erinne Stirling
- Agriculture and Food, CSIRO, Adelaide, South Australia, Australia
- Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Yijun Yu
- Arable Soil Quality and Fertilizer Administration Bureau of Zhejiang Province, Hangzhou, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Chao Tang
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Chuyi Wu
- School of Earth Sciences, Zhejiang University, Hangzhou, China
| | - Baiyu Dong
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Ran Xue
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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3
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Gong JC, Li BH, Hu JW, Li PF, Liu Q, Yang GP, Liu CY. Driving force of tidal pulses on denitrifiers-dominated nitrogen oxide emissions from intertidal wetland sediments. WATER RESEARCH 2023; 247:120770. [PMID: 37897991 DOI: 10.1016/j.watres.2023.120770] [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: 05/19/2023] [Revised: 09/12/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Intertidal wetland sediments are an important source of atmospheric nitrogen oxides (NOx), but their contribution to the global NOx budget remains unclear. In this work, we conducted year-round and diurnal observations in the intertidal wetland of Jiaozhou Bay to explore their regional source-sink patterns and influence factors on NOx emissions (initially in the form of nitric oxide) and used a dynamic soil reactor to further extend the mechanisms underlying the tidal pulse of nitric oxide (NO) observed in our investigations. The annual fluxes of NOx in the vegetated wetland were significantly higher than those in the wetland without vegetation. Their annual variations could be attributed to changes in temperature and the amount of organic carbon in the sediment, which was derived from vegetated plants and promoted the carbon-nitrogen cycle. Anaerobic denitrifiers had advantages in the intertidal wetland sediment and accounted for the major NO production (63.8 %) but were still limited by nitrite and nitrate concentrations in the sediment. Moreover, the tidal pulse was likely a primary driver of NOx emissions from intertidal wetlands over short periods, which was not considered in previous investigations. The annual NO exchange flux considering the tide pulse contribution (8.93 ± 1.72 × 10-2 kg N ha-1 yr-1) was significantly higher than that of the non-pulse period (4.14 ± 1.13 × 10-2 kg N ha-1 yr-1) in our modeling result for the fluxes over the last decade. Therefore, the current measurement of NOx fluxes underestimated the actual gas emission without considering the tidal pulse.
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Affiliation(s)
- Jiang-Chen Gong
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Bing-Han Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jing-Wen Hu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Pei-Feng Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Qian Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Chun-Ying Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Shan Y, Fu Y, Wang L, Yao Y. Response of the nitrogen processing bacterial community to water level fluctuation and nitrate availability in an intact marsh soil column. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:111947-111957. [PMID: 37819472 DOI: 10.1007/s11356-023-30020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Wetlands are known to experience fluctuations in water levels and receive exogenous nitrogen inputs that affect various organisms, including soil microorganisms. To study the impact of these factors on microbial diversity, we collected intact soil columns from a Phragmites australis-dominated site in the Qixing River National Nature Reserve in Northeast China. In a laboratory experiment, we simulated water level fluctuations and exogenous nitrogen inputs to the soil columns and examined the associated changes in the relative abundance of 51 bacterial genera involved in nitrogen cycling processes. Our findings revealed that different bacterial genera exhibited varying relative abundances across treatments. Specifically, Massilia showed the highest total relative abundance at the genus level, while Planctomyces had the second highest, and Campylobacter had the lowest abundance. The DESeq2 model, based on negative binomial distribution, revealed that the tags of bacterial genera were significantly correlated with soil depth, but not with water levels or nitrogen concentrations. However, the addition of a 30 mg/L nitrate solution caused a decrease in the relative abundances of bacterial genera with decreasing water levels, while a 60 mg/L concentration of nitrogen resulted in a decrease and then an increase in the relative abundances of bacterial genera with decreasing water levels. Our study provides valuable insights into the response of nitrogen-cycling bacteria to changes in different environmental conditions.
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Affiliation(s)
- Yuanqi Shan
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Yi Fu
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Lei Wang
- College of Landscape Architectrue, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Yunlong Yao
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China.
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China.
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5
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Purchase ML, Bending GD, Mushinski RM. Spatiotemporal Variations of Soil Reactive Nitrogen Oxide Fluxes across the Anthropogenic Landscape. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16348-16360. [PMID: 37856795 PMCID: PMC10620987 DOI: 10.1021/acs.est.3c05849] [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: 07/21/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
Volatile reactive nitrogen oxides (NOy) are significant atmospheric pollutants, including NOx (nitric oxide [NO] + nitrogen dioxide [NO2]) and NOz (nitrous acid [HONO] + nitric acid [HNO3] + nitrogen trioxide [NO3] + ...). NOy species are products of nitrogen (N) cycle processes, particularly nitrification and denitrification. Biogenic sources, including soil, account for over 50% of natural NOy emissions to the atmosphere, yet emissions from soils are generally not included in atmospheric models as a result of a lack of mechanistic data. This work is a unique investigation of NOy fluxes on a landscape scale, taking a comprehensive set of land-use types, human influence, and seasonality into account to determine large-scale heterogeneity to provide a basis for future modeling and hypothesis generation. By coupling 16S rRNA amplicon sequencing and quantitative polymerase chain reaction, we have linked significant differences in functional potential and activity of nitrifying and denitrifying soil microbes to NOy emissions from soils. Further, we have identified soils subject to increased N deposition that are less microbially active despite increased available N, potentially as a result of poor soil health from anthropogenic pollution. Structural equation modeling suggests human influence on soils to be a more significant effector of soil NOy emissions than land-use type.
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Affiliation(s)
- Megan L Purchase
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ryan M Mushinski
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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6
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Shang S, Song M, Wang C, Dou X, Wang J, Liu F, Zhu C, Wang S. Decrease of nitrogen cycle gene abundance and promotion of soil microbial-N saturation restrain increases in N 2O emissions in a temperate forest with long-term nitrogen addition. CHEMOSPHERE 2023; 338:139378. [PMID: 37419152 DOI: 10.1016/j.chemosphere.2023.139378] [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: 04/04/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Increases in soil available nitrogen (N) influence N-cycle gene abundances and emission of nitrous oxide (N2O), which is primarily due to N-induced soil acidification in forest. Moreover, the extent of microbial-N saturation could control microbial activity and N2O emission. The contributions of N-induced alterations of microbial-N saturation and N-cycle gene abundances to N2O emission have rarely been quantified. Here, the mechanism underlying N2O emission under N additions (three chemical forms of N, i.e., NO3--N, NH4+-N and NH4NO3-N, and each at two rates, 50 and 150 kg N ha-1 year-1, respectively) spanning 2011-2021 was investigated in a temperate forest in Beijing. Results showed N2O emissions increased at both low and high N rates of all the three forms compared with control during the whole experiment. However, N2O emissions were lower in high rate of NH4NO3-N and NH4+-N treatments than the corresponding low N rates in the recent three years. Effects of N on microbial-N saturation and abundances of N-cycle genes were dependent on the N rate and form as well as experimental time. Specifically, negative effects of N on N-cycle gene abundances and positive effects of N on microbial-N saturation were demonstrated in high N rate treatments, particularly with NH4+ addition during 2019-2021. Such effects were associated with soil acidification. A hump-backed trend between microbial-N saturation and N2O emissions was observed, suggesting N2O emissions decreased with increase of the microbial-N saturation. Furthermore, N-induced decreases in N-cycle gene abundances restrained N2O emissions. In particular, the nitrification process, dominated by ammonia-oxidize archaea, is critical to determination of N2O emissions in response to the N addition in the temperate forest. We confirmed N addition promoted soil microbial-N saturation and reduced N-cycle gene abundances, which restrained the continuous increase in N2O emissions. It is important for understanding the forest-N-microbe nexus under climate change.
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Affiliation(s)
- Shuaishuai Shang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Minghua Song
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, A11, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chunmei Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaomin Dou
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxin Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Fangfang Liu
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Chenying Zhu
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Shiqi Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
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Hu X, Gu H, Sun X, Wang Y, Liu J, Yu Z, Li Y, Jin J, Wang G. Distinct influence of conventional and biodegradable microplastics on microbe-driving nitrogen cycling processes in soils and plastispheres as evaluated by metagenomic analysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131097. [PMID: 36898310 DOI: 10.1016/j.jhazmat.2023.131097] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Plastic mulching is one of the large contributors to microplastic (MP) accumulation in agricultural landscapes. However, the effects of conventional (PE-MPs) and biodegradable MPs (BMPs) on microbial functional and genomic information encoding nitrogen (N) cycling have yet to be addressed. Here, a soil microcosmic experiment was conducted by adding PE-MPs and BMPs to a Mollisol at dosage of 5% (w/w) followed by incubation for 90 days. The soils and MPs were examined by metagenomics and genome binning methods. The results revealed that BMPs harbored rougher surfaces and induced stronger alterations in microbial functional and taxonomic profiles in the soil and plastisphere than PE-MPs. In comparison to their respective soils, the plastispheres of PE-MPs and BMPs stimulated the processes of N fixation, N degradation and assimilatory nitrate reduction (ANRA) and reduced the gene abundances encoding nitrification and denitrification, in which BMPs induced stronger influences than PE-MPs. Ramlibacter mainly drove the differences in N cycling processes between the soils containing two types of MPs and was further enriched in the BMP plastisphere. Three high-quality genomes were identified as Ramlibacter stains with higher abundances in the plastisphere of BMP than that of PE-MP. These Ramlibacter strains had the metabolic capacities of N fixation, N degradation, ANRA and ammonium transport, which were potentially attributed to their biosynthesis and the accumulation of soil NH4+-N. Taken together, our results highlight the genetic mechanisms of soil N bioavailability in the presence of biodegradable MPs, which have important implications for maintaining sustainable agriculture and controlling microplastic risk.
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Affiliation(s)
- Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongbin Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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Singavarapu B, Du J, Beugnon R, Cesarz S, Eisenhauer N, Xue K, Wang Y, Bruelheide H, Wubet T. Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity. Microbiol Spectr 2023; 11:e0457822. [PMID: 36951585 PMCID: PMC10111882 DOI: 10.1128/spectrum.04578-22] [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: 11/09/2022] [Accepted: 02/11/2023] [Indexed: 03/24/2023] Open
Abstract
Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Jianqing Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Yanshan Earth Critical Zone National Research Station, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources, Chinese Academy of Sciences, Beijing, China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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10
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Guo Q, Ye J, Zeng J, Chen L, Korpelainen H, Li C. Selenium species transforming along soil-plant continuum and their beneficial roles for horticultural crops. HORTICULTURE RESEARCH 2023; 10:uhac270. [PMID: 36789256 PMCID: PMC9923214 DOI: 10.1093/hr/uhac270] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/01/2022] [Indexed: 05/15/2023]
Abstract
Selenium (Se) acquirement from daily diet can help reduce the risk of many diseases. The edible parts of crop plants are the main source of dietary Se, while the Se content in crops is determined by Se bioavailability in soil. We summarize recent research on the biogeochemical cycle of Se driven by specific microorganisms and emphasize the oxidizing process in the Se cycle. Moreover, we discuss how plant root exudates and rhizosphere microorganisms affect soil Se availability. Finally, we cover beneficial microorganisms, including endophytes, that promote crop quality and improve crop tolerance to environmental stresses. Se availability to plants depends on the balance between adsorption and desorption, reduction, methylation and oxidation, which are determined by interactions among soil properties, microbial communities and plants. Reduction and methylation processes governed by bacteria or fungi lead to declined Se availability, while Se oxidation regulated by Se-oxidizing microorganisms increases Se availability to plants. Despite a much lower rate of Se oxidization compared to reduction and methylation, the potential roles of microbial communities in increasing Se bioavailability are probably largely underestimated. Enhancing Se oxidation and Se desorption are crucial for the promotion of Se bioavailability and uptake, particularly in Se-deficient soils. Beneficial roles of Se are reported in terms of improved crop growth and quality, and enhanced protection against fungal diseases and abiotic stress through improved photosynthetic traits, increased sugar and amino acid contents, and promoted defense systems. Understanding Se transformation along the plant-soil continuum is crucial for agricultural production and even for human health.
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Affiliation(s)
- Qingxue Guo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Jianhui Ye
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianming Zeng
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Liang Chen
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Finland
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11
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Zhang M, Liu S, Cao X, Chen M, Chen J, Xu G, Shi Z. The effects of ectomycorrhizal and saprotropic fungi on soil nitrogen mineralization differ from those of arbuscular and ericoid mycorrhizal fungi on the eastern Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2023; 13:1069730. [PMID: 36684739 PMCID: PMC9846110 DOI: 10.3389/fpls.2022.1069730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Interactions between soil fungi and soil environmental factors regulate soil nitrogen (N) mineralization rates on the eastern Qinghai-Tibetan Plateau. Some studies have also illuminated differences in soil N mineralization rate based on different mycorrhizal forests, but the associated effect of soil fungal functional guilds and soil environmental factors underlying this process are not well-understood. Three primary forests respectively dominated by Abies fargesii var. faxoniana (ectomycorrhizal, EcM), Cupressus chengiana (arbuscular mycorrhizal, AM) and Rhododendron phaeochrysum (ericoid mycorrhizal, ErM) trees were selected in this area. Meanwhile, soil net N mineralization rate, soil fungal composition and soil enzyme activity among these three mycorrhizal forests were studied. Our results showed that there were significant differences in the seasonal variation of soil net N mineralization rates among three mycorrhizal forests. Soil net N mineralization rate in the AM forest was faster. EcM fungi and saprotroph are the main functional guilds in these three mycorrhizal forests. Meanwhile, the relative abundances of soil fungal functional guilds, soil temperature and soil peroxidase activity could explain 85.0% in the difference of soil net ammonification rate among three mycorrhizal forests. In addition, soil temperature, soil water-filled pore space and soil ammonium content play a central role in controlling the differing soil net nitrification rate among three mycorrhizal forests. Our results suggest differences in soil net mineralization among different mycorrhizal forest types are driven mainly by soil net ammonification. Soil fungal functional guilds and temperature regulate the rate of soil net ammonification by modulating soil peroxidase activity.
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Affiliation(s)
- Miaomiao Zhang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Shun Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Xiangwen Cao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Miao Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Jian Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Gexi Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
| | - Zuomin Shi
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County, Sichuan, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
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12
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Guo Q, Liu L, Liu J, Korpelainen H, Li C. Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions. MICROBIOME 2022; 10:191. [PMID: 36333709 PMCID: PMC9636617 DOI: 10.1186/s40168-022-01387-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/09/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Dioecious plants have coevolved with diverse plant microbiomes, which are crucial for the fitness and productivity of their host. Sexual dimorphism in morphology, physiology, or gene expression may relate to different microbial compositions that affect male and female fitness in different environments. However, sex-specific impacts on ecological processes that control the microbiome assembly are not well known. In this study, Populus cathayana males and females were planted in different nitrogen conditions. It was hypothesized that males and females differently affect bacterial and fungal communities in the rhizosphere soil, roots, old leaves, and young leaves. Physiological traits and transcriptome profiles of male and female plants were investigated to reveal potential mechanisms that control the microbiome assembly. RESULTS Our results showed strong niche differentiation that shapes microbial communities leading to a rapid loss of diversity along a decreasing pH gradient from the rhizosphere soil to leaves. Sex had different impacts on the microbial assembly in each niche. Especially fungal endophytes showed great differences in the community structure, keystone species, and community complexity between P. cathayana males and females. For example, the fungal co-occurrence network was more complex and the alpha diversity was significantly higher in young female leaves compared to young male leaves. Transcriptome profiles revealed substantial differences in plant-pathogen interactions and physiological traits that clearly demonstrated divergent internal environments for endophytes inhabiting males and females. Starch and pH of young leaves significantly affected the abundance of Proteobacteria, while tannin and pH of roots showed significant effects on the abundance of Chloroflexi, Actinobacteria, and Proteobacteria, and on the bacterial Shannon diversity. CONCLUSION Our results provided important knowledge for understanding sexual dimorphism that affects microbial assemblies, thus advancing our understanding of plant-microbiome interactions. Video Abstract.
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Affiliation(s)
- Qingxue Guo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Lin Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiantong Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Helsinki, Finland
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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13
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Qiu Q, Mgelwa AS, Jin S, Hu Y. Nitrogen-Induced Changes in Soil Environmental Factors Are More Important Than Nitrification and Denitrification Gene Abundance in Regulating N 2O Emissions in Subtropical Forest Soils. FRONTIERS IN PLANT SCIENCE 2022; 13:950367. [PMID: 35903223 PMCID: PMC9315429 DOI: 10.3389/fpls.2022.950367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Subtropical regions are currently experiencing a dramatic increase in nitrogen (N) deposition; however, the contributions of nitrification and denitrification processes to soil N2O emissions and the underlying mechanisms under increasing N deposition remain unclear. Therefore, a 15N-tracing laboratory experiment with four N application rates (0, 12.5, 25, and 50 μg 15N g-1 soil) was conducted to investigate the response of nitrification- and denitrification-derived N2O to N additions in an evergreen broad-leaved forest (BF) and a Pinus forest (PF) in the Wuyi Mountains in southeastern China. Moreover, the abundance of functional genes related to nitrification (amoA), denitrification (nirK, nirS, and nosZ), and soil properties were measured to clarify the underlying mechanisms. Results showed that nitrification-derived N2O emissions were generally decreased with increasing N input. However, denitrification-derived N2O emissions were a non-linear response to N additions, with maximum N2O emissions at the middle N application rate. Denitrification-derived N2O was the dominant pathway of N2O production, accounting for 64 to 100% of the total N2O fluxes. Soil NH4 +-N content and pH were the predominant factors in regulating nitrification-derived N2O emissions in BF and PF, respectively. Soil pH and the nirS abundance contributed the most to the variations of denitrification-derived N2O emissions in BF and PF, respectively. Our results suggest that N application has the potential to increase the contribution of denitrification to N2O production in subtropical forest soils. Changes in soil chemical properties induced by N addition are more important than the abundance of nitrification and denitrification functional genes in regulating soil nitrification- and denitrification-derived N2O emissions.
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Affiliation(s)
- Qingyan Qiu
- Forest Ecology and Stable Isotope Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Abubakari Said Mgelwa
- College of Natural Resources Management and Tourism, Mwalimu Julius K. Nyerere University of Agriculture and Technology, Musoma, Tanzania
| | - Shaofei Jin
- Department of Geography, Minjiang University, Fuzhou, China
| | - Yalin Hu
- Forest Ecology and Stable Isotope Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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14
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Liu J, Wang X, Liu L, Wu X, Xia Z, Guo Q. Rhizosphere soil bacterial communities and nitrogen cycling affected by deciduous and evergreen tree species. Ecol Evol 2022; 12:e9103. [PMID: 35845380 PMCID: PMC9277416 DOI: 10.1002/ece3.9103] [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: 12/24/2021] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/12/2022] Open
Abstract
Deciduous and evergreen trees differ in their responses to drought and nitrogen (N) demand. Whether or not these functional types affect the role of the bacterial community in the N cycle during drought remains uncertain. Two deciduous tree species (Alnus cremastogyne, an N2-fixing species, and Liquidambar formosana) and two evergreen trees (Cunninghamia lanceolata and Pinus massoniana) were used to assess factors in controlling rhizosphere soil bacterial community and N cycling functions. Photosynthetic rates and biomass production of plants, 16S rRNA sequencing and N-cycling-related genes of rhizosphere soil were measured. The relative abundance of the phyla Actinobacteria and Firmicutes was higher, and that of Proteobacteria, Acidobacteria, and Gemmatimondaetes was lower in rhizosphere soil of deciduous trees than that of evergreen. Beta-diversity of bacterial community also significantly differed between the two types of trees. Deciduous trees showed significantly higher net photosynthetic rates and biomass production than evergreen species both at well water condition and short-term drought. Root biomass was the most important factor in driving soil bacterial community and N-cycling functions than total biomass and aboveground biomass. Furthermore, 44 bacteria genera with a decreasing response and 46 taxa showed an increased response along the root biomass gradient. Regarding N-cycle-related functional genes, copy numbers of ammonia-oxidizing bacteria (AOB) and autotrophic ammonia-oxidizing archaea (AOA), N2 fixation gene (nifH), and denitrification genes (nirK, nirS) were significantly higher in the soil of deciduous trees than in that of the evergreen. Structural equation models explained 50.2%, 47.6%, 48.6%, 49.4%, and 37.3% of the variability in copy numbers of nifH, AOB, AOA, nirK, and nirS, respectively, and revealed that root biomass had significant positive effects on copy numbers of all N-cycle functional genes. In conclusion, root biomass played key roles in affecting bacterial community structure and soil N cycling. Our findings have important implications for our understanding of plants control over bacterial community and N-cycling function in artificial forest ecosystems.
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Affiliation(s)
- Jiantong Liu
- Department of Ecology, College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Xinyu Wang
- Department of Ecology, College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Lin Liu
- Department of Ecology, College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Xuefeng Wu
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station Northeast Normal University Changchun China
| | - Zhichao Xia
- Department of Ecology, College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Qingxue Guo
- Department of Ecology, College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
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15
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Gardner CM, Gerhard WA, Redfern LK, Gunsch CK. Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35319433 DOI: 10.1099/mic.0.001155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r S≥0.70 or r S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.
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Affiliation(s)
- Courtney M Gardner
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Washington State University, Civil and Environmental Engineering, 405 Spokane St., PO Box 642910, Pullman, WA 99164, USA
| | - William A Gerhard
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA
| | - Lauren K Redfern
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Florida Gulf Coast University, Environmental and Civil Engineering, 10501 FGCU Blvd. South, Ft. Myers, FL 33965, USA
| | - Claudia K Gunsch
- Duke University, Civil and Environmental Engineering, Durham, NC 27708, USA.,Present address: Duke University, Durham, NC 27708, USA
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16
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García-Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. GLOBAL CHANGE BIOLOGY 2022. [PMID: 34923712 DOI: 10.6084/m9.figshare.14370896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Feng Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Diego Abalos
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Pablo García-Palacios
- Departamento de Biología y Geología, Física y Química Inorgánica y Analítica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
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17
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García‐Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. GLOBAL CHANGE BIOLOGY 2022; 28:2158-2168. [PMID: 34923712 PMCID: PMC9303726 DOI: 10.1111/gcb.16042] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/10/2021] [Indexed: 05/15/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Feng Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Diego Abalos
- Department of AgroecologyAarhus UniversityTjeleDenmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Dafeng Hui
- Department of Biological SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Pablo García‐Palacios
- Departamento de Biología y GeologíaFísica y Química Inorgánica y AnalíticaEscuela Superior de Ciencias Experimentales y TecnologíaUniversidad Rey Juan CarlosMóstolesSpain
- Instituto de Ciencias AgrariasConsejo Superior de Investigaciones CientíficasMadridSpain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate EcosystemsUniversity of GöttingenGöttingenGermany
- Agro‐Technological InstituteRUDN UniversityMoscowRussia
- Institute of Environmental SciencesKazan Federal UniversityKazanRussia
| | - Jørgen Eivind Olesen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Uffe Jørgensen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Ji Chen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
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18
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Ke P, Kang R, Avery LK, Zhang J, Yu Q, Xie D, Duan L. Temporal variations of soil NO and NO 2 fluxes in two typical subtropical forests receiving contrasting rates of N deposition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118696. [PMID: 34953951 DOI: 10.1016/j.envpol.2021.118696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Soils have been widely acknowledged as important natural sources of nitric oxide (NO) and meanwhile sinks of nitric dioxide (NO2). High nitrogen deposition across South China could potentially result in large NO emissions from subtropical forests soils there. In this study, the dynamic chamber method was applied to monitor NO and NO2 fluxes at two subtropical forest sites in South China, namely "Qianyanzhou" (QYZ) and "Tieshanping" (TSP). Chronically higher N deposition occurred at TSP than that at QYZ. Besides soil water filled pore spaces (WFPS) and temperature, ambient NO concentration could also possibly be important in regulating temporal NO emissions, especially in the winter. For both sites, the optimum soil temperature was above 25 °C, while the optimum WFPS for NO release at QYZ was higher (65-70%) than that at TSP (<23%). Moreover, heavy rainfall could trigger NO emission pulses from moist soils at QYZ, while rainfall-induced NO pulses were only observed after a long drying period at TSP. Distinctly different contents of mineral nitrogen and soil moisture conditions between the two sites might induce the divergent preference of WFPS and responses to rainfall. The cumulative soil emission of NO reached 0.41 ± 0.01 and 0.76 ± 0.01 kg N ha-1 yr-1 at QYZ and TSP, contributing to 2.5% and 1.4% of the annual throughfall N input, respectively. At both sites, NO2 were mainly deposited to soils, accounting for 2% and 21% of soil-emitted NO at QYZ and TSP, respectively. The observed annual NO emissions at these two sites were larger than the median values observed for tropical and temperate forests and unfertilized croplands. Higher N deposition could induce larger NO emission potential, while soil temperature and pH might also be important in regulating regional soil NO emissions as N-loss from subtropical forests.
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Affiliation(s)
- Piaopiao Ke
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Ronghua Kang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Loreena K Avery
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jiawei Zhang
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Qian Yu
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Danni Xie
- School of Land Engineering, Chang'an University, Shanxi, 710064, China
| | - Lei Duan
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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19
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Gill NS, Turner MG, Brown CD, Glassman SI, Haire SL, Hansen WD, Pansing ER, St Clair SB, Tomback DF. Limitations to Propagule Dispersal Will Constrain Postfire Recovery of Plants and Fungi in Western Coniferous Forests. Bioscience 2022. [DOI: 10.1093/biosci/biab139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Many forest species are adapted to long-interval, high-severity fires, but the intervals between severe fires are decreasing with changes in climate, land use, and biological invasions. Although the effects of changing fire regimes on some important recovery processes have previously been considered, the consequences for the dispersal of propagules (plant seeds and fungal spores) in forest communities have not. We characterize three mechanisms by which changing fire regimes disrupt propagule dispersal in mesic temperate, boreal, and high-elevation forests: reduced abundance and altered spatial distributions of propagule source populations, less effective dispersal of propagules by wind, and altered behavior of animal dispersers and propagule predators. We consider how disruptions to propagule dispersal may interact with other factors that are also influenced by fire regime change, potentially increasing risk of forest conversion. Finally, we highlight urgent research topics regarding how dispersal limitation may shape twenty-first century forest recovery after stand-replacing fire.
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Affiliation(s)
- Nathan S Gill
- Texas Tech University, Lubbock, Texas, United States
| | - Monica G Turner
- University of Wisconsin–Madison, Madison, Wisconsin, United States
| | - Carissa D Brown
- Memorial University, St. John's, Newfoundland and Labrador, Canada
| | | | - Sandra L Haire
- Haire Laboratory for Landscape Ecology, Tucson, Arizona, United States
| | | | | | | | - Diana F Tomback
- University of Colorado Denver, Denver, Colorado, United States
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20
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Chuckran PF, Hungate BA, Schwartz E, Dijkstra P. Variation in genomic traits of microbial communities among ecosystems. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ABSTRACT
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size—reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments—a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
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Affiliation(s)
- Peter F Chuckran
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Dijkstra
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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21
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Yang Y, Xiao Y, Li C, Wang B, Gao Y, Zhou G. Nitrogen addition, rather than altered precipitation, stimulates nitrous oxide emissions in an alpine steppe. Ecol Evol 2021; 11:15153-15163. [PMID: 34765167 PMCID: PMC8571595 DOI: 10.1002/ece3.8196] [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: 05/20/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 11/25/2022] Open
Abstract
Anthropogenic-driven global change, including changes in atmospheric nitrogen (N) deposition and precipitation patterns, is dramatically altering N cycling in soil. How long-term N deposition, precipitation changes, and their interaction influence nitrous oxide (N2O) emissions remains unknown, especially in the alpine steppes of the Qinghai-Tibetan Plateau (QTP). To fill this knowledge gap, a platform of N addition (10 g m-2 year-1) and altered precipitation (±50% precipitation) experiments was established in an alpine steppe of the QTP in 2013. Long-term N addition significantly increased N2O emissions. However, neither long-term alterations in precipitation nor the co-occurrence of N addition and altered precipitation significantly affected N2O emissions. These unexpected findings indicate that N2O emissions are particularly susceptible to N deposition in the alpine steppes. Our results further indicated that both biotic and abiotic properties had significant effects on N2O emissions. N2O emissions occurred mainly due to nitrification, which was dominated by ammonia-oxidizing bacteria, rather than ammonia-oxidizing archaea. Furthermore, the alterations in belowground biomass and soil temperature induced by N addition modulated N2O emissions. Overall, this study provides pivotal insights to aid the prediction of future responses of N2O emissions to long-term N deposition and precipitation changes in alpine ecosystems. The underlying microbial pathway and key predictors of N2O emissions identified in this study may also be used for future global-scale model studies.
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Affiliation(s)
- Yang Yang
- Northwest Institute of Plateau BiologyChinese Academy of ScienceXiningChina
- University of Chinese Academy of ScienceBeijingChina
| | - Yuanming Xiao
- Northwest Institute of Plateau BiologyChinese Academy of ScienceXiningChina
- University of Chinese Academy of ScienceBeijingChina
| | - Changbin Li
- College of Agriculture and Animal HusbandryQinghai UniversityXiningChina
| | - Bo Wang
- Northwest Institute of Plateau BiologyChinese Academy of ScienceXiningChina
- University of Chinese Academy of ScienceBeijingChina
| | - Yongheng Gao
- Northwest Institute of Plateau BiologyChinese Academy of ScienceXiningChina
- Institute of Mountain Hazards and EnvironmentChinese Academy of ScienceChengduChina
| | - Guoying Zhou
- Northwest Institute of Plateau BiologyChinese Academy of ScienceXiningChina
- Key Laboratory of Tibetan Medicine ResearchChinese Academy of SciencesXiningChina
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22
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Beidler KV, Oh YE, Pritchard SG, Phillips RP. Mycorrhizal roots slow the decay of belowground litters in a temperate hardwood forest. Oecologia 2021; 197:743-755. [PMID: 34626268 DOI: 10.1007/s00442-021-05051-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/26/2021] [Indexed: 11/24/2022]
Abstract
There is increasing evidence that plant roots and mycorrhizal fungi, whether living or dead, play a central role in soil carbon (C) cycling. Root-mycorrhizal-microbial interactions can both suppress and enhance litter decay, with the net result dependent upon belowground nutrient acquisition strategies and soil nutrient availability. We measured the net effect of living roots and mycorrhizal fungi on the decay of dead roots and fungal hyphae in a hardwood forest dominated by either sugar maple (Acer saccharum) or white oak (Quercus alba) trees. Root and fungal litter were allowed to decompose within root-ingrowth bags and root-exclusion cores. In conjunction with root effects on decay, we assessed foraging responses and root induced changes in soil moisture, nitrogen (N) availability and enzyme activity. After 1 year, maple root production increased, and mycorrhizal fungal colonization decreased in the presence of decaying litter. In addition, we found that actively foraging roots suppressed the decay of root litter (- 14%) more than fungal litter (- 3%), and suppression of root decay was stronger for oak (- 20%) than maple roots (- 8%). Suppressive effects of oak roots on decay were greatest when roots also reduced soil N availability, which corresponded with reductions in hydrolytic enzyme activity and enhanced oxidative enzyme activities. These findings further our understanding of context-dependent drivers of root-mycorrhizal-microbial interactions and demonstrate that such interactions can play an underappreciated role in soil organic matter accumulation and turnover in temperate forests.
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Affiliation(s)
- Katilyn V Beidler
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - Young E Oh
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Seth G Pritchard
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
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23
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Saifuddin M, Bhatnagar JM, Phillips RP, Finzi AC. Ectomycorrhizal fungi are associated with reduced nitrogen cycling rates in temperate forest soils without corresponding trends in bacterial functional groups. Oecologia 2021; 196:863-875. [PMID: 34170396 DOI: 10.1007/s00442-021-04966-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Microbial processes play a central role in controlling the availability of N in temperate forests. While bacteria, archaea, and fungi account for major inputs, transformations, and exports of N in soil, relationships between microbial community structure and N cycle fluxes have been difficult to detect and characterize. Several studies have reported differences in N cycling based on mycorrhizal type in temperate forests, but associated differences in N cycling genes underlying these fluxes are not well-understood. We explored how rates of soil N cycle fluxes vary across gradients of mycorrhizal abundance (hereafter "mycorrhizal gradients") at four temperate forest sites in Massachusetts and Indiana, USA. We paired measurements of N-fixation, net nitrification, and denitrification rates with gene abundance data for specific bacterial functional groups associated with each process. We find that the availability of NO3 and rates of N-fixation, net nitrification, and denitrification are reduced in stands dominated by trees associated with ECM fungi. On average, rates of N-fixation and denitrification in stands dominated by trees associated with arbuscular mycorrhizal fungi were more than double the corresponding rates in stands dominated by trees associated with ectomycorrhizal fungi. Despite the structuring of flux rates across the mycorrhizal gradients, we did not find concomitant shifts in the abundances of N-cycling bacterial genes, and gene abundances were not correlated with process rates. Given that AM-associating trees are replacing ECM-associating trees throughout much of the eastern US, our results suggest that shifts in mycorrhizal dominance may accelerate N cycling independent of changes in the relative abundance of N cycling bacteria, with consequences for forest productivity and N retention.
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