1
|
Fernández-Guisuraga JM, Ansola G, Pinto R, Marcos E, Calvo L, Sáenz de Miera LE. Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:171079. [PMID: 38373460 DOI: 10.1016/j.scitotenv.2024.171079] [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: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha-1 yr-1 for 3-years; and 56 kg N ha-1 yr-1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha-1 yr-1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.
Collapse
Affiliation(s)
- José Manuel Fernández-Guisuraga
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Centro de Investigação e de Tecnologias Agroambientais e Biológicas, Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Elena Marcos
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| |
Collapse
|
2
|
Li D, Meng M, Ren B, Ma X, Bai L, Li J, Bai G, Yao F, Tan C. Different responses of soil fungal and bacterial communities to nitrogen addition in a forest grassland ecotone. Front Microbiol 2023; 14:1211768. [PMID: 37736095 PMCID: PMC10510407 DOI: 10.3389/fmicb.2023.1211768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/14/2023] [Indexed: 09/23/2023] Open
Abstract
Introduction Continuous nitrogen deposition increases the nitrogen content of terrestrial ecosystem and affects the geochemical cycle of soil nitrogen. Forest-grassland ecotone is the interface area of forest and grassland and is sensitive to global climate change. However, the structure composition and diversity of soil microbial communities and their relationship with soil environmental factors at increasing nitrogen deposition have not been sufficiently studied in forest-grassland ecotone. Methods In this study, experiments were carried out with four nitrogen addition treatments (0 kgN·hm-2·a-1, 10 kgN·hm-2·a-1, 20 kgN·hm-2·a-1 and 40 kgN·hm-2·a-1) to simulate nitrogen deposition in a forest-grassland ecotone in northwest Liaoning Province, China. High-throughput sequencing and qPCR technologies were used to analyze the composition, structure, and diversity characteristics of the soil microbial communities under different levels of nitrogen addition. Results and discussion The results showed that soil pH decreased significantly at increasing nitrogen concentrations, and the total nitrogen and ammonium nitrogen contents first increased and then decreased, which were significantly higher in the N10 treatment than in other treatments (N:0.32 ~ 0.48 g/kg; NH4+-N: 11.54 ~ 13 mg/kg). With the increase in nitrogen concentration, the net nitrogen mineralization, nitrification, and ammoniation rates decreased. The addition of nitrogen had no significant effect on the diversity and structure of the fungal community, while the diversity of the bacterial community decreased significantly at increasing nitrogen concentrations. Ascomycetes and Actinomycetes were the dominant fungal and bacterial phyla, respectively. The relative abundance of Ascomycetes was negatively correlated with total nitrogen content, while that of Actinomycetes was positively correlated with soil pH. The fungal community diversity was significantly negatively correlated with nitrate nitrogen, while the diversity of the bacterial community was significantly positively correlated with soil pH. No significant differences in the abundance of functional genes related to soil nitrogen transformations under the different treatments were observed. Overall, the distribution pattern and driving factors were different in soil microbial communities in a forest-grassland ecotone in northwest Liaoning. Our study enriches research content related to factors that affect the forest-grassland ecotone.
Collapse
Affiliation(s)
- Daiyan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Meng Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Baihui Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinwei Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Long Bai
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Jiahuan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Guohua Bai
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
| | - Fengjun Yao
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
| | - Chunming Tan
- Zhangwu County Forest and Grass Development Service Center, Fuxin, Liaoning, China
| |
Collapse
|
3
|
Alcalá-Herrera R, Moreno B, Aguirrebengoa M, Winter S, Robles-Cruz AB, Ramos-Font ME, Benítez E. Role of Agricultural Management in the Provision of Ecosystem Services in Warm Climate Vineyards: Functional Prediction of Genes Involved in Nutrient Cycling and Carbon Sequestration. PLANTS (BASEL, SWITZERLAND) 2023; 12:527. [PMID: 36771611 PMCID: PMC9919410 DOI: 10.3390/plants12030527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
(1) Background: Maintaining soil fertility and crop productivity using natural microbial diversity could be a feasible approach for achieving sustainable development in agriculture. In this study, we compared soils from vineyards under organic and conventional management by predicting functional profiles through metagenomic analysis based on the 16S rRNA gene. (2) Methods: The structure, diversity and predictive functions of soil bacteria related to the biogeochemical cycle of the soil were analyzed, including oxidative and hydrolytic C-cycling enzymes, N-cycling enzymes and P-cycling enzymes. The inter-row spontaneous vegetation in the organic vineyards was also characterized. (3) Results: A clear effect of the farming system (organic vs. conventional) and cover management (herbicides plus tillage, mowing only and mowing plus tillage) on bacterial beta diversity and predicted functions was evidenced. While conventional viticulture increased the potential capacity of the soil to regulate the cycling of inorganic forms of N, organic viticulture in general enhanced those functions involving organic N, P and C substrates. Although the soil bacterial community responded differently to contrasting soil management strategies, nutrient cycling and carbon sequestration functions remained preserved, suggesting a high bacterial functional redundancy in the soil in any case. However, most of the predicted bacterial functions related to soil organic matter turnover were enhanced by organic management. (4) Conclusions: We posit the potential for organic viticulture to adequately address climate change adaptation in the context of sustainable agriculture.
Collapse
Affiliation(s)
- Rafael Alcalá-Herrera
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Beatriz Moreno
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Martin Aguirrebengoa
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| | - Silvia Winter
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Ana Belén Robles-Cruz
- Assessment, Restoration and Protection of Mediterranean Agrosystems Service (SERPAM), Estación Experimental del Zaidín, CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| | - María Eugenia Ramos-Font
- Assessment, Restoration and Protection of Mediterranean Agrosystems Service (SERPAM), Estación Experimental del Zaidín, CSIC, c/Profesor Albareda, 1, 18008 Granada, Spain
| | - Emilio Benítez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, c/Profesor Albareda 1, 18008 Granada, Spain
| |
Collapse
|
4
|
Yang X, Ni K, Shi Y, Yi X, Ji L, Wei S, Jiang Y, Zhang Y, Cai Y, Ma Q, Tang S, Ma L, Ruan J. Metagenomics reveals N-induced changes in carbon-degrading genes and microbial communities of tea (Camellia sinensis L.) plantation soil under long-term fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159231. [PMID: 36216053 DOI: 10.1016/j.scitotenv.2022.159231] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Soil organic carbon (SOC) is an important C pool of the global ecosystem and is affected by various agricultural practices including fertilization. Excessive nitrogen (N) application is an important field management measure in tea plantation systems. However, the mechanism underlying the impact of N fertilization on SOC, especially the microscopic mechanism remain unclear. The present study explored the effects of N fertilization on C-cycling genes, SOC-degrading enzymes and microbes expressing these enzymes by using a metagenomic approach in a tea plantation under long-term fertilization with different N rates. Results showed that N application significantly changed the abundance of C-cycling genes, SOC-degrading enzymes, especially those associated with labile and recalcitrant C degradation. In addition, the beta-glucosidase and chitinase-expressing microbial communities showed a significant difference under different N rates. At the phylum level, microbial taxa involved in C degradation were highly similar and abundant, while at the genus level, only specific taxa performed labile and recalcitrant C degradation; these SOC-degrading microbes were significantly enriched under N application. Redundancy analysis (RDA) revealed that the soil and pruned litter properties greatly influenced the SOC-degrading communities; pH and DOC of the soil and biomass and total polyphenol (TP) of the pruned litter exerted significant effects. Additionally, the random forest (RF) algorithm revealed that soil pH and dominant taxa efficiently predicted the beta-glucosidase abundance, while soil pH and DOC, pruned litter TP, and the highly abundant microbial taxa efficiently predicted chitinase abundance. Our study indicated that long-term N fertilization exerted a significant positive effect on SOC-degrading enzymes and microbes expressing these enzymes, resulting in potential impact on soil C storage in a perennial tea plantation ecosystem.
Collapse
Affiliation(s)
- Xiangde Yang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Kang Ni
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Yuanzhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Xiaoyun Yi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Lingfei Ji
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Sirou Wei
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Yanyan Jiang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Yongli Zhang
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China
| | - Yanjiang Cai
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qingxu Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Sheng Tang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Lifeng Ma
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China.
| | - Jianyun Ruan
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory of Tea Biology and Resource Utilization of Tea, The Ministry of Agriculture, Hangzhou 310008, China.
| |
Collapse
|
5
|
Abstract
Terrestrial ecosystem carbon (C) sequestration plays an important role in ameliorating global climate change. While tropical forests exert a disproportionately large influence on global C cycling, there remains an open question on changes in below-ground soil C stocks with global increases in nitrogen (N) deposition, because N supply often does not constrain the growth of tropical forests. We quantified soil C sequestration through more than a decade of continuous N addition experiment in an N-rich primary tropical forest. Results showed that long-term N additions increased soil C stocks by 7 to 21%, mainly arising from decreased C output fluxes and physical protection mechanisms without changes in the chemical composition of organic matter. A meta-analysis further verified that soil C sequestration induced by excess N inputs is a general phenomenon in tropical forests. Notably, soil N sequestration can keep pace with soil C, based on consistent C/N ratios under N additions. These findings provide empirical evidence that below-ground C sequestration can be stimulated in mature tropical forests under excess N deposition, which has important implications for predicting future terrestrial sinks for both elevated anthropogenic CO2 and N deposition. We further developed a conceptual model hypothesis depicting how soil C sequestration happens under chronic N deposition in N-limited and N-rich ecosystems, suggesting a direction to incorporate N deposition and N cycling into terrestrial C cycle models to improve the predictability on C sink strength as enhanced N deposition spreads from temperate into tropical systems.
Collapse
|
6
|
Zhang S, Shao L, Sun Z, Huang Y, Liu N. An atmospheric pollutant (inorganic nitrogen) alters the response of evergreen broad-leaved tree species to extreme drought. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109750. [PMID: 31655412 DOI: 10.1016/j.ecoenv.2019.109750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Drought and nitrogen (N) deposition are important components of global climate and environmental change. In this greenhouse study, we investigated the ecophysiological responses of the seedlings of three subtropical forest plant species (Schima superba, Castanopsis fissa, and Michelia macclurei) to short-term experimental drought stress, N addition, and their interaction. The results showed that drought stress reduced the activities of antioxidant enzymes [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] and total antioxidant capacity (T-AOC), but increased the malondialdehyde (MDA), abscisic acid (ABA), and proline (PRO) contents in plants. The PRO content, T-AOC, and antioxidant enzyme activities were increased, and ABA and MDA contents were decreased by N addition alone. Furthermore, N addition under drought stress increased antioxidant enzymes activities, PRO content, and T-AOC. The treatments, however, did not significantly affect the chlorophyll fluorescence parameters of the species. T-AOC was positively correlated with antioxidant enzyme activities in each species, indicating that antioxidant enzymes were important for plant resistance to oxidative stress. MDA content increased with the increase of ABA content, indicating that ABA may help regulate stomatal movement and drought-induced oxidative injury in plants. T-AOC was positively correlated with PRO content, probably because PRO participated in osmotic regulation of cells and increased osmotic stress resistance. These results indicate that N addition can reduce drought stress of subtropical forest plants and will help researchers predict how evergreen broad-leaved forests will respond to global change in the future.
Collapse
Affiliation(s)
- Shike Zhang
- CAS Engineering Laboratory for Ecological Restoration of Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Shao
- School of Food Pharmaceutical Engineering, Zhao Qing University, Zhaoqing, 526061, China
| | - Zhongyu Sun
- Guangdong Open Laboratory of Geospatial Information Technology and Application, Guangzhou Institute of Geography, Guangzhou, 510070, China
| | - Yao Huang
- CAS Engineering Laboratory for Ecological Restoration of Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Liu
- CAS Engineering Laboratory for Ecological Restoration of Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| |
Collapse
|
7
|
Argiroff WA, Zak DR, Upchurch RA, Salley SO, Grandy AS. Anthropogenic N deposition alters soil organic matter biochemistry and microbial communities on decaying fine roots. GLOBAL CHANGE BIOLOGY 2019; 25:4369-4382. [PMID: 31314956 DOI: 10.1111/gcb.14770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/06/2019] [Indexed: 06/10/2023]
Abstract
Fine root litter is a primary source of soil organic matter (SOM), which is a globally important pool of C that is responsive to climate change. We previously established that ~20 years of experimental nitrogen (N) deposition has slowed fine root decay and increased the storage of soil carbon (C; +18%) across a widespread northern hardwood forest ecosystem. However, the microbial mechanisms that have directly slowed fine root decay are unknown. Here, we show that experimental N deposition has decreased the relative abundance of Agaricales fungi (-31%) and increased that of partially ligninolytic Actinobacteria (+24%) on decaying fine roots. Moreover, experimental N deposition has increased the relative abundance of lignin-derived compounds residing in SOM (+53%), and this biochemical response is significantly related to shifts in both fungal and bacterial community composition. Specifically, the accumulation of lignin-derived compounds in SOM is negatively related to the relative abundance of ligninolytic Mycena and Kuehneromyces fungi, and positively related to Microbacteriaceae. Our findings suggest that by altering the composition of microbial communities on decaying fine roots such that their capacity for lignin degradation is reduced, experimental N deposition has slowed fine root litter decay, and increased the contribution of lignin-derived compounds from fine roots to SOM. The microbial responses we observed may explain widespread findings that anthropogenic N deposition increases soil C storage in terrestrial ecosystems. More broadly, our findings directly link composition to function in soil microbial communities, and implicate compositional shifts in mediating biogeochemical processes of global significance.
Collapse
Affiliation(s)
- William A Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rima A Upchurch
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Sydney O Salley
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - A Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| |
Collapse
|
8
|
Li R, Tan W, Wang G, Zhao X, Dang Q, Yu H, Xi B. Nitrogen addition promotes the transformation of heavy metal speciation from bioavailable to organic bound by increasing the turnover time of organic matter: An analysis on soil aggregate level. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113170. [PMID: 31520909 DOI: 10.1016/j.envpol.2019.113170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/13/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) addition can change physicochemical properties and biogeochemical processes in soil, but whether or not these changes further affect the transport and transformation of heavy metal speciation is unknown. Here, a long-term (2004-2016) field experiment was conducted to assess the responses of different heavy metal speciation in three soil aggregate fractions to N additions in a temperate agroecosystem of North China. The organic matter turnover time was quantified based on changes in δ13C following the conversion from C3 (wheat) to C4 crop (corn). Averagely, N addition decreases and increases the heavy metal contents in bioavailable and organic bound fractions by 27.5% and 16.6%, respectively, suggesting N addition promotes the transformation of heavy metal speciation from bioavailable to organic bound, and such a promotion in a small aggregate fraction is more remarkable than that in a large aggregate fraction. The transformations of heavy metal speciation from bioavailable to organic bound in all soil aggregate fractions are largely dependent on the increments in the turnover time of organic matter. The increase in organic matter turnover time induced by N addition may inhibit the desorption of heavy metals from organic matter by prolonging the interaction time between heavy metals and organic matter and enhance the capacity of organic matter to adsorb heavy metals by increasing the humification degree and functional group. Our work can provide insights into the accumulation, migration, and transformation of heavy metals in soils in the context of increasing global soil N input from a microenvironmental perspective.
Collapse
Affiliation(s)
- Renfei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guoan Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Hanxia Yu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| |
Collapse
|
9
|
Luo R, Fan J, Wang W, Luo J, Kuzyakov Y, He JS, Chu H, Ding W. Nitrogen and phosphorus enrichment accelerates soil organic carbon loss in alpine grassland on the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:303-312. [PMID: 30199676 DOI: 10.1016/j.scitotenv.2018.09.038] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 05/22/2023]
Abstract
Anthropogenic activities have substantially increased soil nutrient availability, which in turn affects ecosystem processes and functions, especially in nutrient-limited ecosystems such as alpine grasslands. Although considerable efforts have been devoted to understanding the responses of plant productivity and community composition to nitrogen (N) and phosphorus (P) enrichment, the nutrient enrichment effects on soil organic carbon (SOC) and microbial functions are not well understood. A four-year field experiment was established to evaluate the influence of continuous N and P enrichment on plant growth and SOC content in an alpine grassland of the Qinghai-Tibetan Plateau. The study included four treatments: Control without addition, N addition, P addition, and N plus P addition. N addition strongly increased aboveground plant biomass and decreased species richness by promoting growth of the dominant grasses species. In contrast, N and P enrichment significantly decreased SOC, especially the recalcitrant organic C content in the surface layer (0-10 cm) by reducing the slow C pool and enlarging the active C pool. Microbial biomass and activities of C-degrading enzymes (β-glucosidase, cellulase and polyphenol oxidase) and an N-degrading enzyme (chitinase) increased with nutrient inputs. The CO2 emissions during a 300 d incubation period were positively correlated with the cellulase and chitinase activities, while the slow C pool was negatively correlated with the cellulase and polyphenol oxidase activities. Consequently, N and P enrichment accelerated decomposition of the recalcitrant C by stimulating microbial growth and increasing enzyme activities, leading to negative impacts on soil C sequestration. Overall, the results indicate that alpine grassland soils of the Qinghai-Tibetan Plateau may be changing from a C sink to a C source under increasing N and P availability, and improvement of alpine grassland management through nutrient inputs should consider not only the aboveground biomass for grazing, but also the soil C sequestration and ecosystem functioning.
Collapse
Affiliation(s)
- Ruyi Luo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 10049, China
| | - Jianling Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weijin Wang
- Department of Environment and Science, Dutton Park, QLD 4102, Australia; Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Jiafa Luo
- AgResearch Limited, Ruakura Research Centre, Hamilton 3240, New Zealand
| | - Yakov Kuzyakov
- Agro-Technology Institute, RUDN University, Moscow, Russia; Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Büsgenweg 2, Göttingen 37077, Germany; Soil Science Consulting, 37077 Göttingen, Germany
| | - Jin-Sheng He
- College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| |
Collapse
|
10
|
Albright MBN, Johansen R, Lopez D, Gallegos-Graves LV, Steven B, Kuske CR, Dunbar J. Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil. Appl Environ Microbiol 2018; 84:e00598-18. [PMID: 29802185 PMCID: PMC6052259 DOI: 10.1128/aem.00598-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/15/2018] [Indexed: 01/05/2023] Open
Abstract
Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.
Collapse
Affiliation(s)
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | | | - Blaire Steven
- Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| |
Collapse
|
11
|
Anthropogenic N Deposition Alters the Composition of Expressed Class II Fungal Peroxidases. Appl Environ Microbiol 2018; 84:AEM.02816-17. [PMID: 29453258 DOI: 10.1128/aem.02816-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/09/2018] [Indexed: 01/13/2023] Open
Abstract
Here, we present evidence that ca. 20 years of experimental N deposition altered the composition of lignin-decaying class II peroxidases expressed by forest floor fungi, a response which has occurred concurrently with reductions in plant litter decomposition and a rapid accumulation of soil organic matter. This finding suggests that anthropogenic N deposition has induced changes in the biological mediation of lignin decay, the rate limiting step in plant litter decomposition. Thus, an altered composition of transcripts for a critical gene that is associated with terrestrial C cycling may explain the increased soil C storage under long-term increases in anthropogenic N deposition.IMPORTANCE Fungal class II peroxidases are enzymes that mediate the rate-limiting step in the decomposition of plant material, which involves the oxidation of lignin and other polyphenols. In field experiments, anthropogenic N deposition has increased soil C storage in forests, a result which could potentially arise from anthropogenic N-induced changes in the composition of class II peroxidases expressed by the fungal community. In this study, we have gained unique insight into how anthropogenic N deposition, a widespread agent of global change, affects the expression of a functional gene encoding an enzyme that plays a critical role in a biologically mediated ecosystem process.
Collapse
|
12
|
Total C and N Pools and Fluxes Vary with Time, Soil Temperature, and Moisture Along an Elevation, Precipitation, and Vegetation Gradient in Southern Appalachian Forests. Ecosystems 2018. [DOI: 10.1007/s10021-018-0244-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
13
|
Entwistle EM, Zak DR, Argiroff WA. Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi. ECOL MONOGR 2018. [DOI: 10.1002/ecm.1288] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elizabeth M. Entwistle
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
| | - Donald R. Zak
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan 48109 USA
| | - William A. Argiroff
- School of Natural Resources & Environment University of Michigan Ann Arbor Michigan 48109 USA
| |
Collapse
|
14
|
Tan W, Wang G, Huang C, Gao R, Xi B, Zhu B. Physico-chemical protection, rather than biochemical composition, governs the responses of soil organic carbon decomposition to nitrogen addition in a temperate agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:282-288. [PMID: 28445825 DOI: 10.1016/j.scitotenv.2017.04.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/19/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The heterogeneous responses of soil organic carbon (SOC) decomposition in different soil fractions to nitrogen (N) addition remain elusive. In this study, turnover rates of SOC in different aggregate fractions were quantified based on changes in δ13C following the conversion of C3 to C4 vegetation in a temperate agroecosystem. The turnover of both total organic matter and specific organic compound classes within each aggregate fraction was inhibited by N addition. Moreover, the intensity of inhibition increases with decreasing aggregate size and increasing N addition level, but does not vary among chemical compound classes within each aggregate fraction. Overall, the response of SOC decomposition to N addition is dependent on the physico-chemical protection of SOC by aggregates and minerals, rather than the biochemical composition of organic substrates. The results of this study could help to understand the fate of SOC in the context of increasing N deposition.
Collapse
Affiliation(s)
- Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guoan Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Caihong Huang
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Rutai Gao
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Biao Zhu
- College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
| |
Collapse
|
15
|
Ni X, Yang W, Qi Z, Liao S, Xu Z, Tan B, Wang B, Wu Q, Fu C, You C, Wu F. Simple additive simulation overestimates real influence: altered nitrogen and rainfall modulate the effect of warming on soil carbon fluxes. GLOBAL CHANGE BIOLOGY 2017; 23:3371-3381. [PMID: 27935178 DOI: 10.1111/gcb.13588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
Experiments and models have led to a consensus that there is positive feedback between carbon (C) fluxes and climate warming. However, the effect of warming may be altered by regional and global changes in nitrogen (N) and rainfall levels, but the current understanding is limited. Through synthesizing global data on soil C pool, input and loss from experiments simulating N deposition, drought and increased precipitation, we quantified the responses of soil C fluxes and equilibrium to the three single factors and their interactions with warming. We found that warming slightly increased the soil C input and loss by 5% and 9%, respectively, but had no significant effect on the soil C pool. Nitrogen deposition alone increased the soil C input (+20%), but the interaction of warming and N deposition greatly increased the soil C input by 49%. Drought alone decreased the soil C input by 17%, while the interaction of warming and drought decreased the soil C input to a greater extent (-22%). Increased precipitation stimulated the soil C input by 15%, but the interaction of warming and increased precipitation had no significant effect on the soil C input. However, the soil C loss was not significantly affected by any of the interactions, although it was constrained by drought (-18%). These results implied that the positive C fluxes-climate warming feedback was modulated by the changing N and rainfall regimes. Further, we found that the additive effects of [warming × N deposition] and [warming × drought] on the soil C input and of [warming × increased precipitation] on the soil C loss were greater than their interactions, suggesting that simple additive simulation using single-factor manipulations may overestimate the effects on soil C fluxes in the real world. Therefore, we propose that more multifactorial experiments should be considered in studying Earth systems.
Collapse
Affiliation(s)
- Xiangyin Ni
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Advanced Science Research Center, The City University of New York, New York, NY, 10031, USA
- Department of Earth and Environmental Sciences, Brooklyn College of The City University of New York, New York, NY, 11210, USA
| | - Wanqin Yang
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Zemin Qi
- College of Life Science, Neijiang Normal University, Neijiang, 641199, China
| | - Shu Liao
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhenfeng Xu
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Bo Tan
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Bin Wang
- Laboratory of Forestry, Department of Forest and Water Management, Ghent University, Geraardsbergsesteenweg 267, BE-9090, Gontrode (Melle), Belgium
| | - Qinggui Wu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, 621000, China
| | - Changkun Fu
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chengming You
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fuzhong Wu
- Long-Term Research Station of Alpine Forest Ecosystems, Key Laboratory of Ecological Forestry Engineering, Institute of Ecology and Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Center of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| |
Collapse
|
16
|
Eldridge DJ, Delgado-Baquerizo M, Travers SK, Val J, Oliver I, Hamonts K, Singh BK. Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores. Ecology 2017; 98:1922-1931. [DOI: 10.1002/ecy.1879] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/05/2017] [Accepted: 04/19/2017] [Indexed: 11/12/2022]
Affiliation(s)
- David J. Eldridge
- Office of Environment and Heritage; c/o School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Centre for Ecosystem Science; School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
| | - Samantha K. Travers
- Centre for Ecosystem Science; School of Biological, Earth and Environmental Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
| | - James Val
- Office of Environment and Heritage; P.O. Box 363 Buronga New South Wales 2739 Australia
| | - Ian Oliver
- Office of Environment and Heritage; University of New England; P.O. Box U221 Armidale New South Wales 2351 Australia
- School of Environmental and Rural Sciences; University of New England; Armidale New South Wales 2350 Australia
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; Western Sydney University; Penrith New South Wales 2751 Australia
- Global Centre for Land-Based Innovation; Western Sydney University; Penrith New South Wales 2751 Australia
| |
Collapse
|
17
|
Tatariw C, MacRae JD, Fernandez IJ, Gruselle MC, Salvino CJ, Simon KS. Chronic Nitrogen Enrichment at the Watershed Scale Does Not Enhance Microbial Phosphorus Limitation. Ecosystems 2017. [DOI: 10.1007/s10021-017-0140-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Soil ionomic and enzymatic responses and correlations to fertilizations amended with and without organic fertilizer in long-term experiments. Sci Rep 2016; 6:24559. [PMID: 27079657 PMCID: PMC4832195 DOI: 10.1038/srep24559] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/31/2016] [Indexed: 12/03/2022] Open
Abstract
To investigate potential interactions between the soil ionome and enzyme activities affected by fertilization with or without organic fertilizer, soil samples were collected from four long-term experiments over China. Irrespective of variable interactions, fertilization type was the major factor impacting soil ionomic behavior and accounted for 15.14% of the overall impact. Sampling site was the major factor affecting soil enzymatic profile and accounted for 34.25% of the overall impact. The availabilities of Pb, La, Ni, Co, Fe and Al were significantly higher in soil with only chemical fertilizer than the soil with organic amendment. Most of the soil enzyme activities, including α-glucosidase activity, were significantly activated by organic amendment. Network analysis between the soil ionome and the soil enzyme activities was more complex in the organic-amended soils than in the chemical fertilized soils, whereas the network analysis among the soil ions was less complex with organic amendment. Moreover, α-glucosidase was revealed to generally harbor more corrections with the soil ionic availabilities in network. We concluded that some of the soil enzymes activated by organic input can make the soil more vigorous and stable and that the α-glucosidase revealed by this analysis might help stabilize the soil ion availability.
Collapse
|
19
|
Freedman ZB, Upchurch RA, Zak DR, Cline LC. Anthropogenic N Deposition Slows Decay by Favoring Bacterial Metabolism: Insights from Metagenomic Analyses. Front Microbiol 2016; 7:259. [PMID: 26973633 PMCID: PMC4773658 DOI: 10.3389/fmicb.2016.00259] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/16/2016] [Indexed: 12/03/2022] Open
Abstract
Litter decomposition is an enzymatically-complex process that is mediated by a diverse assemblage of saprophytic microorganisms. It is a globally important biogeochemical process that can be suppressed by anthropogenic N deposition. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. Here, we paired extracellular enzyme assays with shotgun metagenomics to assess if anthropogenic N deposition has altered the functional potential of microbial communities inhabiting decaying forest floor. Experimental N deposition significantly reduced the activity of extracellular enzymes mediating plant cell wall decay, which occurred concurrently with changes in the relative abundance of metagenomic functional gene pathways mediating the metabolism of carbohydrates, aromatic compounds, as well as microbial respiration. Moreover, experimental N deposition increased the relative abundance of 50 of the 60 gene pathways, the majority of which were associated with saprotrophic bacteria. Conversely, the relative abundance and composition of fungal genes mediating the metabolism of plant litter was not affected by experimental N deposition. Future rates of atmospheric N deposition have favored saprotrophic soil bacteria, whereas the metabolic potential of saprotrophic fungi appears resilient to this agent of environmental change. Results presented here provide evidence that changes in the functional capacity of saprotrophic soil microorganisms mediate how anthropogenic N deposition increases C storage in soil.
Collapse
Affiliation(s)
- Zachary B Freedman
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Rima A Upchurch
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Donald R Zak
- School of Natural Resources and Environment, University of MichiganAnn Arbor, MI, USA; Department of Ecology, Evolution, and Behavior, University of MichiganAnn Arbor, MI, USA
| | - Lauren C Cline
- School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| |
Collapse
|
20
|
Mueller RC, Gallegos-Graves L, Zak DR, Kuske CR. Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient. MICROBIAL ECOLOGY 2016; 71:57-67. [PMID: 26280745 DOI: 10.1007/s00248-015-0655-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/21/2015] [Indexed: 06/04/2023]
Abstract
Dormancy is thought to promote biodiversity within microbial communities, but how assembly of the active community responds to changes in environmental conditions is unclear. To measure the active and dormant communities of bacteria and fungi colonizing decomposing litter in maple forests, we targeted ribosomal genes and transcripts across a natural environmental gradient. Within bacterial and fungal communities, the active and dormant communities were phylogenetically distinct, but patterns of phylogenetic clustering varied. For bacteria, active communities were significantly more clustered than dormant communities, while the reverse was found for fungi. The proportion of operational taxonomic units (OTUs) classified as active and the degree of phylogenetic clustering of the active bacterial communities declined with increasing pH and decreasing C/N. No significant correlations were found for the fungal community. The opposing pattern of phylogenetic clustering in dormant and active communities and the differential response of active communities to environmental gradients suggest that dormancy differentially structures bacterial and fungal communities.
Collapse
Affiliation(s)
- Rebecca C Mueller
- Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | | | - Donald R Zak
- School of Natural Resources and Environment, Ann Arbor, MI, 48109, USA
| | - Cheryl R Kuske
- Bioscience Division, M888, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| |
Collapse
|
21
|
Peschel AR, Zak DR, Cline LC, Freedman Z. Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function. Ecology 2015; 96:2383-93. [PMID: 26594696 DOI: 10.1890/15-0164.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Saprotrophic microbial communities in soil are primarily structured by the availability of growth-limiting resources (i.e., plant detritus), a bottom-up ecological force. However, foraging by native ungulates can alter plant community composition and the nature of detritus entering soil, plausibly exerting an indirect, top-down ecological force that shapes both the composition and function of soil microbial communities. To test this idea, we used physiological assays and molecular approaches to quantify microbial community composition and function inside and outside of replicate, long-term (60-80 yr) winter-foraging exclosures in sagebrush steppe of Wyoming, USA. Winter foraging exclusion substantially increased shrub biomass (2146 g/m2 vs. 87 g/m2), which, in turn, increased the abundance of bacterial and fungal genes with lignocellulolytic function; microbial respiration (+50%) and net N mineralization (+70%) also were greater in the absence of winter foraging. Our results reveal that winter foraging by native, migratory ungulates in sagebrush steppe exerts an indirect, top-down ecological force that shapes the composition and function of soil microbial communities. Because approximately 25% of the Earth's land surface is influenced by grazing animals, this indirect top-down ecological force could function to broadly shape the community membership and physiological capacity of saprotrophic microbial communities in shrub steppe.
Collapse
|
22
|
Freedman ZB, Zak DR. Atmospheric N deposition alters connectance, but not functional potential among saprotrophic bacterial communities. Mol Ecol 2015; 24:3170-80. [PMID: 25943298 DOI: 10.1111/mec.13224] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 11/28/2022]
Abstract
The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co-occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.
Collapse
Affiliation(s)
- Zachary B Freedman
- School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Donald R Zak
- School of Natural Resources & Environment, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, 48109, USA
| |
Collapse
|
23
|
Hesse CN, Mueller RC, Vuyisich M, Gallegos-Graves LV, Gleasner CD, Zak DR, Kuske CR. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Front Microbiol 2015; 6:337. [PMID: 25954263 PMCID: PMC4407611 DOI: 10.3389/fmicb.2015.00337] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/05/2015] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.
Collapse
Affiliation(s)
- Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Rebecca C Mueller
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Momchilo Vuyisich
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | | | - Cheryl D Gleasner
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Donald R Zak
- Department of Ecology and Evolutionary Biology, School of Natural Resources and Environment, University of Michigan Ann Arbor, MI, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| |
Collapse
|
24
|
Lee SH, Kim SY, Ding W, Kang H. Impact of elevated CO2 and N addition on bacteria, fungi, and archaea in a marsh ecosystem with various types of plants. Appl Microbiol Biotechnol 2015; 99:5295-305. [DOI: 10.1007/s00253-015-6385-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/02/2015] [Accepted: 01/04/2015] [Indexed: 10/24/2022]
|
25
|
Mueller RC, Balasch MM, Kuske CR. Contrasting soil fungal community responses to experimental nitrogen addition using the large subunit rRNA taxonomic marker and cellobiohydrolase I functional marker. Mol Ecol 2014; 23:4406-17. [DOI: 10.1111/mec.12858] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 06/30/2014] [Accepted: 07/09/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Rebecca C. Mueller
- Bioscience Division; Los Alamos National Laboratory; Los Alamos NM 87545 USA
| | - Monica M. Balasch
- Bioscience Division; Los Alamos National Laboratory; Los Alamos NM 87545 USA
| | - Cheryl R. Kuske
- Bioscience Division; Los Alamos National Laboratory; Los Alamos NM 87545 USA
| |
Collapse
|
26
|
Banakar SP, Thippeswamy B. Isolation and partial purification of fungal ligninolytic enzymes from the forest soil fungi isolated from Bhadra Wildlife Sanctuary. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1319-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
Atmospheric N deposition increases bacterial laccase-like multicopper oxidases: implications for organic matter decay. Appl Environ Microbiol 2014; 80:4460-8. [PMID: 24837374 DOI: 10.1128/aem.01224-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anthropogenic release of biologically available nitrogen (N) has increased dramatically over the last 150 years, which can alter the processes controlling carbon (C) storage in terrestrial ecosystems. In a northern hardwood forest ecosystem located in Michigan in the United States, nearly 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This change occurred concomitantly with compositional changes in Basidiomycete fungi and in Actinobacteria, as well as the downregulation of fungal lignocelluloytic genes. Recently, laccase-like multicopper oxidases (LMCOs) have been discovered among bacteria which can oxidize β-O-4 linkages in phenolic compounds (e.g., lignin and humic compounds), resulting in the production of dissolved organic carbon (DOC). Here, we examined how nearly 2 decades of experimental N deposition has affected the abundance and composition of saprotrophic bacteria possessing LMCO genes. In our experiment, LMCO genes were more abundant in the forest floor under experimental N deposition whereas the abundances of bacteria and fungi were unchanged. Experimental N deposition also led to less-diverse, significantly altered bacterial and LMCO gene assemblages, with taxa implicated in organic matter decay (i.e., Actinobacteria, Proteobacteria) accounting for the majority of compositional changes. These results suggest that experimental N deposition favors bacteria in the forest floor that harbor the LMCO gene and represents a plausible mechanism by which anthropogenic N deposition has reduced decomposition, increased soil C storage, and accelerated phenolic DOC production in our field experiment. Our observations suggest that future rates of atmospheric N deposition could fundamentally alter the physiological potential of soil microbial communities.
Collapse
|
28
|
Trivedi P, Anderson IC, Singh BK. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol 2013; 21:641-51. [DOI: 10.1016/j.tim.2013.09.005] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 09/12/2013] [Accepted: 09/17/2013] [Indexed: 10/26/2022]
|
29
|
Weber CF, Vilgalys R, Kuske CR. Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon. Front Microbiol 2013; 4:78. [PMID: 23641237 PMCID: PMC3621283 DOI: 10.3389/fmicb.2013.00078] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/18/2013] [Indexed: 11/13/2022] Open
Abstract
Increasing levels of atmospheric carbon dioxide (CO2) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2) and N-fertilization in spatially separated field samples, in the forest floor, 0–2, 2–5, and 5–10 cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0–2 cm and forest floor intervals. Composition shifted in forest floor, 0–2 and 2–5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0–2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0–2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes.
Collapse
Affiliation(s)
- Carolyn F Weber
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | | | | |
Collapse
|