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Maitra P, Hrynkiewicz K, Szuba A, Jagodziński AM, Al-Rashid J, Mandal D, Mucha J. Metabolic niches in the rhizosphere microbiome: dependence on soil horizons, root traits and climate variables in forest ecosystems. FRONTIERS IN PLANT SCIENCE 2024; 15:1344205. [PMID: 38645395 PMCID: PMC11026606 DOI: 10.3389/fpls.2024.1344205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/18/2024] [Indexed: 04/23/2024]
Abstract
Understanding belowground plant-microbial interactions is important for biodiversity maintenance, community assembly and ecosystem functioning of forest ecosystems. Consequently, a large number of studies were conducted on root and microbial interactions, especially in the context of precipitation and temperature gradients under global climate change scenarios. Forests ecosystems have high biodiversity of plants and associated microbes, and contribute to major primary productivity of terrestrial ecosystems. However, the impact of root metabolites/exudates and root traits on soil microbial functional groups along these climate gradients is poorly described in these forest ecosystems. The plant root system exhibits differentiated exudation profiles and considerable trait plasticity in terms of root morphological/phenotypic traits, which can cause shifts in microbial abundance and diversity. The root metabolites composed of primary and secondary metabolites and volatile organic compounds that have diverse roles in appealing to and preventing distinct microbial strains, thus benefit plant fitness and growth, and tolerance to abiotic stresses such as drought. Climatic factors significantly alter the quantity and quality of metabolites that forest trees secrete into the soil. Thus, the heterogeneities in the rhizosphere due to different climate drivers generate ecological niches for various microbial assemblages to foster beneficial rhizospheric interactions in the forest ecosystems. However, the root exudations and microbial diversity in forest trees vary across different soil layers due to alterations in root system architecture, soil moisture, temperature, and nutrient stoichiometry. Changes in root system architecture or traits, e.g. root tissue density (RTD), specific root length (SRL), and specific root area (SRA), impact the root exudation profile and amount released into the soil and thus influence the abundance and diversity of different functional guilds of microbes. Here, we review the current knowledge about root morphological and functional (root exudation) trait changes that affect microbial interactions along drought and temperature gradients. This review aims to clarify how forest trees adapt to challenging environments by leveraging their root traits to interact beneficially with microbes. Understanding these strategies is vital for comprehending plant adaptation under global climate change, with significant implications for future research in plant biodiversity conservation, particularly within forest ecosystems.
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Affiliation(s)
- Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland
| | - Agnieszka Szuba
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | - Andrzej M. Jagodziński
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
- Department of Game Management and Forest Protection, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Poznań, Poland
| | - Jubair Al-Rashid
- Tianjin Institute of Industrial Biotechnology, University of Chinese Academy of Sciences, Tianjin, China
| | - Dipa Mandal
- Institute of Microbiology, University of Chinese Academy of Sciences, Beijing, China
| | - Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
- Department of Forest Entomology and Pathology, Faculty of Forestry and Wood Technology, Poznań University of Life Sciences, Poznań, Poland
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He L, Sun X, Li S, Zhou W, Yu J, Zhao G, Chen Z, Bai X, Zhang J. Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169905. [PMID: 38190904 DOI: 10.1016/j.scitotenv.2024.169905] [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: 07/24/2023] [Revised: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiantao Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Guanyu Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jinshuo Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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Awad A, Pena R. An improved method for extraction of soil fungal mycelium. MethodsX 2023; 11:102477. [PMID: 38023315 PMCID: PMC10679939 DOI: 10.1016/j.mex.2023.102477] [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: 04/17/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.
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Dejene T, Merga B, Martín-Pinto P. Green trees preservation: A sustainable source of valuable mushrooms for Ethiopian local communities. PLoS One 2023; 18:e0294633. [PMID: 38019803 PMCID: PMC10686473 DOI: 10.1371/journal.pone.0294633] [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: 10/02/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023] Open
Abstract
In Ethiopia, Pinus radiata and Pinus patula are extensively cultivated. Both plantations frequently serve as habitats for edible fungi, providing economic and ecological importance. Our study aims were: (i) to investigate how plantation age and tree species influence the variety of edible fungi and sporocarps production; (ii) to determine edaphic factors contributing to variations in sporocarps composition; and (iii) to establish a relationship between the most influencing edaphic factors and the production of valuable edible mushrooms for both plantation types. Sporocarps were collected weekly from permanent plots (100 m2) established in 5-, 14-, and 28-year-old stands of both species in 2020. From each plot, composite soil samples were also collected to determine explanatory edaphic variables for sporocarps production and composition. A total of 24 edible species, comprising 21 saprophytic and three ectomycorrhizal ones were identified. Agaricus campestroides, Morchella sp., Suillus luteus, Lepista sordida, and Tylopilus niger were found in both plantations. Sporocarp yields showed significant variation, with the highest mean production in 28-year-old stands of both Pinus stands. Differences in sporocarps variety were also observed between the two plantations, influenced by factors such as pH, nitrogen, phosphorus, potassium, and cation exchange capacity. Bovista dermoxantha, Coprinellus domesticus, and A. campestroides made contributions to the variety. The linear regression models indicated that the abundance of specific fungi was significantly predicted by organic matter. This insight into the nutrient requirements of various fungal species can inform for a better plantation management to produce both wood and non-wood forest products. Additionally, higher sporocarps production in older stands suggests that retaining patches of mature trees after the final cut can enhance fungal habitat, promoting diversity and yield. Thus, implementing this approach could provide supplementary income opportunities from mushroom sales and enhance the economic outputs of plantations, while mature trees could serve as a source of fungal inoculum for new plantations.
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Affiliation(s)
- Tatek Dejene
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, Palencia, Spain
- Ethiopian Forestry Development (EFD), Forest Products Innovation Center of Excellency, Addis Ababa, Ethiopia
| | - Bulti Merga
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, Palencia, Spain
| | - Pablo Martín-Pinto
- Sustainable Forest Management Research Institute UVa-INIA, Avenida Madrid, Palencia, Spain
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [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: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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He L, Sun X, Li S, Zhou W, Chen Z, Bai X. The vertical distribution and control factor of microbial biomass and bacterial community at macroecological scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161754. [PMID: 36709888 DOI: 10.1016/j.scitotenv.2023.161754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms exist throughout the soil profile and those microorganisms living in deeper soil horizons likely play key roles in regulating biogeochemical processes. However, the vertical differentiations of microbes along soil depth and their global biogeographical patterns remain poorly understood. Herein, we conducted a global meta-analysis to clarify the vertical changes of microbial biomass, diversity, and microbial relative abundance across the soil profiles. Data was collected from 43 peer-reviewed articles of 110 soil profiles (467 observations in total) from around the world. We found soil microbial biomass and bacterial diversity decreased with depth in soils. Among examined edaphic factors, the depth variation in soil pH exhibited significant negative associations with the depth change in microbial biomass and bacterial Shannon index, while soil total organic carbon (TOC) and total nitrogen (TN) exhibited significant positive associations. For the major bacteria phyla, the relative abundances of Proteobacteria and Bacteroidetes decreased with soil depth, while Chloroflexi, Gemmatimonadetes, and Nitrospirae increased. We found both parallels and differences in the biogeographical patterns of microbial attribute of topsoil vs. subsoil. Microbial biomass was significantly controlled by the soil nutrient concentrations in both topsoil and subsoil compared with climatic factors, while bacterial Shannon index was significantly controlled by the edaphic factors and across latitudes or climatic factors. Moreover, mean annual precipitation can also be used as a predictor of microbial biomass in subsoil which is different from topsoil. Collectively, our results provide a novel integrative view of how microbial biomass and bacterial community response to soil depth change and clarify the controlling factors of the global distribution patterns of microbial biomass and diversity, which are critical to enhance ecosystem simulation models and for formulating sustainable ecosystem management and conservation policies.
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Affiliation(s)
- Libing He
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiangyang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Suyan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Wenzhi Zhou
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Zhe Chen
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xueting Bai
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
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7
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Benucci GMN, Beschoren da Costa P, Wang X, Bonito G. Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche. Environ Microbiol 2023; 25:352-366. [PMID: 36354216 PMCID: PMC10099798 DOI: 10.1111/1462-2920.16269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.
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Affiliation(s)
- Gian Maria Niccolò Benucci
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, USA
| | - Pedro Beschoren da Costa
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Xinxin Wang
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Gregory Bonito
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
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Fungi Present in the Organic and Mineral Layers of Six Broad-Leaved Tree Plantations as Assessed by the Plate Dilution Method. DIVERSITY 2022. [DOI: 10.3390/d15010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This study examined the distribution of culturable fungi and predominant genera in the organic layer and in the upper layers of the mineral soil of six broad-leaved tree plantations in autumn, after the full fall of leaves. In total, 1335 fungal isolates were recovered from an organic layer and two mineral layers (0–4 cm and 5–8 cm) of soil. The structure of fungal genera differed in the tree plantations and in the three studied soil layers. The organic layer was the layer most populated by fungi compared to the mineral layers. In the organic layer, Penicillium and phyllosphere fungi such as Cladosporium and Phoma dominated. Deeper in the soil, the dominance of certain genera decreased with the increase in Trichoderma, Mucor, Mortierella, and entomopathogenic fungi such as Paecilomyces and Beauveria. Penicillium was one of the most abundant fungi in all soil layers studied.
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9
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Gámez S, Harris NC. Conceptualizing the 3D niche and vertical space use. Trends Ecol Evol 2022; 37:953-962. [PMID: 35872027 DOI: 10.1016/j.tree.2022.06.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/24/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
Abstract
Spatial partitioning in ecological communities has predominantly been described in two dimensions, yet habitat is complex and 3D. Complex space use mediates community structure and interaction strength by expanding spatial, temporal, and dietary dimensions. Vertical stratification of resources provides opportunities for novel specializations, creating a 3D niche. Competition and predation are mediated by 3D space use, as individuals use the vertical axis to access prey, flee predators, or avoid competitors. The 3D niche is important for long-term conservation strategies as species must navigate tradeoffs in habitat use between strata-specific threats and suboptimal habitat patches. Ultimately, elucidating the 3D niche has implications for protected area management and corridor design that directly influence species persistence and ecosystem function in a rapidly changing world.
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Affiliation(s)
- Siria Gámez
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA.
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University 195 Prospect Street, New Haven, CT 06511, USA
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Nash JM, Diggs FM, Yanai RD. Length and colonization rates of roots associated with arbuscular or ectomycorrhizal fungi decline differentially with depth in two northern hardwood forests. MYCORRHIZA 2022; 32:213-219. [PMID: 35152303 DOI: 10.1007/s00572-022-01071-8] [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: 10/15/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi are often studied independently, and thus little is known regarding differences in vertical distribution of these two groups in forests where they co-occur. We sampled roots at two soil depths in two northern hardwood stands in Bartlett, New Hampshire, co-dominated by tree species that associate with AM or EM fungi. Root length of both groups declined with depth. More importantly, root length of EM plant species exceeded that of AM plants at 0-10-cm depth, while AM exceeded EM root length at 30-50-cm depth. Colonization rates were similar between mineral and organic portions of the shallow (0-10 cm) samples for EM and AM fungi and declined dramatically with depth (30-50 cm). The ratio of EM to AM fungal colonization declined with depth, but not as much as the decline in root length with depth, resulting in greater dominance by EM fungi near the surface and by AM fungi at depth. The depth distribution of EM and AM roots may have implications for soil carbon accumulation as well as for the success of the associated tree species.
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Affiliation(s)
- Joseph M Nash
- SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Franklin M Diggs
- SUNY College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Ruth D Yanai
- SUNY College of Environmental Science and Forestry, Syracuse, NY, USA.
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11
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Büntgen U, Peter M, Tegel W, Stobbe U, Elburg R, Sproll L, Molinier V, Čejka T, Isaac EL, Egli S. Eco-archaeological excavation techniques reveal snapshots of subterranean truffle growth. Fungal Biol 2021; 125:951-961. [PMID: 34776232 DOI: 10.1016/j.funbio.2021.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023]
Abstract
Despite its status as a highly-prized and coveted fungi in gastronomy, many aspects of the subterranean life cycle of the Burgundy truffle (Tuber aestivum) are still unknown, because in situ observations of the formation and maturation of truffle fruitbodies remain difficult. Here, we adopted a suite of archaeological fine-scale excavating techniques to provide unique spatiotemporal snapshots of Burgundy truffle growth at three sites in southern Germany. We also recorded the relative position, fresh weight, maturity level and genotype composition of all excavated fruitbodies. Varying by a factor of thousand, the fresh weight of 73 truffle ranged from 0.1 to 103.2 g, with individual maturity levels likely representing different life cycle stages from completely unripe to fully ripe and even decaying. While only a slightly positive relationship between fruitbody weight and maturity level was found, our results suggest that genetically distinct specimens can exhibit different life cycle stages at the same period of time and under the same environmental conditions. We therefore argue that truffles are likely able to grow, mature and ripe simultaneously between early summer and late winter of the following year. Our case study should encourage further eco-archaeological truffle excavations under different biogeographic settings and at different seasons of the year to gain deeper insights into the fungi's subterranean ecology. The expected cross-disciplinary findings will help truffle hunters and farmers to improve their harvest practices and management strategies.
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Affiliation(s)
- Ulf Büntgen
- Department of Geography, University of Cambridge, Cambridge, CB2 3EN, UK; Global Change Research Institute of the Czech Academy of Sciences (CzechGlobe), 603 00, Brno, Czech Republic; Department of Geography, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic; Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland.
| | - Martina Peter
- Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland
| | - Willy Tegel
- Chair of Forest Growth and Dendroecology, University of Freiburg, 79106, Freiburg i.Br., Germany
| | | | - Rengert Elburg
- Archaeological Heritage Office Saxony, 01109, Dresden, Germany
| | | | - Virginie Molinier
- Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland
| | - Tomáš Čejka
- Global Change Research Institute of the Czech Academy of Sciences (CzechGlobe), 603 00, Brno, Czech Republic; Department of Geography, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic
| | - Elizabeth L Isaac
- Department of Geography, University of Cambridge, Cambridge, CB2 3EN, UK
| | - Simon Egli
- Swiss Federal Research Institute (WSL), 8903, Birmensdorf, Switzerland
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Ectomycorrhizal Stands Accelerate Decomposition to a Greater Extent than Arbuscular Mycorrhizal Stands in a Northern Deciduous Forest. Ecosystems 2021. [DOI: 10.1007/s10021-021-00712-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Khokon AM, Schneider D, Daniel R, Polle A. Soil Layers Matter: Vertical Stratification of Root-Associated Fungal Assemblages in Temperate Forests Reveals Differences in Habitat Colonization. Microorganisms 2021; 9:2131. [PMID: 34683452 PMCID: PMC8537680 DOI: 10.3390/microorganisms9102131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Ectomycorrhizal and saprotrophic fungi play pivotal roles in ecosystem functioning. Here, we studied the vertical differentiation of root-associated fungi (RAF) in temperate forests. We analysed RAF assemblages in the organic and mineral soil from 150 experimental forest plots across three biogeographic regions spanning a distance of about 800 km. Saprotrophic RAF showed the highest richness in organic and symbiotrophic RAF in mineral soil. Symbiotrophic RAF exhibited higher relative abundances than saprotrophic fungi in both soil layers. Beta-diversity of RAF was mainly due to turnover between organic and mineral soil and showed regional differences for symbiotrophic and saprotrophic fungi. Regional differences were also found for different phylogenetic levels, i.e., fungal orders and indicator species in the organic and mineral soil, supporting that habitat conditions strongly influence differentiation of RAF assemblages. Important exceptions were fungal orders that occurred irrespective of the habitat conditions in distinct soil layers across the biogeographic gradient: Russulales and Cantharellales (ectomycorrhizal fungi) were enriched in RAF assemblages in mineral soil, whereas saprotrophic Polyporales and Sordariales and ectomycorrhizal Boletales were enriched in RAF assemblages in the organic layer. These results underpin a phylogenetic signature for niche partitioning at the rank of fungal orders and suggest that RAF assembly entails two strategies encompassing flexible and territorial habitat colonization by different fungal taxa.
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Affiliation(s)
- Anis Mahmud Khokon
- Department of Forest Botany and Tree Physiology, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.S.); (R.D.)
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany; (D.S.); (R.D.)
| | - Andrea Polle
- Department of Forest Botany and Tree Physiology, University of Göttingen, 37077 Göttingen, Germany;
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14
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Wu W, Kuang L, Li Y, He L, Mou Z, Wang F, Zhang J, Wang J, Li Z, Lambers H, Sardans J, Peñuelas J, Geisen S, Liu Z. Faster recovery of soil biodiversity in native species mixture than in Eucalyptus monoculture after 60 years afforestation in tropical degraded coastal terraces. GLOBAL CHANGE BIOLOGY 2021; 27:5329-5340. [PMID: 34245481 DOI: 10.1111/gcb.15774] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/30/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Afforestation is an effective method to restore degraded land. Afforestation methods vary in their effects on ecosystem multifunctionality, but their effects on soil biodiversity have been largely overlooked. Here, we mapped the biodiversity and functioning of multiple soil organism groups resulting from diverse afforestation methods in tropical coastal terraces. Sixty years after afforestation from bare land (BL), plant species richness and the abundance of plant litter (398 ± 85 g m-2 ) and plant biomass (179 ± 3.7 t ha-1 ) in native tree species mixtures (MF) were restored to the level of native forests (NF; 287 ± 21 g m-2 and 243.0 ± 33 t ha-1 , respectively), while Eucalyptus monoculture (EP) only successfully restored the litter mass (388 ± 43 g m-2 ) to the level of NF. Soil fertility in EP and MF was increased but remained lower than in NF. For example, soil nitrogen and phosphorus concentrations in MF (1.2 ± 0.2 g kg-1 and 408 ± 49 mg kg-1 , respectively; p < 0.05) were lower than in NF (1.8 ± 0.2 g kg-1 and 523 ± 24 mg kg-1 , respectively; p < 0.05). Soil biodiversity, abundance (except for nematodes), and community composition in MF were similar or greater than those in NF. In contrast, restoration with EP only enhanced the diversity of microbes and mites to the level of NF, but not for other soil biota. Together, afforestation with native species mixtures can end up restoring vegetation and most aspects of the taxonomic and functional biodiversity in soil whereas monoculture using fast-growing non-native species cannot. Native species mixtures show a greater potential to reach completely similar levels of soil biodiversity in local natural forests if they are received some more decades of afforestation. Multifunctionality of soil biotic community should be considered to accelerate such processes in future restoration practices.
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Affiliation(s)
- Wenjia Wu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Centre for Plant Ecology, Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Laboratory of Nematology, Wageningen University and Research, Wageningen, the Netherlands
| | - Luhui Kuang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yue Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Lingfeng He
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhijian Mou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Faming Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Centre for Plant Ecology, Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jing Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jun Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhi'an Li
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Valles, Catalonia, Spain
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, the Netherlands
| | - Zhanfeng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems & CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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15
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Carteron A, Beigas M, Joly S, Turner BL, Laliberté E. Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth. MICROBIAL ECOLOGY 2021; 82:377-390. [PMID: 32556393 DOI: 10.1007/s00248-020-01540-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.
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Affiliation(s)
- Alexis Carteron
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada.
| | - Marie Beigas
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada
- Montreal Botanical Garden, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Etienne Laliberté
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, H1X 2B2, Canada
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16
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Ectomycorrhizal fungi and trees: brothers in arms in the face of anthropogenic activities and their consequences. Symbiosis 2021. [DOI: 10.1007/s13199-021-00792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Livne-Luzon S, Perlson O, Avidan Y, Sivan G, Bruns TD, Shemesh H. A non-linear effect of the spatial structure of the soil ectomycorrhizal spore bank on the performance of pine seedlings. MYCORRHIZA 2021; 31:325-333. [PMID: 33620587 DOI: 10.1007/s00572-021-01023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The spatial structure of the environment is known to affect ecological processes. Unlike the spatial structure of negative interactions, such as competition and predation, the role of spatial structure in positive interaction has received less attention. We tested how the spatial structure of spores of ectomycorrhizal fungi (EMF) in the soil affects the growth of Aleppo pine (Pinus halepensis) seedlings. Spores were spatially distributed at four different levels of patchiness (1 patch, 4 patches, 8 patches and complete mixing) in 4 L pots (all pots received the same total amount of spores). Based on previous findings, we hypothesized that plant performance would gradually increase from the single patch treatment to the complete mixing. However, we found a non-linear response to patchiness. Specifically, plants were largest in the single patch and complete mixing while those in the 4 and 8 patch treatments were the smallest. This non-monotonic response, which might be the result of spatially determined colonization timing or community composition, suggests that the spatial structure of EMF spores has a complex effect on seedling growth.
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Affiliation(s)
- Stav Livne-Luzon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Oren Perlson
- Department of Animal Sciences, Tel-Hai College, Galilee, Israel
| | - Yael Avidan
- Department of Desert Ecology, Ben-Gurion University of the Negev, Blaustein Institutes of Desert Research, Mitrani Beersheba, Israel
| | - Guy Sivan
- Department of Animal Sciences, Tel-Hai College, Galilee, Israel
| | - Thomas D Bruns
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, USA
| | - Hagai Shemesh
- Department of Environmental Sciences, Tel-Hai College, Galilee, Israel.
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18
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Karst J, Franklin J, Simeon A, Light A, Bennett JA, Erbilgin N. Assessing the dual-mycorrhizal status of a widespread tree species as a model for studies on stand biogeochemistry. MYCORRHIZA 2021; 31:313-324. [PMID: 33829296 DOI: 10.1007/s00572-021-01029-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Viewing plant species by their mycorrhizal type has explained a range of ecosystem processes. However, mycorrhizal type is confounded with plant phylogeny and the environments in which mycorrhizal partners occur. To circumvent these confounding effects, "dual-mycorrhizal" plant species may be potential models for testing the influence of mycorrhizal type on stand biogeochemistry. To assess their use as models, duality in mycorrhizas within a single host species must be confirmed and factors underlying their variation understood. We surveyed roots, soils, and leaves of mature aspen (Populus tremuloides) across 27 stands in western Canada spanning two biomes: boreal forest and parklands. Aspen roots were mostly ectomycorrhizal with sporadic and rare occurrences of arbuscular mycorrhizas. We further tested whether a climate moisture index predicted abundance of ectomycorrhizal roots (number of ectomycorrhizal root tips m-1 root length) surveyed at two depths (0-20 cm and 20-40 cm) and found that ectomycorrhizal root abundance in subsoils (20-40 cm) was positively related to the index. We subsequently examined the relationships between ectomycorrhizal root abundance, leaf traits, and slow and fast pools of soil organic carbon and nitrogen. The ratio of leaf lignin:N, but not its components, increased along with ectomycorrhizal root abundance in subsoils. Soil carbon and nitrogen pools were independent of ectomycorrhizal root abundance. Our results suggest that (1) categorizing aspen as dual-mycorrhizal may overstate the functional importance of arbuscular mycorrhizas in this species and life stage, (2) water availability influences ectomycorrhizal root abundance, and (3) ectomycorrhizal root abundance coincides with leaf quality.
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Affiliation(s)
- Justine Karst
- Department of Renewable Resources, University of Alberta, Edmonton, Canada.
| | - James Franklin
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Andrea Simeon
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Ashley Light
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
| | - Jonathan A Bennett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
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19
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Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 2021; 97:fiab022. [PMID: 33547899 PMCID: PMC7948073 DOI: 10.1093/femsec/fiab022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - O Janne Kjønaas
- NIBIO, Department of Terrestrial Ecology, NO-1431 Ås, Norway
| | - Luis N Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Yngvild Ransedokken
- Faculty of Environmental and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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20
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Moroenyane I, Tremblay J, Yergeau É. Temporal and spatial interactions modulate the soybean microbiome. FEMS Microbiol Ecol 2021; 97:fiaa2062. [PMID: 33367840 DOI: 10.1093/femsec/fiaa206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked. This study focuses on discerning microbiome successional patterns across all plant organs and tests for evidence of niche differentiation along temporal and spatial axes. Soybean plants were grown in an environmental chamber till seed maturation. Samples from various developmental stages (emergence, growth, flowering and maturation) and compartments (leaf, stem, root and rhizosphere) were collected. Community structure and composition were assessed with 16S rRNA gene and ITS region amplicon sequencing. Overall, the interaction between spatial and temporal dynamics modulated alpha and beta diversity patterns. Time lag analysis on measured diversity indices highlighted a strong temporal dependence of communities. Spatial and temporal interactions influenced the relative abundance of the most abundant genera, whilst random forest predictions reinforced the observed localisation patterns of abundant genera. Overall, our results show that spatial and temporal interactions tend to maintain high levels of biodiversity within the bacterial/archaeal community, whilst in fungal communities OTUs within the same genus tend to have overlapping niches.
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Affiliation(s)
- Itumeleng Moroenyane
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V1B7, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment, Natural Resource Council Canada, 6100 avenue Royalmount, Montréal, Québec, H4P 2R2, Canada
| | - Étienne Yergeau
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec, H7V1B7, Canada
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21
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Newsham KK, Cox F, Sands CJ, Garnett MH, Magan N, Horrocks CA, Dungait JAJ, Robinson CH. A Previously Undescribed Helotialean Fungus That Is Superabundant in Soil Under Maritime Antarctic Higher Plants. Front Microbiol 2020; 11:615608. [PMID: 33391247 PMCID: PMC7775421 DOI: 10.3389/fmicb.2020.615608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
We report a previously undescribed member of the Helotiales that is superabundant in soils at two maritime Antarctic islands under Antarctic Hairgrass (Deschampsia antarctica Desv.). High throughput sequencing showed that up to 92% of DNA reads, and 68% of RNA reads, in soils from the islands were accounted for by the fungus. Sequencing of the large subunit region of ribosomal (r)DNA places the fungus close to the Pezizellaceae, Porodiplodiaceae, and Sclerotiniaceae, with analyses of internal transcribed spacer regions of rDNA indicating that it has affinities to previously unnamed soil and root fungi from alpine, cool temperate and Low Arctic regions. The fungus was found to be most frequent in soils containing C aged to 1,000-1,200 years before present. The relative abundances of its DNA and RNA reads were positively associated with soil carbon and nitrogen concentrations and δ13C values, with the relative abundance of its DNA being negatively associated with soil pH value. An isolate of the fungus produces flask-shaped phialides with a pronounced venter bearing masses of conidia measuring 4.5-6(7) × 1.8-2.5 μm, suggestive of anamorphic Chalara. Enzymatic studies indicate that the isolate strongly synthesizes the extracellular enzyme acid phosphatase, and also exhibits alkaline phosphatase and naphthol-AS-BI-phosphohydrolase activities. Ecophysiological measurements indicate optimal hyphal growth of the isolate at a pH of 4.2-4.5 and a water potential of -0.66 MPa. The isolate is a psychrotroph, exhibiting measureable hyphal growth at -2°C, optimal hyphal extension rate at 15°C and negligible growth at 25°C. It is proposed that the rising temperatures that are predicted to occur in maritime Antarctica later this century will increase the growth rate of the fungus, with the potential loss of ancient C from soils. Analyses using the GlobalFungi Database indicate that the fungus is present in cold, acidic soils on all continents. We advocate further studies to identify whether it is superabundant in soils under D. antarctica elsewhere in maritime Antarctica, and for further isolates to be obtained so that the species can be formally described.
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Affiliation(s)
- Kevin K. Newsham
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Filipa Cox
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
| | - Chester J. Sands
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Mark H. Garnett
- National Environmental Isotope Facility Radiocarbon Laboratory, Glasgow, United Kingdom
| | - Naresh Magan
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, United Kingdom
| | - Claire A. Horrocks
- Sustainable Agriculture Sciences, Rothamsted Research, Okehampton, United Kingdom
| | | | - Clare H. Robinson
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
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22
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Mrak T, Hukić E, Štraus I, Unuk Nahberger T, Kraigher H. Ectomycorrhizal community composition of organic and mineral soil horizons in silver fir (Abies alba Mill.) stands. MYCORRHIZA 2020; 30:541-553. [PMID: 32691152 DOI: 10.1007/s00572-020-00970-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Vertical ectomycorrhizal (ECM) community composition was assessed on silver fir (Abies alba Mill.) in beech-silver fir forests in Bosnia and Herzegovina. Organic and upper mineral horizons were described by pedological analyses. Silver fir root tips were divided into vital ECM, old and non-mycorrhizal for each horizon separately. Morpho-anatomical classification of vital ECM root tips with an assessment of abundance was followed by ITS-based molecular characterization and classification into exploration types. The percentage of vital ECM root tips was not affected by the soil horizon. Altogether, 40 ECM taxa were recorded. Several taxa have not previously been reported for silver fir: Hebeloma laterinum, Inocybe fuscidula, I. glabripes, Lactarius acris, L. albocarneus, L. blennius, L. fluens, Ramaria bataillei, Russula badia, R. lutea, R. mairei, Sistotrema sp., Tarzetta catinus, Tomentella atroarenicolor, T. badia, T. cinerascens, T. bryophylla, and T. ramosissima, indicating high potential for diversity of ECM fungi in silver fir stands. No significant differences in community composition and species richness and diversity were detected between mineral and organic horizons. Community composition was affected by CaCO3, organic carbon concentration, organic carbon stock, total nitrogen stock, C/N ratio and soil bulk density. No significant effects of soil parameters were detected for exploration types. The contact exploration type was dominant in both soil horizons. Significantly different relative abundances of dominant taxa Tomentella stuposa, Cenococcum geophilum and Piloderma sp. 1 were detected in the two horizons. Twelve taxa were limited to the organic horizon and eight to the mineral horizon.
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Affiliation(s)
- Tanja Mrak
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia.
| | - Emira Hukić
- Faculty of Forestry, University of Sarajevo, Zagrebačka 20, 71000, Sarajevo, Bosnia and Herzegovina
| | - Ines Štraus
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
| | | | - Hojka Kraigher
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, Slovenia
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23
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Aas AB, Andrew CJ, Blaalid R, Vik U, Kauserud H, Davey ML. Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms. FEMS Microbiol Ecol 2020; 95:5484836. [PMID: 31049552 DOI: 10.1093/femsec/fiz058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.
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Affiliation(s)
- Anders Bjørnsgaard Aas
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carrie J Andrew
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rakel Blaalid
- Norwegian Institute for Nature Research, Bergen, Norway
| | - Unni Vik
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marie L Davey
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway.,Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway
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Fernandez CW, See CR, Kennedy PG. Decelerated carbon cycling by ectomycorrhizal fungi is controlled by substrate quality and community composition. THE NEW PHYTOLOGIST 2020; 226:569-582. [PMID: 31622518 DOI: 10.1111/nph.16269] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/07/2019] [Indexed: 05/27/2023]
Abstract
Interactions between symbiotic ectomycorrhizal (EM) and free-living saprotrophs can result in significant deceleration of leaf litter decomposition. While this phenomenon is widely cited, its generality remains unclear, as both the direction and magnitude of EM fungal effects on leaf litter decomposition have been shown to vary among studies. Here we explicitly examine how contrasting leaf litter types and EM fungal communities may lead to differential effects on carbon (C) and nitrogen (N) cycling. Specifically, we measured the response of soil nutrient cycling, litter decay rates, litter chemistry and fungal community structure to the reduction of EM fungi (via trenching) with a reciprocal litter transplant experiment in adjacent Pinus- or Quercus-dominated sites. We found clear evidence of EM fungal suppression of C and N cycling in the Pinus-dominated site, but no suppression in the Quercus-dominated site. Additionally, in the Pinus-dominated site, only the Pinus litter decay rates were decelerated by EM fungi and were associated with decoupling of litter C and N cycling. Our results support the hypothesis that EM fungi can decelerate C cycling via N competition, but strongly suggest that the 'Gadgil effect' is dependent on both substrate quality and EM fungal community composition. We argue that understanding tree host traits as well as EM fungal functional diversity is critical to a more mechanistic understanding of how EM fungi mediate forest soil biogeochemical cycling.
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Affiliation(s)
- Christopher W Fernandez
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Craig R See
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
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25
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Koizumi T, Nara K. Ectomycorrhizal fungal communities in ice-age relict forests of Pinus pumila on nine mountains correspond to summer temperature. THE ISME JOURNAL 2020; 14:189-201. [PMID: 31611652 PMCID: PMC6908592 DOI: 10.1038/s41396-019-0524-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 11/09/2022]
Abstract
Ectomycorrhizal (ECM) fungi are critical symbionts of major forest trees, and their communities are affected by various environmental factors including temperature. However, previous knowledge concerning temperature effects does not exclude the effects of host species and coexisting plants, which usually change with temperature, and should be rigorously tested under the same vegetation type. Herein we examined ECM fungal communities in ice-age relict forests dominated by a single host species (Pinus pumila) distributed on nine mountains across >1000 km in Japan. Direct sequencing of rDNA ITS regions identified 154 ECM fungal species from 4134 ECM root-tip samples. Gradient analyses revealed a large contribution of temperature, especially summer temperature, to ECM fungal communities. Additionally, we explored global sequence records of each fungal species to infer its potential temperature niche, and used it to estimate the temperature of the observed communities. The estimated temperature was significantly correlated with the actual temperature of the research sites, especially in summer seasons, indicating inherent temperature niches of the fungal components could determine their distribution among the sites. These results indicate that temperature is still a significant determinant in structuring ECM fungal communities after excluding the effects of host species and coexisting plants. The results also imply that the rising temperature under global warming may have been affecting soil microbes unnoticeably, while such microbial community change may have been contributing to the resilience of the same vegetation.
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Affiliation(s)
- Takahiko Koizumi
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8563, Japan.
- Department of Biosciences, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo, 156-8550, Japan.
| | - Kazuhide Nara
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8563, Japan
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26
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Borovička J, Konvalinková T, Žigová A, Ďurišová J, Gryndler M, Hršelová H, Kameník J, Leonhardt T, Sácký J. Disentangling the factors of contrasting silver and copper accumulation in sporocarps of the ectomycorrhizal fungus Amanita strobiliformis from two sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133679. [PMID: 31400682 DOI: 10.1016/j.scitotenv.2019.133679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Amanita strobiliformis (European Pine Cone Lepidella) is an ectomycorrhizal fungus of the Amanitaceae family known to hyperaccumulate Ag in the sporocarps. Two populations (ecotypes) of A. strobiliformis collected from two urban forest plantations in Prague, Czech Republic, were investigated. The concentrations of Ag, Cu, Cd, and Zn were determined in the mushrooms. The metal mobility and fractionation in the soils was investigated by single extractions and sequential extraction. The soil distribution of A. strobiliformis mycelium was assessed by quantitative polymerase chain reaction (qPCR). The metal uptake from the soil into the mushroom sporocarps was traced by Pb isotopic fingerprinting. The findings suggested that A. strobiliformis (i) accumulates primarily Ag from the topsoil layer (circa 12cm deep) and (ii) accumulates Ag associated with the "reducible soil fraction". The concentrations of all metals, particularly Ag and Cu, were significantly higher in the A. strobiliformis sporocarps from one of the investigated sites (Klíčov). The elevated concentrations of Ag in the sporocarps from Klíčov can possibly be attributed to the higher Ag content in the topsoil layer found at this site. However, the simultaneously elevated concentrations of Cu in A. strobiliformis from Klíčov cannot be explained by the differences in the geochemical background and should be attributed to biological factors.
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Affiliation(s)
- Jan Borovička
- Institute of Geology, Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic; Nuclear Physics Institute, Czech Academy of Sciences, Hlavní 130, 25068 Husinec-Řež, Czech Republic.
| | - Tereza Konvalinková
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - Anna Žigová
- Institute of Geology, Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic
| | - Jana Ďurišová
- Institute of Geology, Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 400 96 Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - Jan Kameník
- Nuclear Physics Institute, Czech Academy of Sciences, Hlavní 130, 25068 Husinec-Řež, Czech Republic
| | - Tereza Leonhardt
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
| | - Jan Sácký
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
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Matsuoka S, Iwasaki T, Sugiyama Y, Kawaguchi E, Doi H, Osono T. Biogeographic Patterns of Ectomycorrhizal Fungal Communities Associated With Castanopsis sieboldii Across the Japanese Archipelago. Front Microbiol 2019; 10:2656. [PMID: 31798567 PMCID: PMC6868053 DOI: 10.3389/fmicb.2019.02656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
Biogeographic patterns in ectomycorrhizal (ECM) fungal communities and their drivers have been elucidated, including effects of host tree species and abiotic (climatic and edaphic) conditions. At these geographic scales, genotypic diversity and composition of single host tree species change with spatial and environmental gradients, reflecting their historical dispersal events. However, whether the host genotypes can be associated with the biogeographic patterns of ECM communities remains unclear. We investigated the biogeographic pattern of ECM fungal community associated with the single host species Castanopsis sieboldii (Fagaceae), whose genotypic diversity and composition across the Japanese archipelago has already been evaluated. ECM communities were investigated in 12 mature Castanopsis-dominated forests covering almost the entire distribution range of C. sieboldii, and we quantified the effect of host genotypes on the biogeographic pattern of ECM fungal communities. Richness and community composition of ECM fungi changed with latitude and longitude; these biogeographic changes of ECM community were significantly correlated with host genotypic variables. Quantitative analyses showed a higher relative explanatory power of climatic and spatial variables than that of host genotypic variables for the biogeographic patterns in the ECM community. Our results suggest historical events of host dispersal can affect the biogeographic patterns of the ECM fungal community, while their explanation power was lower than that for climatic filtering and/or fungal dispersal.
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Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takaya Iwasaki
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eri Kawaguchi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takashi Osono
- Department of Environmental Systems Science, Faculty of Science and Engineering, Doshisha University, Kyoto, Japan
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Robin A, Pradier C, Sanguin H, Mahé F, Lambais GR, de Araujo Pereira AP, Germon A, Santana MC, Tisseyre P, Pablo AL, Heuillard P, Sauvadet M, Bouillet JP, Andreote FD, Plassard C, de Moraes Gonçalves JL, Cardoso EJBN, Laclau JP, Hinsinger P, Jourdan C. How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation. MYCORRHIZA 2019; 29:637-648. [PMID: 31732817 DOI: 10.1007/s00572-019-00917-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.
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Affiliation(s)
- Agnès Robin
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil.
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France.
- ESALQ, University São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - Céline Pradier
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Hervé Sanguin
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Frédéric Mahé
- CIRAD, UMR BGPI, F-34398, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Amandine Germon
- UNESP, University São Paulo, Botucatu, SP, 18610-300, Brazil
| | | | - Pierre Tisseyre
- LSTM, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Anne-Laure Pablo
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Pauline Heuillard
- INRA, US 1426, GeT-PlaGe, Genotoul, F-31320, Castanet-Tolosan, France
| | - Marie Sauvadet
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-Pierre Bouillet
- CIRAD, UMR Eco&Sols, Piracicaba, SP, 13418-900, Brazil
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | - Claude Plassard
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Jean-Paul Laclau
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
| | - Philippe Hinsinger
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Christophe Jourdan
- Eco&Sols, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR Eco&Sols, F-34398, Montpellier, France
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29
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Kluting K, Clemmensen K, Jonaitis S, Vasaitis R, Holmström S, Finlay R, Rosling A. Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest. FEMS Microbiol Ecol 2019; 95:fiz149. [PMID: 31539041 PMCID: PMC6835140 DOI: 10.1093/femsec/fiz149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/19/2019] [Indexed: 11/24/2022] Open
Abstract
In boreal systems, soil profiles typically consist of distinct stratified horizons, with organic layers at the surface overlying deeper mineral horizons providing microhabitat variation along a depth gradient, and vertical stratification of fungal communities along such soil profiles is commonly observed. We studied fungal community structure in a coastal pine forest along a gradient of decreasing influence from the coast. In this system, the vertical stratification pattern of soil microhabitats (defined here as organic, mineral with roots and mineral without roots: O, MR and MN, respectively) is non-uniform; organic horizons are sometimes buried under drifting sand dunes. Our results show that soil microhabitats are distinct with respect to physiochemical characteristics, community composition and OTU richness. While community composition was partly related to depth and distance from the coastal forest edge, microhabitat appeared to have the strongest influence. A closer inspection of the OTUs with the highest relative sequence abundance within each microhabitat revealed that microhabitats support functionally distinct fungal communities with respect to trophic mode and growth morphology. These results suggest that in coastal pine forests, variation in soil microhabitats contributes to the high fungal diversity found belowground and may play an important role in optimizing nutrient cycling.
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Affiliation(s)
- Kerri Kluting
- Evolutionary Biology program, Department of Ecology and Genetics, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Karina Clemmensen
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Box 7026, Sweden
| | | | - Rimvydas Vasaitis
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Box 7026, Sweden
| | - Sara Holmström
- Department of Geological Science, Stockholm University, SE-114 19 Stockholm, Sweden
| | - Roger Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Box 7026, Sweden
| | - Anna Rosling
- Evolutionary Biology program, Department of Ecology and Genetics, Uppsala University, SE-752 36 Uppsala, Sweden
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30
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Assessment of prokaryote to eukaryote ratios in environmental samples by SSU rDNA length polymorphism. Antonie van Leeuwenhoek 2019; 113:175-183. [PMID: 31522373 DOI: 10.1007/s10482-019-01327-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022]
Abstract
Microbial communities are important regulators of many processes in all ecosystems. Understanding of ecosystem processes requires at least an overview of the involved microorganisms. While in-depth identification of microbial species in environmental samples can be achieved by next generation sequencing, profiling of whole microbial communities can be accomplished via less labour-intensive approaches. Especially automated ribosomal intergenic spacer analysis (ARISA) are of interest as they are highly specific even at fine scales and widely applicable for environmental samples. Yet, established protocols lack the possibility to compare prokaryotic and eukaryotic communities as different primer sets are necessary. However, shifts in the eukaryote to prokaryote ratio can be a useful indicator for ecosystem processes like decomposition or nutrient cycling. We propose a protocol to analyse prokaryotic and eukaryotic communities using a single primer pair based reaction based on a region with variable length (V4, which is about 180 bp shorter in prokaryotes compared to eukaryotes) in the small ribosomal subunit flanked by two highly conservative regions. Shifts in the prokaryotic and eukaryotic ratio between samples can be reliably detected by fragment length polymorphism analysis as well as sequencing of this region. Together with established approaches such as ARISA or 16S and ITS rDNA sequencing, this can provide a more complex insight into microbial community shifts and ecosystem processes.
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31
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Bunn RA, Simpson DT, Bullington LS, Lekberg Y, Janos DP. Revisiting the 'direct mineral cycling' hypothesis: arbuscular mycorrhizal fungi colonize leaf litter, but why? THE ISME JOURNAL 2019; 13:1891-1898. [PMID: 30911130 PMCID: PMC6775977 DOI: 10.1038/s41396-019-0403-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/08/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Rebecca A Bunn
- Department of Environmental Sciences, Western Washington University, 516 High St., MS-9181, Bellingham, WA, 98225, USA.
| | - Dylan T Simpson
- Department of Environmental Sciences, Western Washington University, 516 High St., MS-9181, Bellingham, WA, 98225, USA
| | | | - Ylva Lekberg
- MPG Ranch, Missoula, MT, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - David P Janos
- Department of Biology, University of Miami, Miami, FL, USA
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32
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Jiao XL, Zhang XS, Lu XH, Qin R, Bi YM, Gao WW. Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil. Sci Rep 2019; 9:8615. [PMID: 31197229 PMCID: PMC6565631 DOI: 10.1038/s41598-019-44530-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/13/2019] [Indexed: 11/26/2022] Open
Abstract
The production of American ginseng (Panax quinquefolius L.) is severely limited by the replant disorders in China. Crop rotation with maize might reduce the replant problems, but little information is available on the effect of maize rotation on soil cultivated with ginseng. In this study, we analyzed nutrients, phenolic acids, and microbial communities in soils from the fields with continuous maize, mono-culture ginseng, and 1-, 3-, and 5-year maize rotation after ginseng. Pot experiments were also conducted to evaluate the performance of replanting ginseng in these soils. The results showed that Mn, Cu, and 5 phenolic acids in ginseng-cultivated soil were significantly decreased by maize rotation. A 5-year maize rotation significantly increased the relative abundance of beneficial soil bacteria, such as Arthrobacter, rather than decreasing the abundances of potential pathogenic genera. Clustering analysis revealed that the physicochemical properties and microbial communities of 3- and 5-year maize rotation soil were more similar to CM than to G soil. The biomass of replanted ginseng root was improved, and root disease was reduced over 3 years of maize rotation. Overall, the results showed that at least a 3-year maize rotation is needed to overcome the replant failure of American ginseng.
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Affiliation(s)
- Xiao-Lin Jiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xue-Song Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xiao-Hong Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruijun Qin
- Oregon State University-Hermiston Agricultural Research and Extension Center, Hermiston, OR, 97838, USA
| | - Yan-Meng Bi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Wei-Wei Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
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33
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Effect of Deadwood on Ectomycorrhizal Colonisation of Old-Growth Oak Forests. FORESTS 2019. [DOI: 10.3390/f10060480] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the importance of coarse woody debris (CWD) for species diversity is recognized, the effects of coarse woody debris decay class on species composition have received little attention. We examined how the species composition of ectomycorrhizal fungi (ECM) changes with CWD decay. We describe ectomycorrhizal root tips and the diversity of mycorrhizal fungal species at three English oak (Quercus robur L.) sites. DNA barcoding revealed a total of 17 ECM fungal species. The highest degree of mycorrhizal colonization was found in CWDadvanced (27.2%) and CWDearly (27.1%). Based on exploration types, ectomycorrhizae were classified with respect to ecologically relevant soil features. The short distance type was significantly correlated with soil P2O5, while the contact type was correlated with soil C/N. The lowest mean content of soil Corg was found in the CWDabsent site. The difference in total soil N between sites decreased with increasing CWD decomposition, whereas total C/N increased correspondingly. In this study we confirmed that soil CWD stimulates ectomycorrhizal fungi, representing contact or short-distance exploration types of mycelium.
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34
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Cox F, Newsham KK, Robinson CH. Endemic and cosmopolitan fungal taxa exhibit differential abundances in total and active communities of Antarctic soils. Environ Microbiol 2019; 21:1586-1596. [PMID: 30652397 PMCID: PMC6850668 DOI: 10.1111/1462-2920.14533] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 01/13/2019] [Indexed: 01/05/2023]
Abstract
Our understanding of the diversity and community dynamics of soil fungi has increased greatly through the use of DNA-based identification. Community characterization of metabolically active communities via RNA sequencing has previously revealed differences between 'active' and 'total' fungal communities, which may be influenced by the persistence of DNA from nonactive components. However, it is not known how fungal traits influence their prevalence in these contrasting community profiles. In this study, we coextracted DNA and RNA from soil collected from three Antarctic islands to test for differences between total and active soil fungal communities. By matching these geographically isolated fungi against a global dataset of soil fungi, we show that widely dispersed taxa are often more abundant in the total community, whilst taxa restricted to Antarctica are more likely to have higher abundance in the active community. In addition, we find that active communities have lower richness, and show a reduction in the abundance of the most dominant fungi, whilst there are consistent differences in the abundances of certain taxonomic groups between the total and active communities. These results suggest that the views of soil fungal communities offered by DNA- and RNA-based characterization differ in predictable ways.
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Affiliation(s)
- Filipa Cox
- School of Earth & Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK
- NERC British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Kevin K Newsham
- NERC British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Clare H Robinson
- School of Earth & Environmental Sciences, The University of Manchester, Manchester M13 9PL, UK
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Khaliq I, Hardy GESJ, White D, Burgess TI. eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems. FEMS Microbiol Ecol 2019; 94:4944903. [PMID: 29579182 DOI: 10.1093/femsec/fiy048] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Proper isolation and identification of Phytophthora species is critical due to their broad distribution and huge impact on natural ecosystems throughout the world. In this study, five different sites were sampled and seven methods were compared to determine the Phytophthora community. Three traditional isolation methods were conducted (i) soil baiting, (ii) filtering of the bait water and (iii) isolation from field roots using Granny Smith apples. These were compared to four sources of eDNA used for metabarcoding using Phytophthora-specific primers on (i) sieved field soil, (ii) roots from field, (iii) filtered baiting water and (iv) roots from bait plants grown in the glasshouse in soil collected from these sites. Six Phytophthora species each were recovered by soil baiting using bait leaves and from the filtered bait water. No Phytophthora species were recovered from Granny Smith apples. eDNA extracted from field roots detected the highest number of Phytophthora species (25). These were followed by direct DNA isolation from filters (24), isolation from roots from bait plants grown in the glasshouse (19), and DNA extraction from field soil (13). Therefore, roots were determined to be the best substrate for detecting Phytophthora communities using eDNA.
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Affiliation(s)
- Ihsanul Khaliq
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia
| | - Giles E St J Hardy
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia
| | - Diane White
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia
| | - Treena I Burgess
- Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, 6150, Australia
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Grau O, Saravesi K, Ninot JM, Geml J, Markkola A, Ahonen SHK, Peñuelas J. Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties. FEMS Microbiol Ecol 2019; 95:5370081. [DOI: 10.1093/femsec/fiz028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 01/21/2023] Open
Affiliation(s)
- Oriol Grau
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Karita Saravesi
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Josep M Ninot
- Institute for Research in Biodiversity (IRBio) and Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Av. Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - József Geml
- Naturalis Biodiversity Center, Vondellaan 55, P.O. Box 9517, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Annamari Markkola
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Saija HK Ahonen
- Department of Ecology and Genetics, P.O. Box 3000, FI-90014, University of Oulu, Oulu, Finland
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193, Cerdanyola del Vallès, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
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Yang N, Butenschoen O, Rana R, Köhler L, Hertel D, Leuschner C, Scheu S, Polle A, Pena R. Leaf litter species identity influences biochemical composition of ectomycorrhizal fungi. MYCORRHIZA 2019; 29:85-96. [PMID: 30547252 DOI: 10.1007/s00572-018-0876-2] [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: 06/28/2018] [Revised: 10/25/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
In forest ecosystems, ectomycorrhizal (ECM) fungi are important for plant growth and soil biogeochemical processes. The biochemical composition of ECM mycelium is an important fungal effect trait with consequences for its decomposition rate, and consequently on soil carbon pools and plant nutrition. Although the link between ECM fungi and leaf litter-released nutrients is well known, the response of ECM fungal biochemical composition to different leaf litter species remains poorly understood. To determine how leaf litter quality influences ECM fungi's biochemical profiles, we planted young beech trees in an oak forest and replaced the natural leaf litter with that of European beech (Fagus sylvatica), ash (Fraxinus excelsior), maple (Acer pseudoplatanus), or lime (Tilia cordata). We assessed the biochemical profiles of ECM root tips colonized by common fungal taxa in temperate forests (i.e., Cenococcum geophilum, Inocybe sp., and Lactarius subdulcis), using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). ECM fungal biochemical composition changed with leaf litter species. Changes were apparent in the infrared absorption bands assigned to functional groups of lipids, amides, and carbohydrates. C. geophilum and L. subdulcis exhibited large spectral differences corresponding to the initial pattern of leaf litter chemical composition between samples collected in the beech and ash leaf litter treatments. In contrast, Inocybe sp. was influenced by lime, but with no differences between samples from ash or beech leaf litter treatments. Although the spectral bands affected by leaf litter type differed among ECM fungi, they were mainly related to amides, indicating a dynamic response of the fungal proteome to soil nutritional changes. Overall, the results indicate that the biochemical response of ECM fungi to leaf litter species varies among ECM fungal species and suggests that the biochemical composition of ECM mycelium is a fungal response trait, sensitive to environmental changes such as shifts in leaf litter species.
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Affiliation(s)
- Nan Yang
- Forest Botany and Tree Physiology, University of Goettingen, Buesgenweg 2, 37077, Goettingen, Germany
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Olaf Butenschoen
- J. F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
- Senckenberg Biodiversity and Climate Research Centre BiK-F, Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Rumana Rana
- Forest Botany and Tree Physiology, University of Goettingen, Buesgenweg 2, 37077, Goettingen, Germany
- Forestry and Wood Technology Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Lars Köhler
- Plant Ecology and Ecosystem Research, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
| | - Dietrich Hertel
- Plant Ecology and Ecosystem Research, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
| | - Christoph Leuschner
- Plant Ecology and Ecosystem Research, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
| | - Stefan Scheu
- J. F. Blumenbach Institute of Zoology and Anthropology, University of Goettingen, Untere Karspüle 2, 37073, Goettingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Goettingen, 37073, Goettingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Buesgenweg 2, 37077, Goettingen, Germany
- Centre of Biodiversity and Sustainable Land Use, University of Goettingen, 37073, Goettingen, Germany
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Buesgenweg 2, 37077, Goettingen, Germany.
- Centre of Biodiversity and Sustainable Land Use, University of Goettingen, 37073, Goettingen, Germany.
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Deng J, Yin Y, Luo J, Zhu W, Zhou Y. Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. PeerJ 2019; 6:e6251. [PMID: 30648009 PMCID: PMC6330947 DOI: 10.7717/peerj.6251] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
The effects of different revegetation types on soil physical-chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
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Affiliation(s)
- Jiaojiao Deng
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - You Yin
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
| | - Jiyao Luo
- Liaoning Baishi Lazi National Nature Reserve Administration, Dandong, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
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Taniguchi T, Kitajima K, Douhan GW, Yamanaka N, Allen MF. A pulse of summer precipitation after the dry season triggers changes in ectomycorrhizal formation, diversity, and community composition in a Mediterranean forest in California, USA. MYCORRHIZA 2018; 28:665-677. [PMID: 30105498 PMCID: PMC6182365 DOI: 10.1007/s00572-018-0859-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Rapid responses of microbial biomass and community composition following a precipitation event have been reported for soil bacteria and fungi, but measurements characterizing ectomycorrhizal fungi remain limited. The response of ectomycorrhizal fungi after a precipitation event is crucial to understanding biogeochemical cycles and plant nutrition. Here, we examined changes in ectomycorrhizal formation, diversity, and community composition at the end of a summer drought and following precipitation events in a conifer-oak mixed forest under a semiarid, Mediterranean-type climate in CA, USA. To study the effects of different amounts of precipitation, a water addition treatment was also undertaken. Ectomycorrhizal fungal diversity and community composition changed within 6 days following precipitation, with increased simultaneous mortality and re-growth. Ectomycorrhizal diversity increased and community composition changed both in the natural rainfall (less than 10 mm) and water addition (50 mm) treatments, but larger decreases in ectomycorrhizal diversity were observed from 9 to 16 days after precipitation in the water addition treatment. The changes were primarily a shift in richness and abundance of Basidiomycota species, indicating higher drought sensitivity of Basidiomycota species compared with Ascomycota species. Our results indicate that ectomycorrhizal formation, diversity, and community composition rapidly respond to both precipitation events and to the amount of precipitation. These changes affect ecosystem functions, such as nutrient cycling, decomposition, and plant nutrient uptake, in semiarid regions.
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Affiliation(s)
- Takeshi Taniguchi
- Center for Conservation Biology, University of California, Riverside, CA, 92521, USA.
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
| | - Kuni Kitajima
- Center for Conservation Biology, University of California, Riverside, CA, 92521, USA
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- University of California Cooperative Extension, 4437-B S. Laspina St., Tulare, CA, 93274, USA
| | - Norikazu Yamanaka
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - Michael F Allen
- Center for Conservation Biology, University of California, Riverside, CA, 92521, USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Department of Biology, University of California, Riverside, CA, 92521, USA
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40
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Patterns in Ectomycorrhizal Diversity, Community Composition, and Exploration Types in European Beech, Pine, and Spruce Forests. FORESTS 2018. [DOI: 10.3390/f9080445] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ectomycorrhizal (EM) fungi are pivotal drivers of ecosystem functioning in temperate and boreal forests. They constitute an important pathway for plant-derived carbon into the soil and facilitate nitrogen and phosphorus acquisition. However, the mechanisms that drive ectomycorrhizal diversity and community composition are still subject to discussion. We investigated patterns in ectomycorrhizal diversity, community composition, and exploration types on root tips in Fagus sylvatica,Picea abies, and Pinus sylvestris stands across Europe. Host tree species is the most important factor shaping the ectomycorrhizal community as well as the distribution of exploration types. Moreover, abiotic factors such as soil properties, N deposition, temperature, and precipitation, were found to significantly influence EM diversity and community composition. A clear differentiation into functional traits by means of exploration types was shown for all ectomycorrhizal communities across the three analyzed tree species. Contact and short-distance exploration types were clearly significantly more abundant than cord- or rhizomorph-forming long-distance exploration types of EM fungi. Medium-distance exploration types were significantly lower in abundance than contact and short-distance types, however they were the most frequent EM taxa and constituted nearly half of the EM community. Furthermore, EM taxa exhibit distinct ecological ranges, and the type of soil exploration seemed to determine whether EM taxa have small or rather big environmental ranges.
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41
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Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L. Towards robust and repeatable sampling methods in eDNA-based studies. Mol Ecol Resour 2018; 18:940-952. [PMID: 29802793 DOI: 10.1111/1755-0998.12907] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/28/2023]
Abstract
DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.
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Affiliation(s)
- Ian A Dickie
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Stephane Boyer
- Institut de Recherche sur la Biologie de l'Insecte - UMR 7261 CNRS, Université de Tours, Tours, France
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, CHARS Campus, Cambridge Bay, NU, Canada
| | | | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Andreas Makiola
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
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42
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Fungal guilds are evenly distributed along a vertical spruce forest soil profile while individual fungi show pronounced niche partitioning. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1405-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Courty PE, Buée M, Tech JJT, Brulé D, Colin Y, Leveau JHJ, Uroz S. Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino. MYCORRHIZA 2018; 28:343-356. [PMID: 29574496 DOI: 10.1007/s00572-018-0829-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/27/2018] [Indexed: 06/08/2023]
Abstract
Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.
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Affiliation(s)
- P E Courty
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - M Buée
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
| | - J J T Tech
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - D Brulé
- Agroécologie, AgroSup Dijon, CNRS, INRA, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Y Colin
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France
| | - J H J Leveau
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - S Uroz
- INRA, UMR 1136 INRA, Université de Lorraine "Interactions Arbres Micro-organismes", Centre INRA de Nancy, 54280, Champenoux, France.
- INRA UR 1138 "Biogéochimie des Ecosystèmes Forestiers", Centre INRA de Nancy, 54280, Champenoux, France.
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Marupakula S, Mahmood S, Jernberg J, Nallanchakravarthula S, Fahad ZA, Finlay RD. Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition. Environ Microbiol 2017; 19:4736-4753. [PMID: 28967195 DOI: 10.1111/1462-2920.13939] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 08/29/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022]
Abstract
Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonized by different fungi and analyzed differences in microbiome structure related to soils from distinct podzol horizons and effects of short-term additions of N, a growth-limiting nutrient commonly applied as a fertilizer, but known to influence patterns of carbon allocation to roots. Ectomycorrhizal roots growing in soil from different horizons harboured distinct bacterial communities. The fungi colonizing individual roots had a strong effect on the associated bacterial communities. Even closely related species within the same ectomycorrhizal genus had distinct bacterial microbiomes in unfertilized soil, but fertilization removed this specificity. Effects of N were rapid and context dependent, being influenced by both soil type and the particular ectomycorrhizal fungi involved. Fungal community composition changed in soil from all horizons, but bacteria only responded strongly to N in soil from the B horizon where community structure was different and bacterial diversity was significantly reduced, possibly reflecting changed carbon allocation patterns.
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Affiliation(s)
- Srisailam Marupakula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Johanna Jernberg
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Srivathsa Nallanchakravarthula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Zaenab A Fahad
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Roger D Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
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45
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Yao F, Yang S, Wang Z, Wang X, Ye J, Wang X, DeBruyn JM, Feng X, Jiang Y, Li H. Microbial Taxa Distribution Is Associated with Ecological Trophic Cascades along an Elevation Gradient. Front Microbiol 2017; 8:2071. [PMID: 29163383 PMCID: PMC5663944 DOI: 10.3389/fmicb.2017.02071] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 10/10/2017] [Indexed: 12/01/2022] Open
Abstract
The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level. Elevational patterns of the relative abundance of specific microbial taxa could be partially explained by the oligotrophic-copiotrophic theory. Specifically, two dark-coniferous forests, located at mid-elevation sites, were considered to be oligotrophic habitats, with relatively higher soil C/N ratio and [Formula: see text]-N concentrations. As expected, oligotrophic microbial taxa, belonging to the bacterial phyla Acidobacteria and Gemmatimonadetes, and fungal phylum Basidiomycota, were predominant in the two dark-coniferous forests, exhibiting a mid-elevation maximum pattern. In contrast, the broad leaf-Korean pine mixed forest located at the foot of the mountain, Betula ermanii-dominated forest located below the tree line, and alpine tundra at the highest elevation were considered more copiotrophic habitats, characterized by higher substrate-induced-respiration rates and [Formula: see text]-N concentrations. Microbial taxa considered to be so called copiotrophic members, such as bacterial phyla Proteobacteria and Actinobacteria, and fungal phylum Ascomycota, were relatively abundant in these locations, resulting in a mid-elevation minimum pattern. At finer taxonomic levels, the two most abundant proteobacterial classes, alpha- and beta-Proteobacteria, along with Acidobacteria Gp1, 2, 3, 15, and the Basidiomycotal class of Tremellomycetes were classified with the copiotrophic group. Gamma- and delta-Proteobacteria, Acidobacteria Gp4, 6, 7, 16, and Basidiomycotal class of Agaricomycetes were classified as oligotrophic taxa. This work uses the oligotrophic-copiotrophic theory to explain the elevational distribution pattern of the relative abundance of specific microbial taxa, confirming some of the existing trophic classifications of microbial taxa and expanding on the theory to include a broader range of taxonomic levels.
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Affiliation(s)
- Fei Yao
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shan Yang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Zhirui Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji Ye
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Xue Feng
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yong Jiang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Hui Li
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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Essene AL, Shek KL, Lewis JD, Peay KG, McGuire KL. Soil Type Has a Stronger Role than Dipterocarp Host Species in Shaping the Ectomycorrhizal Fungal Community in a Bornean Lowland Tropical Rain Forest. FRONTIERS IN PLANT SCIENCE 2017; 8:1828. [PMID: 29163567 PMCID: PMC5663695 DOI: 10.3389/fpls.2017.01828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/10/2017] [Indexed: 05/12/2023]
Abstract
The role that mycorrhizal fungal associations play in the assembly of long-lived tree communities is poorly understood, especially in tropical forests, which have the highest tree diversity of any ecosystem. The lowland tropical rain forests of Southeast Asia are characterized by high levels of species richness within the family Dipterocarpaceae, the entirety of which has been shown to form obligate ectomycorrhizal (ECM) fungal associations. Differences in ECM assembly between co-occurring species of dipterocarp have been suggested, but never tested in adult trees, as a mechanism for maintaining the coexistence of closely related tree species in this family. Testing this hypothesis has proven difficult because the assembly of both dipterocarps and their ECM associates co-varies with the same edaphic variables. In this study, we used high-throughput DNA sequencing of soils and Sanger sequencing of root tips to evaluate how ECM fungi were structured within and across a clay-sand soil nutrient ecotone in a mixed-dipterocarp rain forest in Malaysian Borneo. We compared assembly patterns of ECM fungi in bulk soil to ECM root tips collected from three ecologically distinct species of dipterocarp. This design allowed us to test whether ECM fungi are more strongly structured by soil type or host specificity. As with previous studies of ECM fungi on this plot, we observed that clay vs. sand soil type strongly structured both the bulk soil and root tip ECM fungal communities. However, we also observed significantly different ECM communities associated with two of the three dipterocarp species evaluated on this plot. These results suggest that ECM fungal assembly on these species is shaped by a combination of biotic and abiotic factors, and that the soil edaphic niche occupied by different dipterocarp species may be mediated by distinct ECM fungal assemblages.
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Affiliation(s)
- Adam L. Essene
- Department of Biological Sciences, Fordham University, New York City, NY, United States
| | - Katherine L. Shek
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - J. D. Lewis
- Department of Biological Sciences, Fordham University, New York City, NY, United States
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Krista L. McGuire
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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Kirker GT, Bishell AB, Jusino MA, Palmer JM, Hickey WJ, Lindner DL. Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites. Front Microbiol 2017; 8:1997. [PMID: 29093702 PMCID: PMC5651271 DOI: 10.3389/fmicb.2017.01997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly between the two sites and that long-term exposure to different preservative chemistries is correlated with different species composition of soil fungi. However, chemical analyses using ICP-OES found levels of select residual preservative actives (copper, chromium and arsenic) to be similar to naturally occurring levels in unexposed areas. A list of indicator species was compiled for each treatment-site combination; functional guild analyses indicate that long-term exposure to wood preservatives may have both detrimental and stimulatory effects on soil fungal species composition. Fungi with demonstrated capacity to degrade industrial pollutants were found to be highly correlated with areas that experienced long-term exposure to preservative testing.
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Affiliation(s)
- Grant T. Kirker
- FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States
| | - Amy B. Bishell
- FPL, United States Department of Agriculture-Forest Service (USDA-FS), Durability and Wood Protection, Madison, WI, United States
| | - Michelle A. Jusino
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
| | - Jonathan M. Palmer
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
| | - William J. Hickey
- Department of Soil Science, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel L. Lindner
- NRS, United States Department of Agriculture-Forest Service (USDA-FS), Center for Forest Mycology Research, Madison, WI, United States
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48
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Ian A. Dickie. THE NEW PHYTOLOGIST 2017; 215:1312-1313. [PMID: 28771814 DOI: 10.1111/nph.14726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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49
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Livne-Luzon S, Ovadia O, Weber G, Avidan Y, Migael H, Glassman SI, Bruns TD, Shemesh H. Small-scale spatial variability in the distribution of ectomycorrhizal fungi affects plant performance and fungal diversity. Ecol Lett 2017; 20:1192-1202. [DOI: 10.1111/ele.12816] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 06/30/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Stav Livne-Luzon
- Department of Life Sciences; Ben-Gurion University of the Negev; POB 653 Beer Sheva Israel
| | - Ofer Ovadia
- Department of Life Sciences; Ben-Gurion University of the Negev; POB 653 Beer Sheva Israel
| | - Gil Weber
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Yael Avidan
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Hen Migael
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
| | - Sydney I. Glassman
- Department of Ecology and Evolutionary Biology; UC Irvine; Irvine CA 92697 USA
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology; UC Berkeley; Berkeley CA 94720-3102 USA
| | - Hagai Shemesh
- Department of Environmental Sciences; Tel-Hai College; Kiryat Shmona 1220800 Israel
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50
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Smith ME, Henkel TW, Williams GC, Aime MC, Fremier AK, Vilgalys R. Investigating niche partitioning of ectomycorrhizal fungi in specialized rooting zones of the monodominant leguminous tree Dicymbe corymbosa. THE NEW PHYTOLOGIST 2017; 215:443-453. [PMID: 28493414 DOI: 10.1111/nph.14570] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
Temperate ectomycorrhizal (ECM) fungi show segregation whereby some species dominate in organic layers and others favor mineral soils. Weak layering in tropical soils is hypothesized to decrease niche space and therefore reduce the diversity of ectomycorrhizal fungi. The Neotropical ECM tree Dicymbe corymbosa forms monodominant stands and has a distinct physiognomy with vertical crown development, adventitious roots and massive root mounds, leading to multi-stemmed trees with spatially segregated rooting environments: aerial litter caches, aerial decayed wood, organic root mounds and mineral soil. We hypothesized that these microhabitats host distinct fungal assemblages and therefore promote diversity. To test our hypothesis, we sampled D. corymbosa ectomycorrhizal root tips from the four microhabitats and analyzed community composition based on pyrosequencing of fungal internal transcribed spacer (ITS) barcode markers. Several dominant fungi were ubiquitous but analyses nonetheless suggested that communities in mineral soil samples were statistically distinct from communities in organic microhabitats. These data indicate that distinctive rooting zones of D. corymbosa contribute to spatial segregation of the fungal community and likely enhance fungal diversity.
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Affiliation(s)
- Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Terry W Henkel
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Alexander K Fremier
- School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, NC, 27708, USA
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