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Chen L, Wei Y, Li C, Zhao Y, Wei Y, Xue Y, Feng Q. Afforestation changed the fungal functional community of paddy fields and dry farmlands differently. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166758. [PMID: 37673251 DOI: 10.1016/j.scitotenv.2023.166758] [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: 01/26/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Afforestation currently makes a great contribution to carbon uptake in terrestrial ecosystems, while dramatically affects soil ecosystem functions too. Little is known, however, about the changes in soil fungal functional groups and their interactions following afforestation. Here, based on high-throughput sequencing and FUNGuild annotation, we investigated the functional characteristics of soil fungi as well as environmental factors in a watershed where paddy field and dry farmland were changed to eucalyptus plantation. The results showed that afforestation on paddy field resulted in greater changes in diversity, community structure and taxon interactions of fungal functional groups than afforestation on dry farmland. The most complex and distinctive community structure was found in eucalyptus plantation, as well as the greatest taxon interactions, and the lowest alpha-diversity of functional guilds of symbiotrophic fungi because of the dominant ectomycorrhizal fungi. Paddy field exhibited the highest proportion of saprotrophic fungi, but the lowest taxonomic diversity of saprotrophic and pathotrophic fungi. The taxonomic diversity of undefined saprotrophic fungi shaped the differences in community structure and network complexity between eucalyptus plantation and cropland. Limited cooperation within dominant fungi was the main reason for the establishment of a loose co-occurrence network in paddy field. From croplands to artificial forests, reduced soil pH boosted the taxonomic diversity of fungal functional groups. All of these findings suggested that afforestation may lead to an increase in the taxonomic diversity of soil fungal functional groups, which would further intensify the taxon interactions.
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Affiliation(s)
- Lijuan Chen
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yuxi Wei
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changsheng Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Plant Protection and Quarantine Station of Gansu Province, Lanzhou 730020, China
| | - Yinjun Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, School of Geography and Planning, Nanning Normal University, Nanning 530001, China
| | - Yongping Wei
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Yuanyuan Xue
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Feng
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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Yuan Z, Zeng Z, Liu F. Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve. Sci Rep 2023; 13:17127. [PMID: 37816825 PMCID: PMC10564911 DOI: 10.1038/s41598-023-44447-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.
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Affiliation(s)
- Zongsheng Yuan
- College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Zhihao Zeng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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Liu S, Vasar M, Öpik M, Koorem K. Disturbance induces similar shifts in arbuscular mycorrhizal fungal communities from grassland and arable field soils. MYCORRHIZA 2023; 33:153-164. [PMID: 36930376 DOI: 10.1007/s00572-023-01108-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 06/08/2023]
Abstract
Anthropogenic disturbances play an increasingly important role in structuring the diversity and functioning of soil organisms such as arbuscular mycorrhizal (AM) fungi. Frequently, multiple land-use practices, which may represent disturbances for AM fungal communities, operate simultaneously in different habitats. It is not known, however, how previous land-use history and specific habitat type influence AM fungal community response to disturbances. We applied mechanical (cutting to stimulate tillage) and chemical (herbicide addition) disturbances to AM fungal communities from meadow and arable field soils. Our results indicated that AM fungal communities from meadows, which previously had experienced mowing, were more species rich than communities from fields that had experienced intensive land-use practices. There were no significant differences, however, in the responses to disturbance of the AM fungal communities from field and meadow soils. We expected mechanical disturbance to promote taxa from the family Glomeraceae which are expected to exhibit a ruderal life-history strategy; instead, the abundance of this family increased in response to chemical disturbance. Simultaneous application of mechanical disturbance and herbicide decreased only the abundance of Diversisporaceae. No AM fungal families increased in abundance when both mechanical and chemical disturbances were applied simultaneously, but all disturbances increased the abundance of culturable AM fungi. Our study demonstrates that although chemical and mechanical forms of disturbance favor different AM fungal families, existing information about family-level characteristics may not adequately characterize the life history strategies of AM fungus species.
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Affiliation(s)
- Siqiao Liu
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia.
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, 2 J. Liivi Street, 50409, Tartu, Estonia
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Yang W, Diao L, Wang Y, Yang X, Zhang H, Wang J, Luo Y, An S, Cheng X. Responses of soil fungal communities and functional guilds to ~160 years of natural revegetation in the Loess Plateau of China. Front Microbiol 2022; 13:967565. [PMID: 36118195 PMCID: PMC9479326 DOI: 10.3389/fmicb.2022.967565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 12/03/2022] Open
Abstract
Natural revegetation has been widely confirmed to be an effective strategy for the restoration of degraded lands, particularly in terms of rehabilitating ecosystem productivity and soil nutrients. Yet the mechanisms of how natural revegetation influences the variabilities and drivers of soil residing fungal communities, and its downstream effects on ecosystem nutrient cycling are not well understood. For this study, we investigated changes in soil fungal communities along with ~160 years of natural revegetation in the Loess Plateau of China, employing Illumina MiSeq DNA sequencing analyses. Our results revealed that the soil fungal abundance was greatly enhanced during the later stages of revegetation. As revegetation progresses, soil fungal richness appeared first to rise and then decline at the climax Quercus liaotungensis forest stage. The fungal Shannon and Simpson diversity indexes were the lowest and highest at the climax forest stage among revegetation stages, respectively. Principal component analysis, Bray–Curtis similarity indices, and FUNGuild function prediction suggested that the composition, trophic modes, and functional groups for soil fungal communities gradually shifted along with natural revegetation. Specifically, the relative abundances of Basidiomycota, Agaricomycetes, Eurotiomycetes, and ectomycorrhizal fungi progressively increased, while that of Ascomycota, Sordariomycetes, Dothideomycetes, Tremellomycetes, saprotrophic, pathotrophic, arbuscular mycorrhizal fungi, and endophyte fungi gradually decreased along with natural revegetation, respectively. The most enriched members of Basidiomycota (e.g., Agaricomycetes, Agaricales, Cortinariaceae, Cortinarius, Sebacinales, Sebacinaceae, Tricholomataceae, Tricholoma, Russulales, and Russulaceae) were found at the climax forest stage. As important carbon (C) sources, the most enriched symbiotic fungi (particularly ectomycorrhizal fungi containing more recalcitrant compounds) can promote organic C and nitrogen (N) accumulation in soils of climax forest. However, the most abundant of saprotrophic fungi in the early stages of revegetation decreased soil organic C and N accumulation by expediting the decomposition of soil organic matter. Our results suggest that natural revegetation can effectively restore soil fungal abundance, and modify soil fungal diversity, community composition, trophic modes, and functional groups by altering plant properties (e.g., plant species richness, diversity, evenness, litter quantity and quality), quantity and quality of soil nutrient substrates, soil moisture and pH. These changes in soil fungal communities, particularly their trophic modes and functional groups along with natural revegetation, impact the accumulation and decomposition of soil C and N and potentially affect ecosystem C and N cycling in the Loess Plateau of China.
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Affiliation(s)
- Wen Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- *Correspondence: Wen Yang,
| | - Longfei Diao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yaqi Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xitong Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Huan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Yiqi Luo
- Department of Biological Sciences, Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, United States
| | - Shuqing An
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaoli Cheng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, China
- Xiaoli Cheng,
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Adnan M, Islam W, Gang L, Chen HYH. Advanced research tools for fungal diversity and its impact on forest ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45044-45062. [PMID: 35460003 DOI: 10.1007/s11356-022-20317-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.
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Affiliation(s)
- Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Gang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Han Y H Chen
- Faculty of Forestry and the Forest Environment, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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Suppressive Effect of Soil Microbiomes Associated with Tropical Fruit Trees on Meloidogyne enterolobii. Microorganisms 2022; 10:microorganisms10050894. [PMID: 35630339 PMCID: PMC9144879 DOI: 10.3390/microorganisms10050894] [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: 03/18/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/16/2022] Open
Abstract
Plant-parasitic nematodes are one of the main biotic factors limiting agricultural production worldwide, with root-knot nematodes (Meloidogyne spp.) being the most damaging group. This study was conducted to evaluate the efficacy of soil microbiomes, associated with various subtropical fruit trees, on the management of a Meloidogyne enterolobii population. Of 14 soil microbiomes tested for nematode suppression, 9 samples in the first experiment and 10 samples in the repeat experiment had significantly (p ≤ 0.05) lower numbers of eggs and J2 compared to the untreated control. The highest nematode suppression was recorded for SA12 extracted from a papaya orchard with a 38% reduction in the nematode population density. In addition, the presence of some bacteria (Bacillus aryabhattai, B. funiculus and B. simplex) and fungi (Metarhizium marquandii, Acremonium sp. and Mortierella sp.) was correlated to a higher suppression potential in some samples. Substantial variations were observed for the diversity of bacterial and fungal isolates among the samples collected from various crop hosts and regions. This suggests that the nematode suppression potential of different soil microbiomes highly depends on the abundance and diversity of fungal and bacterial strains present in the soil. The study confirmed that among all variables, soil dryness, pH, Fe, Zn, organic matter, altitude, and crop cultivar strongly influenced the soil microbial composition.
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Gong J, Hou W, Liu J, Malik K, Kong X, Wang L, Chen X, Tang M, Zhu R, Cheng C, Liu Y, Wang J, Yi Y. Effects of Different Land Use Types and Soil Depths on Soil Mineral Elements, Soil Enzyme Activity, and Fungal Community in Karst Area of Southwest China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053120. [PMID: 35270817 PMCID: PMC8910417 DOI: 10.3390/ijerph19053120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 02/06/2023]
Abstract
The current research was aimed to study the effects of different land use types (LUT) and soil depth (SD) on soil enzyme activity, metal content, and soil fungi in the karst area. Soil samples with depths of 0–20 cm and 20–40 cm were collected from different land types, including grassland, forest, Zanthoxylum planispinum land, Hylocereus spp. land and Zea mays land. The metal content and enzyme activity of the samples were determined, and the soil fungi were sequenced. The results showed that LUT had a significant effect on the contents of soil K, Mg, Fe, Cu and Cr; LUT and SD significantly affected the activities of invertase, urease, alkaline phosphatase and catalase. In addition, Shannon and Chao1 index of soil fungal community was affected by different land use types and soil depths. Ascomycota, Basidiomycota and Mortierellomycota were the dominant phyla at 0–20 cm and 20–40 cm soil depths in five different land types. Land use led to significant changes in soil fungal structure, while soil depth had no significant effect on soil fungal structure, probably because the small-scale environmental changes in karst areas were not the dominant factor in changing the structure of fungal communities. Additionally, metal element content and enzyme activity were related to different soil fungal communities. In conclusion, soil mineral elements content, enzyme activity, and soil fungal community in the karst area were strongly affected by land use types and soil depths. This study provides a theoretical basis for rational land use and ecological restoration in karst areas.
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Affiliation(s)
- Jiyi Gong
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Wenpeng Hou
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (W.H.); (C.C.); (Y.L.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Jie Liu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Kamran Malik
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Xin Kong
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Li Wang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Xianlei Chen
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Ming Tang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
| | - Ruiqing Zhu
- Qinghai Provincial Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibet Plateau, Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining 810008, China;
| | - Chen Cheng
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (W.H.); (C.C.); (Y.L.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Yinglong Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (W.H.); (C.C.); (Y.L.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
| | - Jianfeng Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China; (W.H.); (C.C.); (Y.L.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China;
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Correspondence: (J.W.); (Y.Y.)
| | - Yin Yi
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang 550025, China; (J.G.); (J.L.); (X.K.); (L.W.); (X.C.); (M.T.)
- Correspondence: (J.W.); (Y.Y.)
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Soil Fungal Community Composition Correlates with Site-Specific Abiotic Factors, Tree Community Structure, and Forest Age in Regenerating Tropical Rainforests. BIOLOGY 2021; 10:biology10111120. [PMID: 34827113 PMCID: PMC8614695 DOI: 10.3390/biology10111120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Simple Summary Regenerating forests represent over half of all tropical forests. While regeneration processes of trees and animal groups have been studied, there is surprisingly little information about how the diversity and community composition of fungi and other microorganisms change and what ecological roles play in tropical forest regeneration. In this study, we compared the diversity and community composition of trees and soil fungi among primary forests and regenerating forests of different ages in two sampling areas in southern Costa Rica. Our study shows that while forest age has a significant influence, environmental factors, such as mesoclimate and soil chemistry, have stronger effects on both fungal and tree communities. Moreover, we observed that the more dissimilar tree communities are between any two sites, the more dissimilar the composition of fungal communities. The results presented here contribute to a better understanding of the successional processes of tropical forests in different regions and inform land use and forest management strategies, including, but not limited to, conservation, restoration, and sustainable use. Abstract Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data to compare richness and community composition along secondary forest succession in Costa Rica and assessed the potential roles of abiotic factors influencing them. We found a strong coupling of tree and soil fungal community structure in wet tropical primary and regenerating secondary forests. Forest age, edaphic variables, and regional differences in climatic conditions all had significant effects on tree and fungal richness and community composition in all functional groups. Furthermore, we observed larger site-to-site compositional differences and greater influence of edaphic and climatic factors in secondary than in primary forests. The results suggest greater environmental heterogeneity and greater stochasticity in community assembly in the early stages of secondary forest succession and a certain convergence on a set of taxa with a competitive advantage in the more persisting environmental conditions in old-growth forests. Our work provides unprecedented insights into the successional dynamics of fungal communities during secondary tropical forest succession.
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Zhang W, Bahadur A, Sajjad W, Wu X, Zhang G, Liu G, Chen T. Seasonal Variation in Fungal Community Composition Associated with Tamarix chinensis Roots in the Coastal Saline Soil of Bohai Bay, China. MICROBIAL ECOLOGY 2021; 82:652-665. [PMID: 33598747 DOI: 10.1007/s00248-021-01680-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Coastal salinity typically alters the soil microbial communities, which subsequently affect the biogeochemical cycle of nutrients in the soil. The seasonal variation of the soil fungal communities in the coastal area, closely associated with plant population, is poorly understood. This study provides an insight into the fungal community's variations from autumn to winter and spring to summer at a well-populated area of salt-tolerant Tamarix chinensis and beach. The richness and diversity of fungal community were higher in the spring season and lower in the winter season, as showed by high throughput sequencing of the 18S rRNA gene. Ascomycota was the predominant phylum reported in all samples across the region, and higher difference was reported at order level across the seasonal variations. The redundancy analysis suggested that the abundance and diversity of fungal communities in different seasons are mainly correlated to total organic carbon and total nitrogen. Additionally, the saprotrophic and pathotrophic fungi decreased while symbiotic fungi increased in the autumn season. This study provides a pattern of seasonal variation in fungal community composition that further broadens our limited understanding of how the density of the salt-tolerant T. chinensis population of the coastal saline soil could respond to their seasonal variations.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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Zhou X, Wu F. Land-use conversion from open field to greenhouse cultivation differently affected the diversities and assembly processes of soil abundant and rare fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147751. [PMID: 34023613 DOI: 10.1016/j.scitotenv.2021.147751] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/03/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Soil fungal communities, consisting of a few abundant taxa but many rare taxa, play critical roles in terrestrial ecosystem functioning. However, little is known about ecological processes governing the assembly of abundant and rare sub-communities in response to agricultural intensification, which can threaten soil biodiversity. Here, we performed a regional-scale survey of soil fungal community assembly in different land-use types with an increasing gradient of agricultural intensity, i.e., open field cultivation of main crops (CF) or vegetables (VF), and greenhouse cultivation of vegetables (VG). Results showed that greenhouse cultivation decreased the alpha diversity and spatial turnover rate of soil fungal community. The abundant sub-community was more sensitive to land-use conversion than the rare sub-community. Partitioning the Bray-Curtis dissimilarity found that balanced variation in abundance (i.e., the substitution of individuals by the same number of individuals of a different species), rather than abundance gradients (i.e., one assemblage is a subset of another), accounted for the major shift in fungal beta diversity. Moreover, greenhouse cultivation reduced potential inter-species interactions, and the rare sub-community plays an important role in fungal co-occurrence network. Conversions from CF to VF or VG promoted deterministic processes, which was, to a large extent, associated with changes in soil physicochemical properties. However, conversion from VF to VG decreased deterministic processes. Compared with the rare sub-community, the abundant sub-community with wider niche breadths was more influenced by stochastic processes. Changes in the assembly processes induced by land-use conversion differed between abundant and rare sub-communities. Overall, abundant and rare sub-communities exhibited differential responses to land-use conversion and rare taxa might play a crucial role in maintaining the stability of fungal community.
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Affiliation(s)
- Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; Department of Horticulture, Northeast Agricultural University, Harbin 150030, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China; Department of Horticulture, Northeast Agricultural University, Harbin 150030, China.
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11
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Wang K, Bi Y, Cao Y, Peng S, Christie P, Ma S, Zhang J, Xie L. Shifts in composition and function of soil fungal communities and edaphic properties during the reclamation chronosequence of an open-cast coal mining dump. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144465. [PMID: 33434846 DOI: 10.1016/j.scitotenv.2020.144465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/06/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The diversity, composition and ecological guilds of soil fungal communities in relation to revegetation were assessed during an open-cast mining dump reclamation chronosequence of the soil <1, 5, 10, 15 and 20 years after the start of reclamation. Soil pH and electrical conductivity, total nitrogen (TN), soil organic carbon (SOC), available potassium (AK), and available phosphorus (AP) contents, and soil phosphatase (Pha), urease (U) and invertase (INV) activities were measured. Using high-throughput sequence analysis on internal transcribed spacer (ITS) sequences, 1059 soil fungal operational taxonomic units (OTUs) were identified belonging to 64 orders and these were further categorized by ecological guild. Soil fungal diversity indices were significantly different between the early (<1 year) and later reclamation communities. Nonmetric multidimensional scaling (NMDS) analysis indicates that the composition and ecological guilds of soil fungal communities were significantly different early in the process and at the end of reclamation (P < 0.05). Co-occurrence network and structural equation model analyses show that soil fungal community structure and ecological guilds were correlated with edaphic properties and had an indirect effect on soil available nutrients through direct action on soil enzymes. Overall, the data suggest that soil fungal community composition and function within an open-cast coal mining dump reclamation chronosequence changed during the period following artificial re-vegetation, with interactions between edaphic properties and soil fungal communities associated with these changes.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Yinli Bi
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China; College of Geology and Environment, Xi'an University of Science and Technology, Shaanxi 710054, China.
| | - Yong Cao
- Shehua Group Zhungeer Energy CO., LTD, Ordos 017000, China
| | - Suping Peng
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Peter Christie
- College of Geology and Environment, Xi'an University of Science and Technology, Shaanxi 710054, China
| | - Shaopeng Ma
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Jiayu Zhang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
| | - Linlin Xie
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology, Beijing 100083, China
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12
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Jakovac CC, Junqueira AB, Crouzeilles R, Peña-Claros M, Mesquita RCG, Bongers F. The role of land-use history in driving successional pathways and its implications for the restoration of tropical forests. Biol Rev Camb Philos Soc 2021; 96:1114-1134. [PMID: 33709566 PMCID: PMC8360101 DOI: 10.1111/brv.12694] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 01/29/2023]
Abstract
Secondary forests are increasingly important components of human‐modified landscapes in the tropics. Successional pathways, however, can vary enormously across and within landscapes, with divergent regrowth rates, vegetation structure and species composition. While climatic and edaphic conditions drive variations across regions, land‐use history plays a central role in driving alternative successional pathways within human‐modified landscapes. How land use affects succession depends on its intensity, spatial extent, frequency, duration and management practices, and is mediated by a complex combination of mechanisms acting on different ecosystem components and at different spatial and temporal scales. We review the literature aiming to provide a comprehensive understanding of the mechanisms underlying the long‐lasting effects of land use on tropical forest succession and to discuss its implications for forest restoration. We organize it following a framework based on the hierarchical model of succession and ecological filtering theory. This review shows that our knowledge is mostly derived from studies in Neotropical forests regenerating after abandonment of shifting cultivation or pasture systems. Vegetation is the ecological component assessed most often. Little is known regarding how the recovery of belowground processes and microbiota communities is affected by previous land‐use history. In published studies, land‐use history has been mostly characterized by type, without discrimination of intensity, extent, duration or frequency. We compile and discuss the metrics used to describe land‐use history, aiming to facilitate future studies. The literature shows that (i) species availability to succession is affected by transformations in the landscape that affect dispersal, and by management practices and seed predation, which affect the composition and diversity of propagules on site. Once a species successfully reaches an abandoned field, its establishment and performance are dependent on resistance to management practices, tolerance to (modified) soil conditions, herbivory, competition with weeds and invasive species, and facilitation by remnant trees. (ii) Structural and compositional divergences at early stages of succession remain for decades, suggesting that early communities play an important role in governing further ecosystem functioning and processes during succession. Management interventions at early stages could help enhance recovery rates and manipulate successional pathways. (iii) The combination of local and landscape conditions defines the limitations to succession and therefore the potential for natural regeneration to restore ecosystem properties effectively. The knowledge summarized here could enable the identification of conditions in which natural regeneration could efficiently promote forest restoration, and where specific management practices are required to foster succession. Finally, characterization of the landscape context and previous land‐use history is essential to understand the limitations to succession and therefore to define cost‐effective restoration strategies. Advancing knowledge on these two aspects is key for finding generalizable relations that will increase the predictability of succession and the efficiency of forest restoration under different landscape contexts.
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Affiliation(s)
- Catarina C Jakovac
- International Institute for Sustainability, Estrada Dona Castorina, 124, Rio de Janeiro, 22460-320, Brazil.,Forest Ecology and Management Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands
| | - André B Junqueira
- International Institute for Sustainability, Estrada Dona Castorina, 124, Rio de Janeiro, 22460-320, Brazil.,Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, Carrer de les Columnes s/n, Cerdanyola del Vallès, Barcelona, 08193, Spain
| | - Renato Crouzeilles
- International Institute for Sustainability, Estrada Dona Castorina, 124, Rio de Janeiro, 22460-320, Brazil.,International Institute for Sustainability Australia, Canberra, ACT, 2602, Australia.,Mestrado Profissional em Ciências do Meio Ambiente, Universidade Veiga de Almeida, Rio de Janeiro, 20271-901, Brazil
| | - Marielos Peña-Claros
- Forest Ecology and Management Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands
| | - Rita C G Mesquita
- Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Manaus, 69083-000, Brazil
| | - Frans Bongers
- Forest Ecology and Management Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands
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13
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Effects of Spartina alterniflora Invasion on Soil Microbial Community Structure and Ecological Functions. Microorganisms 2021; 9:microorganisms9010138. [PMID: 33435501 PMCID: PMC7827921 DOI: 10.3390/microorganisms9010138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/23/2022] Open
Abstract
It has been reported that the invasion of Spartina alterniflora changed the soil microbial community in the mangrove ecosystem in China, especially the bacterial community, although the response of soil fungal communities and soil microbial ecological functions to the invasion of Spartina alterniflora remains unclear. In this study, we selected three different communities (i.e., Spartina alterniflora community (SC), Spartina alterniflora–mangrove mixed community (TC), and mangrove community (MC)) in the Zhangjiangkou Mangrove Nature Reserve in China. High-throughput sequencing technology was used to analyze the impact of Spartina alterniflora invasion on mangrove soil microbial communities. Our results indicate that the invasion of Spartina alterniflora does not cause significant changes in microbial diversity, but it can alter the community structure of soil bacteria. The results of the LEfSe (LDA Effect Size) analysis show that the relative abundance of some bacterial taxa is not significantly different between the MC and SC communities, but different changes have occurred during the invasion process (i.e., TC community). Different from the results of the bacterial community, the invasion of Spartina alterniflora only cause a significant increase in few fungal taxa during the invasion process, and these taxa are at some lower levels (such as family, genus, and species) and classified into the phylum Ascomycota. Although the invasion of Spartina alterniflora changes the taxa with certain ecological functions, it may not change the potential ecological functions of soil microorganisms (i.e., the potential metabolic pathways of bacteria, nutritional patterns, and fungal associations). In general, the invasion of Spartina alterniflora changes the community structure of soil microorganisms, but it may not affect the potential ecological functions of soil microorganisms.
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14
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Eisenhauer N, Buscot F, Heintz-Buschart A, Jurburg SD, Küsel K, Sikorski J, Vogel HJ, Guerra CA. The multidimensionality of soil macroecology. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2021; 30:4-10. [PMID: 33692654 PMCID: PMC7116881 DOI: 10.1111/geb.13211] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The recent past has seen a tremendous surge in soil macroecological studies and new insights into the global drivers of one-quarter of the biodiversity of the Earth. Building on these important developments, a recent paper in Global Ecology and Biogeography outlined promising methods and approaches to advance soil macroecology. Among other recommendations, White and colleagues introduced the concept of a spatial three-dimensionality in soil macroecology by considering the different spheres of influence and scales, as soil organism size ranges vary from bacteria to macro- and megafauna. Here, we extend this concept by discussing three additional dimensions (biological, physical, and societal) that are crucial to steer soil macroecology from pattern description towards better mechanistic understanding. In our view, these are the requirements to establish it as a predictive science that can inform policy about relevant nature and management conservation actions. We highlight the need to explore temporal dynamics of soil biodiversity and functions across multiple temporal scales, integrating different facets of biodiversity (i.e., variability in body size, life-history traits, species identities, and groups of taxa) and their relationships to multiple ecosystem functions, in addition to the feedback effects between humans and soil biodiversity. We also argue that future research needs to consider effective soil conservation policy and management in combination with higher awareness of the contributions of soil-based nature's contributions to people. To verify causal relationships, soil macroecology should be paired with local and globally distributed experiments. The present paper expands the multidimensional perspective on soil macroecology to guide future research contents and funding. We recommend considering these multiple dimensions in projected global soil biodiversity monitoring initiatives.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - François Buscot
- Institute of Biology, Leipzig University, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Stephanie D. Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kirsten Küsel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Johannes Sikorski
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Hans-Jörg Vogel
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Carlos A. Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Martin Luther University Halle Wittenberg, Halle (Saale), Germany
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15
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Yang C, Sun J. Soil Salinity Drives the Distribution Patterns and Ecological Functions of Fungi in Saline-Alkali Land in the Yellow River Delta, China. Front Microbiol 2020; 11:594284. [PMID: 33424797 PMCID: PMC7786015 DOI: 10.3389/fmicb.2020.594284] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
High soil salinity is the main factor that limits soil microbial activity in the Yellow River Delta (YRD); however, its effects on fungal community and ecological function are unknown. Here, we comparatively investigated the diversity and structures of soil fungal communities targeting the internally transcribed fungal spacer gene using Illumina MiSeq sequencing methods under a salt gradient with five levels, namely, Low: low-salinity soil, Medium: medium-salinity soil, High: high-salinity soil, Extreme: extreme-salinity soil, and a non-salted site as the control (Non-saline). The results show that bulk density (BD) values significantly increased (p < 0.05), while significantly lower values of soil total carbon (TC), total nitrogen (TN), and fungal Shannon and Chao indexes were observed as the salinization gradient increased (p < 0.05). The relatively high levels of the families Nectriaceae and Cladosporiaceae distinguished two of the clusters, indicating two enterotypes of low (Non-saline and Low) and high (Medium, High, and Extreme) salinity soils, respectively. The family Nectriaceae was most abundant in the networks, and the positive correlations were more pronounced than negative correlations; however, Cladosporiaceae was the family most negatively correlated with others based on the network analysis. At the ecological function level, plant saprotrophs and litter saprotroph were significantly less abundant in extremely saline soil than non-saline soil. The change in soil properties (TC, TN, and BD) caused by soil salinization [salt and electrical conductivity (EC)] regulated the diversity of soil fungal communities, and ecological function, as indicated by Pearson correlation analyses. We suggest further investigation into the ecological functions of soil microorganisms in the extremely saline-alkaline soils of the YRD.
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Affiliation(s)
- Chao Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Juan Sun
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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16
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Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations. Microorganisms 2020; 8:microorganisms8101577. [PMID: 33066264 PMCID: PMC7656304 DOI: 10.3390/microorganisms8101577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.
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17
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Ma S, De Frenne P, Boon N, Brunet J, Cousins SAO, Decocq G, Kolb A, Lemke I, Liira J, Naaf T, Orczewska A, Plue J, Wulf M, Verheyen K. Plant species identity and soil characteristics determine rhizosphere soil bacteria community composition in European temperate forests. FEMS Microbiol Ecol 2020; 95:5485637. [PMID: 31054240 DOI: 10.1093/femsec/fiz063] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/02/2019] [Indexed: 11/12/2022] Open
Abstract
Soil bacteria and understorey plants interact and drive forest ecosystem functioning. Yet, knowledge about biotic and abiotic factors that affect the composition of the bacterial community in the rhizosphere of understorey plants is largely lacking. Here, we assessed the effects of plant species identity (Milium effusum vs. Stachys sylvatica), rhizospheric soil characteristics, large-scale environmental conditions (temperature, precipitation and nitrogen (N) deposition), and land-use history (ancient vs. recent forests) on bacterial community composition in rhizosphere soil in temperate forests along a 1700 km latitudinal gradient in Europe. The dominant bacterial phyla in the rhizosphere soil of both plant species were Acidobacteria, Actinobacteria and Proteobacteria. Bacterial community composition differed significantly between the two plant species. Within plant species, soil chemistry was the most important factor determining soil bacterial community composition. More precisely, soil acidity correlated with the presence of multiple phyla, e.g. Acidobacteria (negatively), Chlamydiae (negatively) and Nitrospirae (positively), in both plant species. Large-scale environmental conditions were only important in S. sylvatica and land-use history was not important in either of the plant species. The observed role of understorey plant species identity and rhizosphere soil characteristics in determining soil bacterial community composition extends our understanding of plant-soil bacteria interactions in forest ecosystem functioning.
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Affiliation(s)
- Shiyu Ma
- Forest & Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090 Gontrode, Belgium
| | - Pieter De Frenne
- Forest & Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090 Gontrode, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Environment, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Jörg Brunet
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Sundsvägen 5, 23053 Alnarp, Sweden
| | - Sara A O Cousins
- Department of Physical Geography, Stockholm University, Svante Arrhenius väg 8, 10691 Stockholm, Sweden
| | - Guillaume Decocq
- Plant Biodiversity Lab, University of Picardy Jules Verne, 1 rue des Louvels, 80037 Amiens, France
| | - Annette Kolb
- Vegetation Ecology and Conservation Biology, Faculty of Biology/Chemistry (FB 02), University of Bremen, Bibliothekstraße 1, 28359, Bremen, Germany
| | - Isa Lemke
- Vegetation Ecology and Conservation Biology, Faculty of Biology/Chemistry (FB 02), University of Bremen, Bibliothekstraße 1, 28359, Bremen, Germany
| | - Jaan Liira
- Department of Botany, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Tobias Naaf
- Biotic Interactions between Forest and Agricultural Land, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Straße 84, 15374 Müncheberg, Germany
| | - Anna Orczewska
- Department of Ecology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40032 Katowice, Poland
| | - Jan Plue
- Department of Physical Geography, Stockholm University, Svante Arrhenius väg 8, 10691 Stockholm, Sweden.,School of Natural Sciences, Technology and Environmental Studies, Södertörn University. Alfred Nobels allé 7 Flemingsberg, 14189 Huddinge, Sweden
| | - Monika Wulf
- Biotic Interactions between Forest and Agricultural Land, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Straße 84, 15374 Müncheberg, Germany
| | - Kris Verheyen
- Forest & Nature Lab, Department of Environment, Ghent University, Geraardsbergsesteenweg 267, 9090 Gontrode, Belgium
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18
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Wang C, Wei M, Wang S, Wu B, Du D. Cadmium influences the litter decomposition of Solidago canadensis L. and soil N-fixing bacterial communities. CHEMOSPHERE 2020; 246:125717. [PMID: 31918081 DOI: 10.1016/j.chemosphere.2019.125717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
It is important to illuminate the effects of litter decomposition of invasive alien species on soil N-fixing bacterial communities (SoNiBa), especially under heavy metal pollution to better outline the mechanisms for invasion success of invasive alien species. This study attempts to identify the effects of litter decomposition of Solidago canadensis L. on SoNiBa under cadmium (Cd) pollution with different concentrations (i.e., low concentration, 7.5 mg/kg soil; high concentration, 15 mg/kg soil) via a polyethylene litterbags-experiment. Electrical conductivity and total N of soil were the most important environmental factors for determining the variations of SoNiBa composition. S. canadensis did not significantly affect the alpha diversity of SoNiBa but significantly affect the beta diversity of SoNiBa and SoNiBa composition. Thus, SoNiBa composition, rather than alpha diversity of SoNiBa, was the most important determinant of the invasion success of S. canadensis. Cd with 15 mg/kg soil did not address distinct effects on alpha diversity of SoNiBa, but Cd with 7.5 mg/kg soil noticeably raised the number of species and species richness of SoNiBa mainly due to the hormonal effects. The combined S. canadensis and Cd with 15 mg/kg soil obviously decreased cumulative mass losses and the rate of litter decomposition (k) of S. canadensis, but the combined S. canadensis and Cd with 7.5 mg/kg soil evidently accelerated cumulative mass losses and k of S. canadensis. Thus, Cd with 7.5 mg/kg soil can accelerate litter decomposition of S. canadensis, but Cd with 15 mg/kg soil can decline litter decomposition of S. canadensis.
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Affiliation(s)
- Congyan Wang
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, 200092, PR China.
| | - Mei Wei
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Shu Wang
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Bingde Wu
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Daolin Du
- Institute of Environment and Ecology & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
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19
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Bachelot B, Lee CT. Disturbances Can Promote and Hinder Coexistence of Competitors in Ongoing Partner Choice Mutualisms. Am Nat 2020; 195:445-462. [DOI: 10.1086/707258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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20
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Shu X, Zhang K, Zhang Q, Wang W. Ecophysiological responses of Jatropha curcas L. seedlings to simulated acid rain under different soil types. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 185:109705. [PMID: 31561080 DOI: 10.1016/j.ecoenv.2019.109705] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/09/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Acid rain is a global environmental problem. Acid rain can affect plants directly by damaging the leaves and indirectly by soil acidifying. Many studies have been conducted to investigate the impacts of acid rain on plant under a single soil type. However, there is little information on the effect of acid rain on plant under different soil types. Jatropha curcas L. is an energy plant widely distributed in acid rain pollution area with various soil types. In this study, we investigated the effects of acid rain (pH2.5, pH3.5, pH4.5, pH5.6) on the growth, physiology, nutrient elements and bacterial community of J. curcas seedlings under different soil types [Red soils (RS), Yellow soils (YS), Yellow-brown soils (YBS), and Purplish soils (PS)]. Acid rain and soil types significantly influence the growth of J. curcas seedlings, and there was a significant interaction between acid rain and soil types. Acid rain (pH 4.5) was beneficial to the growth of J. curcas seedlings, whereas acid rain (pH 2.5 or 3.5) inhibited growth of J. curcas seedlings. The growth of J. curcas seedlings could resist the stress of acid rain by scavenging and detoxification of active oxygen species in leaves. Combined with the increase in relative growth rate of seedlings treated with simulated acid rain at pH 4.5, we inferred that K can stimulate the growth of seedlings. The lower soil pH, cation exchange capacity and base saturation had stronger inhibitory effects on growth of J. curcas seedlings. YBS and PS were beneficial for growth of J. curcas seedlings by higher buffering capacity under acid rain treatments. The phylum Proteobacteria was found to predominate in rhizosphere soils. YBS was favorable to support Proteobacteria growth and reproduction. The redundancy analysis showed that the Cyanobacteria were favorable to growth of J. curcas seedlings.
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Affiliation(s)
- Xiao Shu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - KeRong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - QuanFa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - WeiBo Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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21
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Yang W, Zhang D, Cai X, Xia L, Luo Y, Cheng X, An S. Significant alterations in soil fungal communities along a chronosequence of Spartina alterniflora invasion in a Chinese Yellow Sea coastal wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133548. [PMID: 31369894 DOI: 10.1016/j.scitotenv.2019.07.354] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023]
Abstract
Plant invasion typically alters the microbial communities of soils, which affects ecosystem carbon (C) and nitrogen (N) cycles. The responses of the soil fungal communities to plant invasion along its chronosequence remain poorly understood. For this study, we investigated variations in soil fungal communities through Illumina MiSeq sequencing analyses of the fungal internal transcribed spacer (ITS) region, and quantitative polymerase chain reaction (qPCR), along a chronosequence (i.e., 9-, 13-, 20- and 23-year-old) of invasive Spartina alterniflora. We compared these variations with those of bare flat in a Chinese Yellow Sea coastal wetland. Our results highlighted that the abundance of soil fungi, the number of operational taxonomic units (OTUs), species richness, and Shannon diversity indices for soil fungal communities were highest in 9-year-old S. alterniflora soil, which gradually declined along the invasion chronosequence. The relative abundance of copiotrophic Basidiomycota revealed significant decreasing trend, while the relative abundance of oligotrophic Ascomycota gradually increased along the S. alterniflora invasion chronosequence. The relative abundance of soil saprotrophic fungi (e.g., undefined saprotrophs) was gradually reduced while symbiotic fungi (e.g., ectomycorrhizal fungi) and pathotrophic fungi (e.g., plant and animal pathogens) progressively increased along the S. alterniflora invasion chronosequence. Our results suggested that S. alterniflora invasion significantly altered soil fungal abundance and diversity, community composition, trophic modes, and functional groups along a chronosequence, via substantially reduced soil litter inputs, and gradually decreased soil pH, moisture, and soil nutrient substrates along the invasion chronosequence, from 9 to 23 years. These changes in soil fungal communities, particularly their trophic modes and functional groups along the S. alterniflora invasion chronosequence could well impact the decomposition and accumulation of soil C and N, while potentially altering ecosystem C and N sinks in a Chinese Yellow Sea coastal wetland.
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Affiliation(s)
- Wen Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China.
| | - Di Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China
| | - Xinwen Cai
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, PR China
| | - Lu Xia
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing 210023, PR China
| | - Yiqi Luo
- Center for Ecosystem Science and Society (Ecoss), Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Xiaoli Cheng
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China.
| | - Shuqing An
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing 210023, PR China
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22
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Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests. Microorganisms 2019; 7:microorganisms7110547. [PMID: 31717669 PMCID: PMC6921041 DOI: 10.3390/microorganisms7110547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 11/17/2022] Open
Abstract
Soil fungi are a highly diverse group of microorganisms that provide many ecosystem services. The mechanisms of soil fungal community assembly must therefore be understood to reliably predict how global changes such as climate warming and biodiversity loss will affect ecosystem functioning. To this end, we assessed fungal communities in experimental subtropical forests by pyrosequencing of the internal transcribed spacer 2 (ITS2) region, and constructed tree-fungal bipartite networks based on the co-occurrence of fungal operational taxonomic units (OTUs) and tree species. The characteristics of the networks and the observed degree of fungal specialization were then analyzed in relation to the level of tree species diversity. Unexpectedly, plots containing two tree species had higher network connectance and fungal generality values than those with higher tree diversity. Most of the frequent fungal OTUs were saprotrophs. The degree of fungal specialization was highest in tree monocultures. Ectomycorrhizal fungi had higher specialization coefficients than saprotrophic, arbuscular mycorrhizal, and plant pathogenic fungi. High tree species diversity plots with 4 to 16 different tree species sustained the greatest number of fungal species, which is assumed to be beneficial for ecosystem services because it leads to more effective resource exploitation and greater resilience due to functional redundancy.
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Responses of Rhizosphere Fungal Communities to the Sewage Sludge Application into the Soil. Microorganisms 2019; 7:microorganisms7110505. [PMID: 31671795 PMCID: PMC6920848 DOI: 10.3390/microorganisms7110505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/17/2022] Open
Abstract
Due to the increasing sewage sludge production in the world and problems with its disposal, an application of sludge to the soil appears to be a suitable solution considering its fertilizer properties and ability to improve the soil physical conditions. On the other hand, the sludge may also contain undesirable and toxic substances. Since soil microorganisms are sensitive to environmental changes, they can be used as indicators of soil quality. In this study, we used sewage sludge (SS) from two municipal wastewater treatment plants (SS-A and SS-B) in the dose of 5 t/ha and 15 t/ha in order to determine possible changes in the fungal community diversity, especially arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Arundo donax L. Rhizosphere samples were collected in summer and autumn for two consecutive years and the fungal diversity was examined using terminal restriction fragment length polymorphism and 18S rDNA sequencing. Fungal alpha diversity was more affected by SS-A than SS-B probably due to the higher heavy metal content. However, based on principal component analysis and ANOSIM, significant changes in overall fungal diversity were not observed. Simultaneously, 18S rDNA sequencing showed that more various fungal taxa were detected in the sample with sewage sludge than in the control. Glomus sp. as a representative of AMF was the most represented. Moreover, Funneliformis in both samples and Rhizophagus in control with Septoglomus in the sludge sample were other representatives of AMF. Our results indicate that the short-term sewage sludge application into the soil does not cause a shift in the fungal community composition.
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Wang K, Zhang Y, Tang Z, Shangguan Z, Chang F, Jia F, Chen Y, He X, Shi W, Deng L. Effects of grassland afforestation on structure and function of soil bacterial and fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 676:396-406. [PMID: 31048170 DOI: 10.1016/j.scitotenv.2019.04.259] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/27/2019] [Accepted: 04/17/2019] [Indexed: 05/20/2023]
Abstract
Grassland afforestation strongly influences the structure and function of soil microorganisms. Yet the mechanisms of how afforestation could simultaneously alter both the soil fungal and bacterial communities and its implications for ecosystem management are poorly understood, especially in nitrogen-limited ecosystems. Using high-throughput sequencing of 16S rRNA and ITS rRNA genes, the present study investigated the changes in soil properties and soil microorganisms after afforestation of natural grasslands with Chinese pine (Pinus tabuliformis) on the Loess Plateau in China. Results showed that soil bacterial diversity had no significant differences among the grassland (GL), forest-grassland transition zone (TZ), and forestland (FL), while soil fungal diversity in the GL was significantly higher than that in the FL and TZ (P < 0.05). The proportion of shared OTUs in the soil bacterial community was higher than that in the soil fungal community among the three land use types. The dominant bacterial phylum shifted from Proteobacteria to Actinobacteria, while the dominant fungal phylum shifted from Ascomycota to Basidiomycota after the GL conversion to the FL. The functional groups of ECM fungi increased significantly while biotrophic fungi decreased significantly after grassland afforestation. Both the soil bacterial and fungal communities in the TZ showed great similarity with those in the FL. In addition, among all examined soil properties, soil nitrogen (N) showed a more significant effect on the soil microbial communities. The reduction of soil N after grassland afforestation resulted in both the structure and function changes in soil microbial communities. Our results demonstrated simultaneously differential changes in the composition and diversity of both soil bacterial and fungal communities after afforestation from grasslands to planted forests.
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Affiliation(s)
- Kaibo Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710075, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongwang Zhang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China
| | - Zhuangsheng Tang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhouping Shangguan
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China
| | - Fan Chang
- Microbial Metabolism Research Center, Microbiology Institute of Shaanxi, Xi'an 710043, China
| | - Feng'an Jia
- Microbial Metabolism Research Center, Microbiology Institute of Shaanxi, Xi'an 710043, China
| | - Yiping Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, Shaanxi 710075, China
| | - Xinhua He
- College of Natural Resources and Environment, Southwest University, Beibei, Chongqing 400715, China; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Weiyu Shi
- Chongqing Engineering Research Center for Remote Sensing Big Data Application, School of Geographical Sciences, Southwest University, Chongqing 400715, China.
| | - Lei Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, China.
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25
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Miller ET, Bohannan BJM. Life Between Patches: Incorporating Microbiome Biology Alters the Predictions of Metacommunity Models. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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26
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Ma S, De Frenne P, Vanhellemont M, Wasof S, Boeckx P, Brunet J, Cousins SA, Decocq G, Kolb A, Lemke I, Liira J, Naaf T, Orczewska A, Plue J, Wulf M, Verheyen K. Local soil characteristics determine the microbial communities under forest understorey plants along a latitudinal gradient. Basic Appl Ecol 2019. [DOI: 10.1016/j.baae.2019.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Schlatter DC, Yin C, Burke I, Hulbert S, Paulitz T. Location, Root Proximity, and Glyphosate-Use History Modulate the Effects of Glyphosate on Fungal Community Networks of Wheat. MICROBIAL ECOLOGY 2018; 76:240-257. [PMID: 29218372 DOI: 10.1007/s00248-017-1113-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Glyphosate is the most-used herbicide worldwide and an essential tool for weed control in no-till cropping systems. However, concerns have been raised regarding the long-term effects of glyphosate on soil microbial communities. We examined the impact of repeated glyphosate application on bulk and rhizosphere soil fungal communities of wheat grown in four soils representative of the dryland wheat production region of Eastern Washington, USA. Further, using soils from paired fields, we contrasted the response of fungal communities that had a long history of glyphosate exposure and those that had no known exposure. Soil fungal communities were characterized after three cycles of wheat growth in the greenhouse followed by termination with glyphosate or manual clipping of plants. We found that cropping system, location, year, and root proximity were the primary drivers of fungal community compositions, and that glyphosate had only small impacts on fungal community composition or diversity. However, the taxa that responded to glyphosate applications differed between rhizosphere and bulk soil and between cropping systems. Further, a greater number of fungal OTUs responded to glyphosate in soils with a long history of glyphosate use. Finally, fungal co-occurrence patterns, but not co-occurrence network characteristics, differed substantially between glyphosate-treated and non-treated communities. Results suggest that most fungi influenced by glyphosate are saprophytes that likely feed on dying roots.
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Affiliation(s)
- Daniel C Schlatter
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Ian Burke
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Scot Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Timothy Paulitz
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA.
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28
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Bachelot B, Uriarte M, Muscarella R, Forero-Montaña J, Thompson J, McGuire K, Zimmerman J, Swenson NG, Clark JS. Associations among arbuscular mycorrhizal fungi and seedlings are predicted to change with tree successional status. Ecology 2018; 99:607-620. [PMID: 29281752 DOI: 10.1002/ecy.2122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/22/2017] [Accepted: 12/07/2017] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi in the soil may influence tropical tree dynamics and forest succession. The mechanisms are poorly understood, because the functional characteristics and abundances of tree species and AM fungi are likely to be codependent. We used generalized joint attribute modeling to evaluate if AM fungi are associated with three forest community metrics for a sub-tropical montane forest in Puerto Rico. The metrics chosen to reflect changes during forest succession are the abundance of seedlings of different successional status, the amount of foliar damage on seedlings of different successional status, and community-weighted mean functional trait values (adult specific leaf area [SLA], adult wood density, and seed mass). We used high-throughput DNA sequencing to identify fungal operational taxonomic units (OTUs) in the soil. Model predictions showed that seedlings of mid- and late-successional species had less leaf damage when the 12 most common AM fungi were abundant compared to when these fungi were absent. We also found that seedlings of mid-successional species were predicted to be more abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. In contrast, early-successional tree seedlings were predicted to be less abundant when the 12 most common AM fungi were abundant compared to when these fungi were absent. Finally, we showed that, among the 12 most common AM fungi, different AM fungi were correlated with functional trait characteristics of early- or late-successional species. Together, these results suggest that early-successional species might not rely as much as mid- and late-successional species on AM fungi, and AM fungi might accelerate forest succession.
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Affiliation(s)
| | - María Uriarte
- Department of Ecology Evolution and Environmental Biology, Columbia University, New York, New York, 10027, USA
| | - Robert Muscarella
- Section for Ecoinformatics & Biodiversity, Department of Bisocience, Aarhus University, Aarhus, 8000, Denmark
| | - Jimena Forero-Montaña
- Department of Environmental Science, University of Puerto Rico-Rıo Piedras, San Juan, Puerto Rico, 00931, USA
| | - Jill Thompson
- Department of Environmental Science, University of Puerto Rico-Rıo Piedras, San Juan, Puerto Rico, 00931, USA.,Centre for Ecology & Hydrology, Penicuik, Midlothian, EH26 0QB, United Kingdom
| | - Krista McGuire
- Department of Biology, University of Oregon, Eugene, Oregon, 97403, USA
| | - Jess Zimmerman
- Department of Environmental Science, University of Puerto Rico-Rıo Piedras, San Juan, Puerto Rico, 00931, USA
| | - Nathan G Swenson
- Department of Biology, The University of Maryland, College Park, Maryland, 20742, USA
| | - James S Clark
- Nicholas School of the Environment and Department of Statistical Science, Duke University, Durham, North Carolina, 27708, USA
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29
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Liu S, Wang H, Deng Y, Tian P, Wang Q. Forest conversion induces seasonal variation in microbial β-diversity. Environ Microbiol 2018; 20:111-123. [DOI: 10.1111/1462-2920.14017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Shengen Liu
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Hang Wang
- National Plateau Wetlands Research Center; Southwest Forestry University; Kunming 650224 China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science; Chinese Academy of Sciences; Beijing 100085 China
| | - Peng Tian
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Qingkui Wang
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
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30
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Wang C, Zhou J, Liu J, Jiang K, Xiao H, Du D. Responses of the soil fungal communities to the co-invasion of two invasive species with different cover classes. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:151-159. [PMID: 29030899 DOI: 10.1111/plb.12646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Soil fungal communities play an important role in the successful invasion of non-native species. It is common for two or more invasive plant species to co-occur in invaded ecosystems. This study aimed to determine the effects of co-invasion of two invasive species (Erigeron annuus and Solidago canadensis) with different cover classes on soil fungal communities using high-throughput sequencing. Invasion of E. annuus and/or S. canadensis had positive effects on the sequence number, operational taxonomic unit (OTU) richness, Shannon diversity, abundance-based cover estimator (ACE index) and Chao1 index of soil fungal communities, but negative effects on the Simpson index. Thus, invasion of E. annuus and/or S. canadensis could increase diversity and richness of soil fungal communities but decrease dominance of some members of these communities, in part to facilitate plant further invasion, because high soil microbial diversity could increase soil functions and plant nutrient acquisition. Some soil fungal species grow well, whereas others tend to extinction after non-native plant invasion with increasing invasion degree and presumably time. The sequence number, OTU richness, Shannon diversity, ACE index and Chao1 index of soil fungal communities were higher under co-invasion of E. annuus and S. canadensis than under independent invasion of either individual species. The co-invasion of the two invasive species had a positive synergistic effect on diversity and abundance of soil fungal communities, partly to build a soil microenvironment to enhance competitiveness of the invaders. The changed diversity and community under co-invasion could modify resource availability and niche differentiation within the soil fungal communities, mediated by differences in leaf litter quality and quantity, which can support different fungal/microbial species in the soil.
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Affiliation(s)
- C Wang
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - J Zhou
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - J Liu
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - K Jiang
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - H Xiao
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - D Du
- Institute of Environment and Ecology, Academy of Environmental Health and Ecological Security & School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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31
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Zhang C, Liu G, Song Z, Qu D, Fang L, Deng L. Natural succession on abandoned cropland effectively decreases the soil erodibility and improves the fungal diversity. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:2142-2154. [PMID: 28681951 DOI: 10.1002/eap.1598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
Changes in plants and soils during natural succession have been evaluated, but little is known about the effects of succession on the activities of soil microbes and their interactions with soil erodibility. We conducted a field study on the Chinese Loess Plateau, typical of this semiarid area, to determine the effect of secondary succession on the stability of soil structure against erosion and on the composition of soil fungal communities. Characteristics of plant, soil, and fungal communities were assessed across a 30-yr chronosequence of grassland developed from abandoned cropland. The diversity and composition of the fungal communities were determined using high-throughput sequencing of the internal transcribed spacer. Six grasslands were selected to represent different successional age classes: 0 (cropland), 5, 10, 15, 20, and 30 yr. Short-term decreases (initial 5 yr) in the amounts of soil organic carbon, total nitrogen, available phosphorus, and fungal biomass and in fungal diversity had returned to original levels (i.e., cropland) within 15 yr and were much higher after continued succession. Abandoning cropland for succession caused the soil erodibility (K) decrease and the aboveground coverage, soil nutrient levels, content of larger (>5 mm) water-stable aggregate, mean aggregate weight diameter, and diversity of the fungal communities improvement including arbuscular mycorrhizas (AMF), ectomycorrhizas (EMF), and saprotrophs. The fungal communities were dominated by Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota during the succession. The successional patterns of the plant and fungal communities were similar, although distinct fungal communities were not observed in the two initial stages, suggesting that fungal succession may develop more slowly than plant succession. Plant root biomass, EMF, and soil organic carbon content accounted for most of the variation of soil erodibility (28.6%, 19.5%, and 11.8%, respectively), indicating their importance in shaping soil structure to prevent erosion. Our results demonstrated that abandoning cropland for natural succession could decrease soil erodibility and increase fungal diversity. EMF plays an important role in soil stability against erosion in the Loess Plateau. Abandoning cropland for natural succession should be recommended for alleviating soil erosion and improving the degraded soils in this area.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
| | - Zilin Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Dong Qu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
| | - Lei Deng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, China
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32
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Fernandez RD, Bulacio N, Álvarez A, Pajot H, Aragón R. Fungal decomposers of leaf litter from an invaded and native mountain forest of NW Argentina. Antonie van Leeuwenhoek 2017; 110:1207-1218. [PMID: 28553697 DOI: 10.1007/s10482-017-0893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/22/2017] [Indexed: 11/27/2022]
Abstract
The impact of plant species invasions on the abundance, composition and activity of fungal decomposers of leaf litter is poorly understood. In this study, we isolated and compared the relative abundance of ligninocellulolytic fungi of leaf litter mixtures from a native forest and a forest invaded by Ligustrum lucidum in a lower mountain forest of Tucuman, Argentina. In addition, we evaluated the relationship between the relative abundance of ligninocellulolytic fungi and properties of the soil of both forest types. Finally, we identified lignin degrading fungi and characterized their polyphenol oxidase activities. The relative abundance of ligninocellulolytic fungi was higher in leaf litter mixtures from the native forest. The abundance of cellulolytic fungi was negatively related with soil pH while the abundance of ligninolytic fungi was positively related with soil humidity. We identified fifteen genera of ligninolytic fungi; four strains were isolated from both forest types, six strains only from the invaded forest and five strains were isolated only from the native forest. The results found in this study suggest that L. Lucidum invasion could alter the abundance and composition of fungal decomposers. Long-term studies that include an analysis of the nutritional quality of litter are needed, for a more complete overview of the influence of L. Lucidum invasion on fungal decomposers and on leaf litter decomposition.
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Affiliation(s)
- Romina Daiana Fernandez
- Instituto de Ecología Regional (IER, UNT- CONICET), Casilla de Correo 34(4107), Yerba Buena, Tucumán, Argentina.
| | - Natalia Bulacio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Analía Álvarez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
- Facultad de Ciencias Naturales e IML (UNT), Miguel Lillo 205(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Hipólito Pajot
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Avenida Belgrano y Pasaje Caseros(4000), San Miguel De Tucumán, Tucumán, Argentina
| | - Roxana Aragón
- Instituto de Ecología Regional (IER, UNT- CONICET), Casilla de Correo 34(4107), Yerba Buena, Tucumán, Argentina
- Facultad de Ciencias Naturales e IML (UNT), Miguel Lillo 205(4000), San Miguel De Tucumán, Tucumán, Argentina
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33
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Wang C, Zhou J, Jiang K, Liu J, Du D. Responses of soil N-fixing bacteria communities to invasive plant species under different types of simulated acid deposition. Naturwissenschaften 2017; 104:43. [DOI: 10.1007/s00114-017-1463-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/10/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]
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34
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Affiliation(s)
- Lucas C R Silva
- Environmental Studies Program, Department of Geography, Institute of Ecology and Evolution, University of Oregon, OR 97405, USA.
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Bachelot B, Uriarte M, McGuire KL, Thompson J, Zimmerman J. Arbuscular mycorrhizal fungal diversity and natural enemies promote coexistence of tropical tree species. Ecology 2017; 98:712-720. [DOI: 10.1002/ecy.1683] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/19/2016] [Accepted: 11/30/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Benedicte Bachelot
- Department of Biology; Duke University; 130 Science Drive Durham North Carolina 27701 USA
| | - María Uriarte
- Department of Ecology, Evolution and Environmental Biology; Columbia University; 1200 Amsterdam Avenue New York City New York 10027 USA
| | - Krista L. McGuire
- Department of Ecology, Evolution and Environmental Biology; Columbia University; 1200 Amsterdam Avenue New York City New York 10027 USA
- Department of Biology; Barnard College; Columbia University; New York City New York 10027 USA
| | - Jill Thompson
- Department of Environmental Sciences; University of Puerto Rico; Río Piedras Campus San Juan Puerto Rico 00936 USA
- Centre for Ecology & Hydrology; Bush Estate Penicuik; Midlothian EH26 0QB United Kingdom
| | - Jess Zimmerman
- Department of Environmental Sciences; University of Puerto Rico; Río Piedras Campus San Juan Puerto Rico 00936 USA
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Pec GJ, Karst J, Taylor DL, Cigan PW, Erbilgin N, Cooke JEK, Simard SW, Cahill JF. Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak. THE NEW PHYTOLOGIST 2017; 213:864-873. [PMID: 27659418 DOI: 10.1111/nph.14195] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi.
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Affiliation(s)
- Gregory J Pec
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
| | - Justine Karst
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - D Lee Taylor
- Department of Biology, University of New Mexico, Castetter Hall 104, Albuquerque, NM, 87131, USA
| | - Paul W Cigan
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, University of British Columbia, Forest Sciences Centre #3601-2424 Main Hall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, B717a Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
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