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Wang X, Wang Z, Chen F, Zhang Z, Fang J, Xing L, Zeng J, Zhang Q, Liu H, Liu W, Ren C, Yang G, Zhong Z, Zhang W, Han X. Deterministic assembly of grassland soil microbial communities driven by climate warming amplifies soil carbon loss. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171418. [PMID: 38460701 DOI: 10.1016/j.scitotenv.2024.171418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Perturbations in soil microbial communities caused by climate warming are expected to have a strong impact on biodiversity and future climate-carbon (C) feedback, especially in vulnerable habitats that are highly sensitive to environmental change. Here, we investigate the impact of four-year experimental warming on soil microbes and C cycling in the Loess Hilly Region of China. The results showed that warming led to soil C loss, mainly from labile C, and this C loss is associated with microbial response. Warming significantly decreased soil bacterial diversity and altered its community structure, especially increasing the abundance of heat-tolerant microorganisms, but had no effect on fungi. Warming also significantly increased the relative importance of homogeneous selection and decreased "drift" of bacterial and fungal communities. Moreover, warming decreased bacterial network stability but increased fungal network stability. Notably, the magnitude of soil C loss was significantly and positively correlated with differences in bacterial community characteristics under ambient and warming conditions, including diversity, composition, network stability, and community assembly. This result suggests that microbial responses to warming may amplify soil C loss. Combined, these results provide insights into soil microbial responses and C feedback in vulnerable ecosystems under climate warming scenarios.
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Affiliation(s)
- Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zhengchen Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Fang Chen
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zhenjiao Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Jingbo Fang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Liheng Xing
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Jia Zeng
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Qi Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Hanyu Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Weichao Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Chengjie Ren
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Gaihe Yang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China
| | - Zekun Zhong
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Wei Zhang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Xinhui Han
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, PR China; Shaanxi Engineering Research Center of Circular Agriculture, Yangling 712100, Shaanxi, PR China.
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Yang M, Luo X, Cai Y, Mwangi BN, Khan MS, Haider FU, Huang W, Cheng X, Yang Z, Zhou H, Liu S, Zhang Q, Luo M, Ou J, Xiong S, Li Y. Effect of fire and post-fire management on soil microbial communities in a lower subtropical forest ecosystem after a mountain fire. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119885. [PMID: 38147772 DOI: 10.1016/j.jenvman.2023.119885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
Wildfires and post-fire management exert profound effects on soil properties and microbial communities in forest ecosystems. Understanding microbial community recovery from fire and what the best post-fire management should be is very important but needs to be sufficiently studied. In light of these gaps in our understanding, this study aimed to assess the short-term effects of wildfire and post-fire management on both bacteria and fungi community composition, diversity, structure, and co-occurrence networks, and to identify the principal determinants of soil processes influencing the restoration of these communities. Specifically, we investigated soil bacterial and fungal community composition, diversity, structure, and co-occurrence networks in lower subtropical forests during a short-term (<3 years) post-fire recovery period at four main sites in Guangdong Province, southern China. Our results revealed significant effects of wildfires on fungal community composition, diversity, and co-occurrence patterns. Network analysis indicated reduced bacterial network complexity and connectivity post-fire, while the same features were enhanced in fungal networks. However, post-fire management effects on microbial communities were negligible. Bacterial diversity correlated positively with soil microbial biomass nitrogen, soil organic carbon, and soil total nitrogen. Conversely, based on the best random forest model, fungal community dynamics were negatively linked to nitrate-nitrogen and soil water content. Spearman's correlation analysis suggested positive associations between bacterial networks and soil factors, whereas fungal networks exhibited predominantly negative associations. This study elucidates the pivotal role of post-fire management in shaping ecological outcomes. Additionally, it accentuates the discernible distinctions between bacterial and fungal responses to fire throughout a short-term recovery period. These findings contribute novel insights that bear significance in evaluating the efficacy of environmental management strategies.
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Affiliation(s)
- Mengmeng Yang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuan Luo
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Ying Cai
- Xiamen University, Xiamen, 361000, China.
| | - Brian N Mwangi
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Muhammad Sadiq Khan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Fasih Ullah Haider
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Wanxuan Huang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xianli Cheng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Hubei University, Wuhan, 430062, China.
| | - Zefan Yang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongen Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China University of Technology, Guangzhou, 510641, China.
| | - Shizhong Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Qianmei Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Mingdao Luo
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Jinwei Ou
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Shiyang Xiong
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Yuelin Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Sardans J, Llusià J, Ogaya R, Vallicrosa H, Filella I, Gargallo-Garriga A, Peguero G, Van Langenhove L, Verryckt LT, Stahl C, Courtois EA, Bréchet LM, Tariq A, Zeng F, Alrefaei AF, Wang W, Janssens IA, Peñuelas J. Foliar elementome and functional traits relationships identify tree species niche in French Guiana rainforests. Ecology 2023; 104:e4118. [PMID: 37282712 DOI: 10.1002/ecy.4118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 06/08/2023]
Abstract
Biogeochemical niche (BN) hypothesis aims to relate species/genotype elemental composition with its niche based on the fact that different elements are involved differentially in distinct plant functions. We here test the BN hypothesis through the analysis of the 10 foliar elemental concentrations and 20 functional-morphological of 60 tree species in a French Guiana tropical forest. We observed strong legacy (phylogenic + species) signals in the species-specific foliar elemental composition (elementome) and, for the first time, provide empirical evidence for a relationship between species-specific foliar elementome and functional traits. Our study thus supports the BN hypothesis and confirms the general niche segregation process through which the species-specific use of bio-elements drives the high levels of α-diversity in this tropical forest. We show that the simple analysis of foliar elementomes may be used to test for BNs of co-occurring species in highly diverse ecosystems, such as tropical rainforests. Although cause and effect mechanisms of leaf functional and morphological traits in species-specific use of bio-elements require confirmation, we posit the hypothesis that divergences in functional-morphological niches and species-specific biogeochemical use are likely to have co-evolved.
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Affiliation(s)
- Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Joan Llusià
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Romà Ogaya
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Helen Vallicrosa
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Iolanda Filella
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Albert Gargallo-Garriga
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Guille Peguero
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Leandro Van Langenhove
- Research Group of Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Antwerpen, Belgium
| | - Lore T Verryckt
- Research Group of Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Antwerpen, Belgium
| | - Clément Stahl
- INRAE, UMR EcoFoG, CNRS, CIRAD, AgroParisTech, Université des Antilles, Université de Guyane, Kourou, France
| | - Elodie A Courtois
- INRAE, UMR EcoFoG, CNRS, CIRAD, AgroParisTech, Université des Antilles, Université de Guyane, Kourou, France
| | - Laëtitia M Bréchet
- Research Group of Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Antwerpen, Belgium
- INRAE, UMR EcoFoG, CNRS, CIRAD, AgroParisTech, Université des Antilles, Université de Guyane, Kourou, France
| | - Akash Tariq
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Fanjiang Zeng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | | | - Weiqi Wang
- Key Laboratory of Humid Subtropical Eco-Geographical Process, Ministry of Education, Fujian Normal University, Fuzhou, China
- College of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Ivan A Janssens
- Research Group of Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Antwerpen, Belgium
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Spain
- CREAF, Cerdanyola del Vallès, Spain
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Dong X, Jiang F, Duan D, Tian Z, Liu H, Zhang Y, Hou F, Nan Z, Chen T. Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species. J Fungi (Basel) 2023; 9:1016. [PMID: 37888272 PMCID: PMC10608051 DOI: 10.3390/jof9101016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.
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Affiliation(s)
- Xin Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Feifei Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Dongdong Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China
| | - Zhen Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Huining Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Yinan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Tao Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
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Osburn ED, Moon C, Stephenson T, Kittipalawattanapol K, Jones M, Strickland MS, Lynch LM. Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities. FEMS Microbiol Ecol 2023; 99:fiad085. [PMID: 37481693 DOI: 10.1093/femsec/fiad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 07/24/2023] Open
Abstract
Forest disturbance has well-characterized effects on soil microbial communities in tropical and northern hemisphere ecosystems, but little is known regarding effects of disturbance in temperate forests of the southern hemisphere. To address this question, we collected soils from intact and degraded Eucalyptus forests along an east-west transect across Tasmania, Australia, and characterized prokaryotic and fungal communities using amplicon sequencing. Forest degradation altered soil microbial community composition and function, with consistent patterns across soil horizons and regions of Tasmania. Responses of prokaryotic communities included decreased relative abundance of Acidobacteriota, nitrifying archaea, and methane-oxidizing prokaryotes in the degraded forest sites, while fungal responses included decreased relative abundance of some saprotrophic taxa (e.g. litter saprotrophs). Forest degradation also reduced network connectivity in prokaryotic communities and increased the importance of dispersal limitation in assembling both prokaryotic and fungal communities, suggesting recolonization dynamics drive microbial composition following disturbance. Further, changes in microbial functional groups reflected changes in soil chemical properties-reductions in nitrifying microorganisms corresponded with reduced NO3-N pools in the degraded soils. Overall, our results show that soil microbiota are highly responsive to forest degradation in eucalypt forests and demonstrate that microbial responses to degradation will drive changes in key forest ecosystem functions.
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Affiliation(s)
- Ernest D Osburn
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Cooper Moon
- Department of Environmental Science, University of Idaho, 875 Perimeter Dr. MS 1139, Moscow, ID 83844, USA
| | - Torrey Stephenson
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Kawinwit Kittipalawattanapol
- School of Natural Sciences, University of Tasmania, Life Sciences Building, Biological Sciences, Hobart, Tasmania 7001, Australia
| | - Menna Jones
- School of Natural Sciences, University of Tasmania, Life Sciences Building, Biological Sciences, Hobart, Tasmania 7001, Australia
| | - Michael S Strickland
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
| | - Laurel M Lynch
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Dr. MS 2340, Moscow, ID 83844, USA
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Mishcherikova V, Lynikienė J, Marčiulynas A, Gedminas A, Prylutskyi O, Marčiulynienė D, Menkis A. Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe. J Fungi (Basel) 2023; 9:829. [PMID: 37623600 PMCID: PMC10455207 DOI: 10.3390/jof9080829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
We assessed the diversity and composition of fungal communities in different functional tissues and the rhizosphere soil of Pinus sylvestris and Picea abies stands along the latitudinal gradient of these tree species distributions in Europe to model possible changes in fungal communities imposed by climate change. For each tree species, living needles, shoots, roots, and the rhizosphere soil were sampled and subjected to high-throughput sequencing. Results showed that the latitude and the host tree species had a limited effect on the diversity and composition of fungal communities, which were largely explained by the environmental variables of each site and the substrate they colonize. The mean annual temperature and mean annual precipitation had a strong effect on root fungal communities, isothermality on needle fungal communities, mean temperature of the warmest quarter and precipitation of the driest month on shoot fungal communities, and precipitation seasonality on soil fungal communities. Fungal communities of both tree species are predicted to shift to habitats with a lower annual temperature amplitude and with increasing precipitation during the driest month, but the suitability of these habitats as compared to the present conditions is predicted to decrease in the future.
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Affiliation(s)
- Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Oleh Prylutskyi
- Department of Mycology and Plant Resistance, V.N. Karazin Kharkiv National University, Svobody Sq., 61022 Kharkiv, Ukraine;
| | - Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas, Lithuania; (V.M.); (J.L.); (A.M.); (A.G.)
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
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Janowski D, Leski T. Landscape-scale mapping of soil fungal distribution: proposing a new NGS-based approach. Sci Rep 2023; 13:10280. [PMID: 37355666 PMCID: PMC10290699 DOI: 10.1038/s41598-023-37538-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/23/2023] [Indexed: 06/26/2023] Open
Abstract
Soil fungi play an indispensable role in the functioning of terrestrial habitats. Most landscape-scale studies of soil fungal diversity try to identify the fungal taxa present at a study site and define the relationships between their abundance and environmental factors. The specific spatial distribution of these fungi over the site, however, is not addressed. Our study's main objective is to propose a novel approach to landscape-scale mapping of soil fungi distribution using next generation sequencing and geographic information system applications. Furthermore, to test the proposed approach and discuss its performance, we aimed to conduct a case study mapping the spatial distribution of soil fungi on the Wielka Żuława island. The case study was performed on the Wielka Żuława island in northern Poland, where soil samples were collected every 100 m in an even grid. The fungal taxa and their relative abundance in each sample were assessed using the Illumina platform. Using the data obtained for the sampled points, maps of soil fungi spatial distribution were generated using three common interpolators: inverted distance weighted (IDW), B-spline, and ordinary Kriging. The proposed approach succeeded in creating maps of fungal distribution on Wielka Żuława. The most abundant groups of soil fungi were Penicillium on the genus level, Aspergillaceae on the family level, and ectomycorrhizal fungi on the trophic group level. Ordinary Kriging proved to be the most accurate at predicting relative abundance values for the groups of fungi significantly spatially autocorrelated at the sampled scale. For the groups of fungi not displaying spatial autocorrelation at the sampled scale, IDW provided the most accurate predictions of their relative abundance. Although less accurate at predicting exact relative abundance values, B-spline performed best in delineating the spatial patterns of soil fungi distribution. The proposed approach to landscape-scale mapping of soil fungi distribution could provide new insights into the ecology of soil fungi and terrestrial ecosystems in general. Producing maps of predicted fungal distribution in landscape-scale soil fungi diversity studies would also facilitate the reusability and replicability of the results. Outside the area of research, mapping the distribution of soil fungi could prove helpful in areas such as agriculture and forestry, nature conservation, and urban planning.
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Affiliation(s)
- Daniel Janowski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland.
- Department of Natural Environmental Studies, The University of Tokyo, Kashiwa, Chiba, Japan.
| | - Tomasz Leski
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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Hogan JA, Jusino MA, Smith ME, Corrales A, Song X, Hu YH, Yang J, Cao M, Valverde-Barrantes OJ, Baraloto C. Root-associated fungal communities are influenced more by soils than by plant-host root traits in a Chinese tropical forest. THE NEW PHYTOLOGIST 2023; 238:1849-1864. [PMID: 36808625 DOI: 10.1111/nph.18821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/14/2023] [Indexed: 05/04/2023]
Abstract
Forest fungal communities are shaped by the interactions between host tree root systems and the associated soil conditions. We investigated how the soil environment, root morphological traits, and root chemistry influence root-inhabiting fungal communities in three tropical forest sites of varying successional status in Xishuangbanna, China. For 150 trees of 66 species, we measured root morphology and tissue chemistry. Tree species identity was confirmed by sequencing rbcL, and root-associated fungal (RAF) communities were determined using high-throughput ITS2 sequencing. Using distance-based redundancy analysis and hierarchical variation partitioning, we quantified the relative importance of two soil variables (site average total phosphorus and available phosphorus), four root traits (dry matter content, tissue density, specific tip abundance, and forks), and three root tissue elemental concentrations (nitrogen, calcium, and manganese) on RAF community dissimilarity. The root and soil environment collectively explained 23% of RAF compositional variation. Soil phosphorus explained 76% of that variation. Twenty fungal taxa differentiated RAF communities among the three sites. Soil phosphorus most strongly affects RAF assemblages in this tropical forest. Variation in root calcium and manganese concentrations and root morphology among tree hosts, principally an architectural trade-off between dense, highly branched vs less-dense, herringbone-type root systems, are important secondary determinants.
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Affiliation(s)
- J Aaron Hogan
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, 33199, USA
| | - Michelle A Jusino
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- USDA Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, WI, 53726, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, 111221, Colombia
| | - Xiaoyang Song
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Yue-Hua Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, 666303, China
| | - Oscar J Valverde-Barrantes
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, 33199, USA
| | - Christopher Baraloto
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, 33199, USA
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Liu Z, Michalet R, Wang C, Wang Y, Chen J, Cui H, Song H, Wang J, Yang Z, An L, Xiao S, Chen S. Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160154. [PMID: 36375548 DOI: 10.1016/j.scitotenv.2022.160154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In alpine systems, cushion plants act as foundation species by ameliorating local environmental conditions. Empirical studies indicate that contrasting phenotypes of alpine cushion species have different effects on understory plant species, either facilitative or competitive. Furthermore, dependent species within each community type might also exhibit different responses to each cushion phenotype, which can be clustered into several "response groups". Additionally, these species-groups specific responses to alpine cushion species phenotypes could alter community assembly. However, very few studies have assessed responses of dependent communities at species-group levels, in particular for both above- and below-ground communities. Here, we selected a loose and a tight phenotype of the alpine cushion species Thylacospermum caespitosum in two sites of northwest China, and use the relative intensity of interactions index to quantify cushion plant effects on subordinate communities of plants and soil fungi and bacteria. We assessed variations in responses of both above- and below-ground organisms to cushion plant effects at species-group level. Species-group level analyses showed that the effects of the phenotype varied among groups of each of the three community types, and different species-groups were composed by unique taxa. Additionally, we found that loose cushions enhanced stochastic processes in community assembly, for plants and soil fungi but not for soil bacteria. These variations of phenotypic effects on different species-group induced contrasting taxonomic composition between groups, and alter community assembly thereby. Our study highlights the occurrence of contrasting effects of two phenotypes of a foundation cushion plant on understory plants, soil fungi and bacteria community composition, but not necessarily on their richness. We also showed that assessing responses of understory species at the species-group level allows a more realistic and mechanistic understanding of biotic interactions both for above- and below-ground communities.
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Affiliation(s)
- Ziyang Liu
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Richard Michalet
- Environnements et Paléoenvironnements Océaniques et Continentaux, University of Bordeaux, Bordeaux, France
| | - Chenyue Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Yajun Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Lizhe An
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China.
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10
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Stanek M, Kushwaha P, Murawska-Wlodarczyk K, Stefanowicz AM, Babst-Kostecka A. Quercus rubra invasion of temperate deciduous forest stands alters the structure and functions of the soil microbiome. GEODERMA 2023; 430:116328. [PMID: 37600960 PMCID: PMC10438910 DOI: 10.1016/j.geoderma.2023.116328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Invasive plants can modify the diversity and taxonomical structure of soil microbiomes. However, it is difficult to generalize the underlying factors as their influence often seems to depend on the complex plant-soil-microbial interactions. In this paper, we investigated how Quercus rubra impacts on the soil microbiome across two soil horizons in relation to native woodland. Five paired adjacent invaded vs native vegetation plots in a managed forest in southern Poland were investigated. Soil microbial communities were assessed along with soil enzyme activities and soil physicochemical parameters, separately for both organic and mineral horizons, as well as forest stand characteristics to explore plant-soil-microbe interactions. Although Q. rubra did not significantly affect pH, organic C, total N, available nutrients nor enzymatic activity, differences in soil abiotic properties (except C to N ratio) were primarily driven by soil depth for both vegetation types. Further, we found significant differences in soil microbiome under invasion in relation to native vegetation. Microbial richness and diversity were lower in both horizons of Q. rubra vs control plots. Moreover, Q. rubra increased relative abundance of unique amplicon sequence variants in both horizons and thereby significantly changed the structure of the core soil microbial communities, in comparison to the control plots. In addition, predicted microbial functional groups indicated a predominant soil depth effect in both vegetation plots with higher abundance of aerobic chemoheterotrophic bacteria and endophytic fungi in the organic horizon and greater abundance of methanotrophic and methylotrophic bacteria, and ectomycorrhizal fungi in the mineral horizon. Overall, our results indicate strong associations between Q. rubra invasion and changes in soil microbiome and associated functions, a finding that needs to be further investigated to predict modifications in ecosystem functioning caused by this invasive species.
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Affiliation(s)
- Małgorzata Stanek
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Priyanka Kushwaha
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | | | - Anna M. Stefanowicz
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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11
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Barros KO, Alvarenga FBM, Magni G, Souza GFL, Abegg MA, Palladino F, da Silva SS, Rodrigues RCLB, Sato TK, Hittinger CT, Rosa CA. The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species. Yeast 2023; 40:84-101. [PMID: 36582015 DOI: 10.1002/yea.3837] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
This study investigated the diversity of yeast species associated with rotting wood in Brazilian Amazonian rainforests. A total of 569 yeast strains were isolated from rotting wood samples collected in three Amazonian areas (Universidade Federal do Amazonas-Universidade Federal do Amazonas [UFAM], Piquiá, and Carú) in the municipality of Itacoatiara, Amazon state. The samples were cultured in yeast nitrogen base (YNB)-d-xylose, YNB-xylan, and sugarcane bagasse and corncob hemicellulosic hydrolysates (undiluted and diluted 1:2 and 1:5). Sugiyamaella was the most prevalent genus identified in this work, followed by Kazachstania. The most frequently isolated yeast species were Schwanniomyces polymorphus, Scheffersomyces amazonensis, and Wickerhamomyces sp., respectively. The alpha diversity analyses showed that the dryland forest of UFAM was the most diverse area, while the floodplain forest of Carú was the least. Additionally, the difference in diversity between UFAM and Carú was the highest among the comparisons. Thirty candidates for new yeast species were obtained, representing 36% of the species identified and totaling 101 isolates. Among them were species belonging to the clades Spathaspora, Scheffersomyces, and Sugiyamaella, which are recognized as genera with natural xylose-fermenting yeasts that are often studied for biotechnological and ecological purposes. The results of this work showed that rotting wood collected from the Amazonian rainforest is a tremendous source of diverse yeasts, including candidates for new species.
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Affiliation(s)
- Katharina O Barros
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Flávia B M Alvarenga
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Giulia Magni
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gisele F L Souza
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maxwel A Abegg
- Institute of Exact Sciences and Technology (ICET), Federal University of Amazonas (UFAM), Itacoatiara, Brazil
| | - Fernanda Palladino
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sílvio S da Silva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Rita C L B Rodrigues
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carlos A Rosa
- Departmento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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12
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Yang Y, Dou Y, Wang B, Xue Z, Wang Y, An S, Chang SX. Deciphering factors driving soil microbial life-history strategies in restored grasslands. IMETA 2023; 2:e66. [PMID: 38868332 PMCID: PMC10989924 DOI: 10.1002/imt2.66] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/12/2022] [Accepted: 11/06/2022] [Indexed: 06/14/2024]
Abstract
In macroecology, the concept of r- and K-strategy has been widely applied, yet, there have been limited studies on microbial life-history strategies in temperate grasslands using multiple sequencing approaches. Total phospholipid fatty acid (PLFA) analysis, high-throughput meta-genomic sequencing, and GeoChip technologies were used to examine the changes in microbial life-history traits in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration). Grassland restoration increased the relative abundances of Actinobacteria, Proteobacteria, and Bacteroidetes but reduced the relative abundances of Acidobacteria, Planctomycetes, and Chloroflexi. PLFA analysis revealed that grassland restoration reduced the fungi:bacteria and Gram-positive:Gram-negative bacteria ratios. Combined with the meta-genomic data, we found that grassland restoration shifted microorganisms from oligotrophic (K-) to copiotrophic (r-) groups, consistent with the increased rRNA operon copy number of the microbial community. Structural equation modeling showed that soil properties positively (p < 0.05) while plant properties negatively (p < 0.05) affected microbial life-history traits. We built a framework to highlight the importance of plant and soil properties in driving microbial life-history traits during grassland restoration. Finally, by incorporating meta-genomic and other microbiological data, this study showed that microbial life-history traits support the idea that rRNA operon copy number is a trait that reflects resource availability to soil microorganisms.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'anChina
- Chinese Academy of Sciences Center for Excellence in Quaternary Science and Global ChangeXi'anChina
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau in ShaanxiXi'anChina
| | - Yanxing Dou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Zhijing Xue
- College of Geography and TourismShaanxi Normal UniversityXi'anChina
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of SciencesXi'anChina
- Chinese Academy of Sciences Center for Excellence in Quaternary Science and Global ChangeXi'anChina
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau in ShaanxiXi'anChina
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess PlateauNorthwest A&F UniversityYanglingChina
| | - Scott X. Chang
- Department of Renewable ResourcesUniversity of AlbertaEdmontonCanada
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Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, Chu H. Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China. SCIENCE CHINA LIFE SCIENCES 2022; 66:1134-1150. [PMID: 36462107 DOI: 10.1007/s11427-022-2174-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022]
Abstract
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, 50409, Estonia
- College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Miao Sun
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Han-Yang Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210003, China
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Effects of Invasive Plant Diversity on Soil Microbial Communities. DIVERSITY 2022. [DOI: 10.3390/d14110992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Native plant communities can be invaded by different numbers of alien plant species or by the same number of alien plant species with different levels of evenness. However, little is known about how alien invasive plant species richness and evenness affect soil microbial communities. We constructed native herbaceous plant communities invaded by exotic plants with different richness (1, 2, 4 and 8 species) and evenness (high and low) and analyzed soil physico-chemical properties and the diversity and composition of soil fungal and bacterial communities by high-throughput Illumina sequencing. Overall, the species richness and evenness of invasive plants had no significant effect on bacterial and fungal alpha diversity (OTUs, Shannon, Simpson, Chao1 and ACE) or the soil physico-chemical properties. However, invasive species richness had a significant impact on the relative abundance of the most dominant fungi, Ascomycota and Bipolaris, and the dominant bacteria, Actinobacteriota, which increased with increasing invasive species richness. The relative abundance of the dominant microbial groups was significantly correlated with the relative abundance of some specific invasive plants in the community. This study sheds new light on the effects of plant co-invasion on soil microbial communities, which may help us understand the underlying mechanisms of multiple alien plant invasion processes from the perspective of soil microorganisms.
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Li J, Chen L, Wang H, Ouyang S, Liu X, Lu J. Pattern and drivers of soil fungal community along elevation gradient in the Abies georgei forests of Segila mountains, Southeast Tibet. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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16
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Marčiulynienė D, Marčiulynas A, Mishcherikova V, Lynikienė J, Gedminas A, Franic I, Menkis A. Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris. J Fungi (Basel) 2022; 8:jof8101112. [PMID: 36294677 PMCID: PMC9604598 DOI: 10.3390/jof8101112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.
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Affiliation(s)
- Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
- Correspondence:
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Iva Franic
- Department of Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden;
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007 Uppsala, Sweden;
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17
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Merino‐Martín L, Hernández‐Cáceres D, Reverchon F, Angeles‐Alvarez G, Zhang G, Dunoyer de Segonzac D, Dezette D, Stokes A. Habitat partitioning of soil microbial communities along an elevation gradient: from plant root to landscape scale. OIKOS 2022. [DOI: 10.1111/oik.09034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Merino‐Martín
- Depto de Biología y Geología, Física y Química inorgánica, ESCET, Univ. Rey Juan Carlos Madrid Spain
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ. Paul Valéry Montpellier 3 Montpellier France
| | | | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Inst. de Ecología, A.C. Pátzcuaro Michoacán México
| | | | - Guangqi Zhang
- Univ. Montpellier, AMAP, INRAE, CIRAD, CNRS, IRD Montpellier France
| | | | - Damien Dezette
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro Montpellier France
| | - Alexia Stokes
- Univ. Montpellier, AMAP, INRAE, CIRAD, CNRS, IRD Montpellier France
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18
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Dueñas JF, Hempel S, Homeier J, Suárez JP, Rillig MC, Camenzind T. Root associated fungal lineages of a tropical montane forest show contrasting sensitivities to the long-term addition of nitrogen and phosphorus. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:775-784. [PMID: 36085412 DOI: 10.1111/1758-2229.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Root associated fungal (RAF) communities can exert strong effects on plant communities and are potentially sensitive to shifts in soil fertility. As increased atmospheric nitrogen (N) and phosphorus (P) deposition can alter the nutrient balance in natural ecosystems, we assessed the response of RAF communities to a fertilization experiment deployed on a highly diverse Andean forest. The stand level fine root fraction was sampled after 7 years of systematic N and P additions and RAF communities were characterized by a deep sequencing approach. We expected that fertilization will enhance competition of fungal taxa for limiting nutrients, thus eliciting diversity reductions and alterations in the structure of RAF communities. Fertilization treatments did not reduce RAF richness but affected community composition. At the phylum level fertilization reduced richness exclusively among Glomeromycota. In contrast, N and P additions (alone or in combination) altered the composition of several fungal phyla. The lack of a generalized response to long-term fertilization among RAF lineages suggests that most of these lineages will not be directly and immediately affected by the increasing rates of atmospheric N and P deposition expected for this region by 2050.
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Affiliation(s)
- Juan F Dueñas
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jürgen Homeier
- Plant Ecology and Ecosystems Research, University of Göttingen, Göttingen, Germany
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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19
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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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20
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Chen J, Shi Z, Liu S, Zhang M, Cao X, Chen M, Xu G, Xing H, Li F, Feng Q. Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine-Gorge Region on the Eastern Qinghai-Tibetan Plateau. J Fungi (Basel) 2022; 8:807. [PMID: 36012795 PMCID: PMC9410234 DOI: 10.3390/jof8080807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022] Open
Abstract
Soil fungi play an integral and essential role in maintaining soil ecosystem functions. The understanding of altitude variations and their drivers of soil fungal community composition and diversity remains relatively unclear. Mountains provide an open, natural platform for studying how the soil fungal community responds to climatic variability at a short altitude distance. Using the Illumina MiSeq high-throughput sequencing technique, we examined soil fungal community composition and diversity among seven vegetation types (dry valley shrub, valley-mountain ecotone broadleaved mixed forest, subalpine broadleaved mixed forest, subalpine coniferous-broadleaved mixed forest, subalpine coniferous forest, alpine shrub meadow, alpine meadow) along a 2582 m altitude gradient in the alpine-gorge region on the eastern Qinghai-Tibetan Plateau. Ascomycota (47.72%), Basidiomycota (36.58%), and Mortierellomycota (12.14%) were the top three soil fungal dominant phyla in all samples. Soil fungal community composition differed significantly among the seven vegetation types along altitude gradients. The α-diversity of soil total fungi and symbiotic fungi had a distinct hollow pattern, while saprophytic fungi and pathogenic fungi showed no obvious pattern along altitude gradients. The β-diversity of soil total fungi, symbiotic fungi, saprophytic fungi, and pathogenic fungi was derived mainly from species turnover processes and exhibited a significant altitude distance-decay pattern. Soil properties explained 31.27-34.91% of variation in soil fungal (total and trophic modes) community composition along altitude gradients, and the effects of soil nutrients on fungal community composition varied by trophic modes. Soil pH was the main factor affecting α-diversity of soil fungi along altitude gradients. The β-diversity and turnover components of soil total fungi and saprophytic fungi were affected by soil properties and geographic distance, while those of symbiotic fungi and pathogenic fungi were affected only by soil properties. This study deepens our knowledge regarding altitude variations and their drivers of soil fungal community composition and diversity, and confirms that the effects of soil properties on soil fungal community composition and diversity vary by trophic modes along altitude gradients in the alpine-gorge region.
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Affiliation(s)
- Jian Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Zuomin Shi
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Shun Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miaomiao Zhang
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Xiangwen Cao
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Miao Chen
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Gexi Xu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Hongshuang Xing
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Feifan Li
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China; (J.C.); (S.L.); (M.Z.); (X.C.); (M.C.); (G.X.); (H.X.); (F.L.)
- Miyaluo Research Station of Alpine Forest Ecosystem, Lixian County 623100, China
| | - Qiuhong Feng
- Ecological Restoration and Conservation on Forest and Wetland Key Laboratory of Sichuan Province, Sichuan Academy of Forestry, Chengdu 610081, China;
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21
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Zeng Q, Man X, Lebreton A, Dai Y, Martin FM. The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan. Front Microbiol 2022; 13:916337. [PMID: 35966686 PMCID: PMC9372452 DOI: 10.3389/fmicb.2022.916337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Yucheng Dai,
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
- Francis M. Martin,
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22
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Salama ES, Jeon BH, Wang J, Abou-Shanab RAI, Xiong JQ. Editorial: Microbial advances towards sustainable environment: Microbiome structure & integrated technologies. Front Microbiol 2022; 13:971696. [PMID: 35923399 PMCID: PMC9343073 DOI: 10.3389/fmicb.2022.971696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, China
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, South Korea
| | - Junling Wang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, China
| | - Reda A. I. Abou-Shanab
- College of Biological Sciences, BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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23
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Gan H, Li X, Wang Y, Lü P, Ji N, Yao H, Li S, Guo L. Plants Play Stronger Effects on Soil Fungal than Bacterial Communities and Co-Occurrence Network Structures in a Subtropical Tree Diversity Experiment. Microbiol Spectr 2022; 10:e0013422. [PMID: 35475656 PMCID: PMC9241759 DOI: 10.1128/spectrum.00134-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/11/2022] [Indexed: 01/04/2023] Open
Abstract
Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. However, the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in association with tree species richness gradients are poorly documented. Here, we examined soil fungal and bacterial communities in a Chinese subtropical tree species richness experiment (from 1 to 16 species) using amplicon sequencing targeting the internal transcribed spacer 2 and V4 hypervariable region of the rRNA genes, respectively. Tree species richness had no significant effect on the diversity of either fungi or bacteria. In addition to soil and spatial distance, tree species richness and composition had a significant effect on fungal community composition but not on bacterial community composition. In fungal rather than bacterial co-occurrence networks, the average degree, degree centralization, and clustering coefficient significantly decreased, but the modularity significantly increased with increasing tree species richness. Fungal co-occurrence network structure was influenced by tree species richness and community composition as well as the soil carbon: nitrogen ratio, but the bacterial co-occurrence network structure was affected by soil pH and spatial distance. This study demonstrates that the community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria differ in the subtropical forest. IMPORTANCE Increasing biodiversity loss profoundly affects community structure and ecosystem functioning. Therefore, revealing the mechanisms associated with community assembly and co-occurrence network structure of microbes along plant species diversity gradients is very important for understanding biodiversity maintenance and community stability in response to plant diversity loss. Here, we compared the differences in community assembly and potential drivers of the co-occurrence network structure of soil fungi and bacteria in a subtropical tree diversity experiment. In addition to soil and spatial distance, plants are more strongly predictive of the community and co-occurrence network structure of fungi than those of bacteria. The study highlighted that plants play more important roles in shaping community assembly and interactions of fungi than of bacteria in the subtropical tree diversity experiment.
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Affiliation(s)
- Huiyun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xingchun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Pengpeng Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Niuniu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- DOE Center for Advanced Bioenergy & Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shan Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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24
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Zeng Q, Lebreton A, Man X, Jia L, Wang G, Gong S, Buée M, Wu G, Dai Y, Yang Z, Martin FM. Ecological Drivers of the Soil Microbial Diversity and Composition in Primary Old-Growth Forest and Secondary Woodland in a Subtropical Evergreen Broad-Leaved Forest Biome in the Ailao Mountains, China. Front Microbiol 2022; 13:908257. [PMID: 35770159 PMCID: PMC9234548 DOI: 10.3389/fmicb.2022.908257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/20/2022] [Indexed: 12/13/2022] Open
Abstract
Replacement of primary old-growth forests by secondary woodlands in threatened subtropical biomes drives important changes at the level of the overstory, understory and forest floor, but the impact on belowground microbial biodiversity is yet poorly documented. In the present study, we surveyed by metabarcoding sequencing, the diversity and composition of soil bacteria and fungi in the old-growth forest, dominated by stone oaks (Lithocarpus spp.) and in the secondary Yunnan pine woodland of an iconic site for biodiversity research, the Ailaoshan National Nature Reserve (Ailao Mountains, Yunnan province, China). We assessed the effect of forest replacement and other environmental factors, including soil horizons, soil physicochemical characteristics and seasonality (monsoon vs. dry seasons). We showed that tree composition and variation in soil properties were major drivers for both bacterial and fungal communities, with a significant influence from seasonality. Ectomycorrhizal Operational Taxonomic Units (OTUs) dominated the functional fungal guilds. Species richness and diversity of the bacterial and fungal communities were higher in the pine woodland compared to the primary Lithocarpus forest, although prominent OTUs were different. The slightly lower complexity of the microbiome in the primary forest stands likely resulted from environmental filtering under relatively stable conditions over centuries, when compared to the secondary pine woodlands. In the old-growth forest, we found a higher number of species, but that communities were homogeneously distributed, whereas in the pine woodlands, there is a slightly lower number of species present but the communities are heterogeneously distributed. The present surveys of the bacterial and fungal diversity will serve as references in future studies aiming to assess the impact of the climate change on soil microbial diversity in both old-growth forests and secondary woodlands in Ailaoshan.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Liukun Jia
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
| | - Gengshen Wang
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Sai Gong
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
| | - Marc Buée
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
| | - Gang Wu
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhuliang Yang
- Chinese Academy of Sciences Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Kunming, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming, China
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst-Nancy, Université de Lorraine, Champenoux, France
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25
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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: 6] [Impact Index Per Article: 3.0] [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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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Khan NF, Reshi ZA. Diversity of root-associated mycobiome of Betula utilis D. Don: a treeline species in Kashmir Himalaya. Trop Ecol 2022. [DOI: 10.1007/s42965-022-00230-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang XW, Jiang JH, Liu SL, Gafforov Y, Zhou LW. Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants. PHYTOPATHOLOGY 2022; 112:404-413. [PMID: 34170760 DOI: 10.1094/phyto-05-21-0181-r] [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] [Indexed: 06/13/2023]
Abstract
Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.
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Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yusufjon Gafforov
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100125, Uzbekistan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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Zhou Z, Zheng M, Xia J, Wang C. Nitrogen addition promotes soil microbial beta diversity and the stochastic assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150569. [PMID: 34597552 DOI: 10.1016/j.scitotenv.2021.150569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/17/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) deposition is one of major environmental concerns and alters the microbial communities in the pedosphere. A central debate in governing microbial community is on the relative importance of deterministic (ecological selection) vs. stochastic processes (dispersal, drift, diversification or speciation), which consequently limited our understanding of microbial assembly in response to N addition. Here, we conducted a global analysis of high-throughput sequencing data to reveal the mechanisms of N-addition effects on soil microbial communities. The results show that N addition significantly shifted the microbial community structure and promoted microbial beta diversity, particularly in the N-limited ecosystems. Changes in microbial structure and beta diversity increased significantly as the N addition rate, study duration, and the degree of soil acidification increased. The stochastic processes are more important than the deterministic processes for microbial community assembly, while N addition significantly increase the importance of stochastic processes whether the phylogenetic relationship is considered or not. Overall, the current study highlights the important of ecological stochasticity in regulating microbial assembly under N deposition scenarios.
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Affiliation(s)
- Zhenghu Zhou
- Center for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Mianhai Zheng
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jianyang Xia
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Chuankuan Wang
- Center for Ecological Research, Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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Zhang B, Xue K, Zhou S, Wang K, Liu W, Xu C, Cui L, Li L, Ran Q, Wang Z, Hu R, Hao Y, Cui X, Wang Y. Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas. eLife 2022; 11:70164. [PMID: 35073255 PMCID: PMC8828049 DOI: 10.7554/elife.70164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.
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Affiliation(s)
- Biao Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Kui Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Wenjing Liu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Cong Xu
- Aerospace Information Research Institute, University of Chinese Academy of Sciences
| | - Lizhen Cui
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Linfeng Li
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Qinwei Ran
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Zongsong Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Ronghai Hu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Xiaoyong Cui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, University of Chinese Academy of Sciences
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences
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Segnitz RM, Russo SE, Peay KG. Interactions with soil fungi alter density dependence and neighborhood effects in a locally abundant dipterocarp species. Ecol Evol 2022; 12:e8478. [PMID: 35127017 PMCID: PMC8796921 DOI: 10.1002/ece3.8478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/05/2021] [Accepted: 11/25/2021] [Indexed: 11/10/2022] Open
Abstract
Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and the presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition and also modify the density-dependent spread of natural enemies such as pathogens or invertebrate predators. Intrinsic correlation between proximity to adult conspecifics (i.e., recruitment neighborhood) and local seedling density, arising from dispersal, makes it difficult to separate the independent and interactive factors that contribute to recruitment success. Here, we present a field experiment in which we manipulated both the recruitment neighborhood and seedling density to explore how they interact to influence the growth and survival of Dryobalanops aromatica, a dominant ectomycorrhizal tree species in a Bornean tropical rainforest. First, we found that both local seedling density and recruitment neighborhood had effects on performance of D. aromatica seedlings, though the nature of these impacts varied between growth and survival. Second, we did not find strong evidence that the effect of density on seedling survival is dependent on the presence of conspecific adult trees. However, accumulation of mutualistic fungi beneath conspecifics adults does facilitate establishment of D. aromatica seedlings. In total, our results suggest that recruitment near adult conspecifics was not associated with a performance cost and may have weakly benefitted recruiting seedlings. Positive effects of conspecifics may be a factor facilitating the regional hyperabundance of this species. Synthesis: Our results provide support for the idea that dominant species in diverse forests may escape the localized recruitment suppression that limits abundance in rarer species.
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Affiliation(s)
- R. Max Segnitz
- Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Sabrina E. Russo
- School of Biological SciencesUniversity of NebraskaLincolnNebraskaUSA
- Center for Plant Science InnovationUniversity of NebraskaLincolnNebraskaUSA
| | - Kabir G. Peay
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
- Woods Institute for the EnvironmentStanfordCaliforniaUSA
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Chang Y, Chen F, Zhu Y, You Y, Cheng Y, Ma J. Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China. Front Microbiol 2022; 13:992816. [PMID: 36090080 PMCID: PMC9453671 DOI: 10.3389/fmicb.2022.992816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.
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Affiliation(s)
- Yuanyuan Chang
- School of Public Policy and Management, China University of Mining and Technology, Xuzhou, China
| | - Fu Chen
- School of Public Policy and Management, China University of Mining and Technology, Xuzhou, China
- School of Public Administration, Hohai University, Nanjing, China
- *Correspondence: Fu Chen,
| | - Yanfeng Zhu
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Yunnan You
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Yanjun Cheng
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- School of Public Administration, Hohai University, Nanjing, China
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Cheng Y, Zhou L, Liang T, Man J, Wang Y, Li Y, Chen H, Zhang T. Deciphering Rhizosphere Microbiome Assembly of Castanea henryi in Plantation and Natural Forest. Microorganisms 2021; 10:microorganisms10010042. [PMID: 35056492 PMCID: PMC8779262 DOI: 10.3390/microorganisms10010042] [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: 11/12/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022] Open
Abstract
Based on the importance and sensitivity of microbial communities to changes in the forest ecosystem, soil microorganisms can be used to indicate the health of the forest system. The metagenome sequencing was used to analyze the changes of microbial communities between natural and plantation Castanea henryi forests for understanding the effect of forest types on soil microbial communities. Our result showed the soil microbial diversity and richness were higher in the natural forests than in the plantation. Proteobacteria, Actinobacteria, and Acidobacteria are the dominant categories in the C. henryi rhizosphere, and Proteobacteria and Actinobacteria were significantly enriched in the natural forest while Acidobacteria was significantly enriched in the plantation. Meanwhile, the functional gene diversity and the abundance of functions in the natural forest were higher than that of the plantation. Furthermore, we found that the microbial network in the natural forests had more complex than in the plantation. We also emphasized the low-abundance taxa may play an important role in the network structure. These results clearly showed that microbial communities, in response to different forest types, provide valuable information to manipulate microbiomes to improve soil conditions of plantation.
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Affiliation(s)
- Yuanyuan Cheng
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lexin Zhou
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Tian Liang
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Jiayin Man
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yinghao Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Li
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
| | - Hui Chen
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- Correspondence: (H.C.); (T.Z.); Tel.: +86-139-5034-3791 (H.C.); +86-180-0691-1945 (T.Z.)
| | - Taoxiang Zhang
- Oil Tea Research Center of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.C.); (L.Z.); (T.L.); (Y.L.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.M.); (Y.W.)
- International Joint Laboratory of Forest Symbiology, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (H.C.); (T.Z.); Tel.: +86-139-5034-3791 (H.C.); +86-180-0691-1945 (T.Z.)
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Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, Miller AN, Hernández-Restrepo M. Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi. J Fungi (Basel) 2021; 7:1097. [PMID: 34947079 PMCID: PMC8704094 DOI: 10.3390/jof7121097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Jana Nekvindová
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Kamila Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- CEITEC—Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - František Sklenář
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA;
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Wang Y, Liu Y, Li J, Bai S, Tian T. Fungal community composition and diversity in the rhizosphere soils of Argentina (syn. Potentilla) anserina, on the Qinghai Plateau. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Peguero G, Ferrín M, Sardans J, Verbruggen E, Ramírez-Rojas I, Van Langenhove L, Verryckt LT, Murienne J, Iribar A, Zinger L, Grau O, Orivel J, Stahl C, Courtois EA, Asensio D, Gargallo-Garriga A, Llusià J, Margalef O, Ogaya R, Richter A, Janssens IA, Peñuelas J. Decay of similarity across tropical forest communities: integrating spatial distance with soil nutrients. Ecology 2021; 103:e03599. [PMID: 34816429 DOI: 10.1002/ecy.3599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 11/09/2022]
Abstract
Understanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m2 sampling point vs. 2,500-m2 plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance-decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales.
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Affiliation(s)
- Guille Peguero
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain
| | - Miquel Ferrín
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Erik Verbruggen
- Department of Biology, Centre of Excellence PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Irene Ramírez-Rojas
- Department of Biology, Centre of Excellence PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Leandro Van Langenhove
- Department of Biology, Centre of Excellence PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Lore T Verryckt
- Department of Biology, Centre of Excellence PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Amaia Iribar
- Laboratoire Evolution et Diversité Biologique (UMR5174), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Lucie Zinger
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Oriol Grau
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain.,UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310, Kourou, France
| | - Jerome Orivel
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310, Kourou, France
| | - Clément Stahl
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université des Antilles, Université de Guyane, 97310, Kourou, France
| | - Elodie A Courtois
- Laboratoire Ecologie, évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, 97300, Cayenne, France
| | - Dolores Asensio
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Albert Gargallo-Garriga
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Joan Llusià
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Olga Margalef
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Romà Ogaya
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria
| | - Ivan A Janssens
- Department of Biology, Centre of Excellence PLECO (Plants and Ecosystems), University of Antwerp, 2610, Wilrijk, Belgium
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913, Bellaterra, Spain.,CREAF, 08913, Cerdanyola del Vallès, Spain
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Kuang J, Han S, Chen Y, Bates CT, Wang P, Shu W. Root-associated fungal community reflects host spatial co-occurrence patterns in a subtropical forest. ISME COMMUNICATIONS 2021; 1:65. [PMID: 36755184 PMCID: PMC9723750 DOI: 10.1038/s43705-021-00072-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022]
Abstract
Plant roots harbor and interact with diverse fungal species. By changing these belowground fungal communities, focal plants can affect the performance of surrounding individuals and the outcome of coexistence. Although highly host related, the roles of these root-associated fungal communities per se in host plant spatial co-occurrence is largely unknown. Here, we evaluated the host dependency of root-associated communities for 39-plant species spatially mapped throughout a 50-ha subtropical forest plot with relevant environmental properties. In addition, we explored whether the differentiation in root fungal associations among plant species can reflect their observed co-occurrence patterns. We demonstrated a strong host-dependency by discriminating the differentiation of root-associated fungal communities regardless of background soil heterogeneity. Furthermore, Random Forest modeling indicated that these nonrandom root fungal associations significantly increased our ability to explain spatial co-occurrence patterns, and to a greater degree than the relative abundance, phylogenetic relatedness, and functional traits of the host plants. Our results further suggested that plants harbor more abundant shared, "generalist" pathogens are likely segregated, while hosting more abundant unique, "specialist" ectomycorrhizal fungi might be an important strategy for promoting spatial aggregation, particularly between early established trees and the heterospecific adults. Together, we provide a conceptual and testable approach to integrate this host-dependent root fungal "fingerprinting" into the plant diversity patterns. We highlight that this approach is complementary to the classic cultivation-based scheme and can deepen our understanding of the community-level effect from overall fungi and its contribution to the pairwise plant dynamics in local species-rich communities.
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Affiliation(s)
- Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, China.
| | - Shun Han
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Colin T Bates
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China.
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38
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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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39
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Zhou J, Gui H, Yang S, Yang X, Shi L. Fungal Interactions Matter: Tricholoma matsutake Domination Affect Fungal Diversity and Function in Mountain Forest Soils. BIOLOGY 2021; 10:1051. [PMID: 34681150 PMCID: PMC8533266 DOI: 10.3390/biology10101051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022]
Abstract
Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called 'shiro', which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.
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Affiliation(s)
- Jie Zhou
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, 37075 Göttingen, Germany; (J.Z.); (L.S.)
| | - Heng Gui
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China;
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
| | - Shujiao Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
| | - Xuefei Yang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming 650201, China;
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Mengla 666303, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
| | - Lingling Shi
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, 37075 Göttingen, Germany; (J.Z.); (L.S.)
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China;
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40
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Zhao J, Ma J, Yang Y, Yu H, Zhang S, Chen F. Response of Soil Microbial Community to Vegetation Reconstruction Modes in Mining Areas of the Loess Plateau, China. Front Microbiol 2021; 12:714967. [PMID: 34512593 PMCID: PMC8424123 DOI: 10.3389/fmicb.2021.714967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/30/2021] [Indexed: 11/25/2022] Open
Abstract
Vegetation reconstruction and restoration is vital to the health of the mine land ecosystem. Different vegetations might change microbial community structure and function of soil, mediating the biogeochemical cycle and nutrition supply to the soil. To clarify the response of soil microbes to different vegetation reconstruction modes in the mining areas of the Loess Plateau, China, soil microbial community structures and functions were determined by the MiSeq high-throughput sequencing along with PICRUSt2 and FUNGuild tools. The fungal community richness was observed to be the highest in grassland soil and positively correlated with soil organic matter, total nitrogen, and nitrate-nitrogen. The bacterial and fungal community structures were similar in grassland and brushland areas, but were significantly differentiated in the coniferous and broadleaf forest, and the leading factors were soil pH and nitrate-nitrogen. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla under different vegetation reconstruction modes. The dominant phyla of fungi were Ascomycota, Basidiomycota, and Mortierellomycota. Different vegetation reconstruction modes did not affect the bacterial functional communities but shaped different functional groups of fungi. The grassland soil was dominated by saprotrophic fungi, while symbiotrophic fungi dominated the coniferous and broadleaf forests. The results suggested that shifts in vegetation reconstruction modes may alter the mining soil bacterial and fungal community structures and function. These findings improve the understanding of microbial ecology in the reclaimed mine soil and provide a reference for the ecological restoration of fragile mining ecosystems.
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Affiliation(s)
- Jiao Zhao
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
| | - Yongjun Yang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Haochen Yu
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Shaoliang Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Fu Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China.,Low Carbon Energy Institute, China University of Mining and Technology, Xuzhou, China
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41
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Petrolli R, Augusto Vieira C, Jakalski M, Bocayuva MF, Vallé C, Cruz EDS, Selosse MA, Martos F, Kasuya MCM. A fine-scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids. THE NEW PHYTOLOGIST 2021; 231:2002-2014. [PMID: 33983644 DOI: 10.1111/nph.17459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Approximately 10% of vascular plants are epiphytes and, even though this has long been ignored in past research, are able to interact with a variety of fungi, including mycorrhizal taxa. However, the structure of fungal communities on bark, as well as their relationship with epiphytic plants, is largely unknown. To fill this gap, we conducted environmental metabarcoding of the ITS-2 region to understand the spatial structure of fungal communities of the bark of tropical trees, with a focus on epiphytic orchid mycorrhizal fungi, and tested the influence of root proximity. For all guilds, including orchid mycorrhizal fungi, fungal communities were more similar when spatially close on bark (i.e. they displayed positive spatial autocorrelation). They also showed distance decay of similarity with respect to epiphytic roots, meaning that their composition on bark increasingly differed, compared to roots, with distance from roots. We first showed that all of the investigated fungal guilds exhibited spatial structure at very small scales. This spatial structure was influenced by the roots of epiphytic plants, suggesting the existence of an epiphytic rhizosphere. Finally, we showed that orchid mycorrhizal fungi were aggregated around them, possibly as a result of reciprocal influence between the mycorrhizal partners.
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Affiliation(s)
- Rémi Petrolli
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Conrado Augusto Vieira
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Marcin Jakalski
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Melissa F Bocayuva
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Clément Vallé
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Everaldo Da Silva Cruz
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, EPHE, Sorbonne Université, CP 39, 57 rue Cuvier, Paris, F-75005, France
| | - Maria Catarina M Kasuya
- Department of Microbiology, Viçosa Federal University (UFV), P. H. Rolfs Street CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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42
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Liu W, Liu L, Yang X, Deng M, Wang Z, Wang P, Yang S, Li P, Peng Z, Yang L, Jiang L. Long-term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland. GLOBAL CHANGE BIOLOGY 2021; 27:3939-3950. [PMID: 33993594 DOI: 10.1111/gcb.15681] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Anthropogenic nitrogen (N) input is known to alter plant and microbial α-diversity, but how N enrichment influences β-diversity of plant and microbial communities remains poorly understood. Using a long-term multilevel N addition experiment in a temperate steppe, we show that plant, soil bacterial and fungal communities exhibited different responses in their β-diversity to N input. Plant β-diversity decreased linearly as N addition increased, as a result of increased directional environmental filtering, where soil environmental properties largely explained variation in plant β-diversity. Soil bacterial β-diversity first increased then decreased with increasing N input, which was best explained by corresponding changes in soil environmental heterogeneity. Soil fungal β-diversity, however, remained largely unchanged across the N gradient, with plant β-diversity, soil environmental properties, and heterogeneity together explaining an insignificant fraction of variation in fungal β-diversity, reflecting the importance of stochastic community assembly. Our study demonstrates the divergent effect of N enrichment on the assembly of plant, soil bacterial and fungal communities, emphasizing the need to examine closely associated fundamental components (i.e., plants and microorganisms) of ecosystems to gain a more complete understanding of ecological consequences of anthropogenic N enrichment.
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Affiliation(s)
- Weixing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lingli Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Meifeng Deng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhou Wang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Provincial Key Laboratory of Applied Botany, Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Sen Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ziyang Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lu Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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43
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Singavarapu B, Beugnon R, Bruelheide H, Cesarz S, Du J, Eisenhauer N, Guo LD, Nawaz A, Wang Y, Xue K, Wubet T. Tree mycorrhizal type and tree diversity shape the forest soil microbiota. Environ Microbiol 2021; 24:4236-4255. [PMID: 34327789 DOI: 10.1111/1462-2920.15690] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/27/2021] [Indexed: 01/04/2023]
Abstract
There is limited knowledge on how the association of trees with different mycorrhizal types shapes soil microbial communities in the context of changing tree diversity levels. We used arbuscular (AM) and ectomycorrhizal (EcM) tree species as con- and heterospecific tree species pairs (TSPs), which were established in plots of three tree diversity levels including monocultures, two-species mixtures and multi-tree species mixtures in a tree diversity experiment in subtropical China. We found that the tree mycorrhizal type had a significant effect on fungal but not bacterial alpha diversity. Furthermore, only EcM but not AM TSPs fungal alpha diversity increased with tree diversity, and the differences between AM and EcM TSPs disappeared in multi-species mixtures. Tree mycorrhizal type, tree diversity and their interaction had significant effects on fungal community composition. Neither fungi nor bacteria showed any significant compositional variation in TSPs located in multi-species mixtures. Accordingly, the most influential taxa driving the tree mycorrhizal differences at low tree diversity were not significant in multi-tree species mixtures. Collectively, our results indicate that tree mycorrhizal type is an important factor determining the diversity and community composition of soil microbes, and higher tree diversity levels promote convergence of the soil microbial communities. SIGNIFICANCE STATEMENT: More than 90% of terrestrial plants have symbiotic associations with mycorrhizal fungi which could influence the coexisting microbiota. Systematic understanding of the individual and interactive effects of tree mycorrhizal type and tree species diversity on the soil microbiota is crucial for the mechanistic comprehension of the role of microbes in forest soil ecological processes. Our tree species pair (TSP) concept coupled with random sampling within and across the plots, allowed us the unbiased assessment of tree mycorrhizal type and tree diversity effects on the tree-tree interaction zone soil microbiota. Unlike in monocultures and two-species mixtures, we identified species-rich and converging fungal and bacterial communities in multi-tree species mixtures. Consequently, we recommend planting species-rich mixtures of EcM and AM trees, for afforestation and reforestation regimes. Specifically, our findings highlight the significance of tree mycorrhizal type in studying 'tree diversity - microbial diversity - ecosystem function' relationships.
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Affiliation(s)
- Bala Singavarapu
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, Halle, 06108, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Rémy Beugnon
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany.,Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, 04103, Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, Halle, 06108, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
| | - Simone Cesarz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany.,Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, 04103, Germany
| | - Jianqing Du
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany.,Institute of Biology, Leipzig University, Puschstrasse 4, Leipzig, 04103, Germany
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ali Nawaz
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Department of Civil, Geo and Environmental Engineering, Technical University of Munich, Am Coulombwall 3, Garching, 85748, Germany
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Centre for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Xue
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Centre for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tesfaye Wubet
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, Leipzig, 04103, Germany
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44
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y. Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions. MICROBIAL ECOLOGY 2021; 82:202-214. [PMID: 32322922 DOI: 10.1007/s00248-020-01509-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.
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Affiliation(s)
- Muke Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Liwei Chai
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Dalin Jiang
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Weiqian Jia
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Yi Huang
- College of Environmental Science and Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China.
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Teng J, Tian J, Barnard R, Yu G, Kuzyakov Y, Zhou J. Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests. Front Microbiol 2021; 12:633751. [PMID: 34177822 PMCID: PMC8222577 DOI: 10.3389/fmicb.2021.633751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Soil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale.
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Affiliation(s)
- Jialing Teng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Romain Barnard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche Comté, Dijon, France
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany.,Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Jeong M, Choi DH, Cheon WJ, Kim JG. Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju. J Microbiol Biotechnol 2021; 31:686-695. [PMID: 33782219 PMCID: PMC9705868 DOI: 10.4014/jmb.2103.03021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.
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Affiliation(s)
- Minji Jeong
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Doo-Ho Choi
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Woo-Jae Cheon
- Department of Forest Environment, Gyeongsangbuk-do Forest Environment Research Institute, Gyeong-ju 38174, Republic of Korea
| | - Jong-Guk Kim
- Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea,Corresponding author Phone: +82-53-950-5379 Fax: +82-53-955-5379 E-mail:
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Plant Diversity Enhances Soil Fungal Diversity and Microbial Resistance to Plant Invasion. Appl Environ Microbiol 2021; 87:AEM.00251-21. [PMID: 33741636 DOI: 10.1128/aem.00251-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/14/2021] [Indexed: 11/20/2022] Open
Abstract
Interactions and feedbacks between aboveground and belowground biomes are fundamental in controlling ecosystem functions and stability. However, the relationship between plant diversity and soil microbial diversity is elusive. Moreover, it remains unknown whether plant diversity loss will cause the stability of soil microbial communities to deteriorate. To shed light on these questions, we conducted a pot-based experiment to manipulate the plant richness gradient (1, 2, 4, or 8 species) and plant [Symphyotrichum subulatum (Michx.) G. L. Nesom] invasion status. We found that, in the noninvasion treatment, soil fungal diversity significantly and positively correlated with plant diversity, while the relationship between bacterial and plant diversity was not significant. Under plant invasion conditions, the coupling of plant-fungal alpha diversity relationship was enhanced, but the plant-fungal beta diversity relationship was decoupled. We also found significant positive relationships between plant diversity and soil microbial resistance. The observed positive relationships were determined by turnover (species substitution) and nestedness (species loss) processes for bacterial and fungal communities, respectively. Our study demonstrated that plant diversity enhanced soil fungal diversity and microbial resistance in response to plant invasion. This study expands our knowledge about the aboveground-belowground diversity relationship and the diversity-stability relationship.IMPORTANCE Our study newly showed that plant invasion significantly altered relationships between aboveground and belowground diversity. Specifically, plant richness indirectly promoted soil fungal richness through the increase of soil total carbon (TC) without plant invasion, while plant richness had a direct positive effect on soil fungal richness under plant invasion conditions. Our study highlights the effect of plant diversity on soil fungal diversity, especially under plant invasion conditions, and the plant diversity effect on microbial resistance in response to plant invasion. These novel findings add important knowledge about the aboveground-belowground diversity relationship and the diversity-stability relationship.
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Yang W, Jeelani N, Cai A, Cheng X, An S. Coastal reclamation alters soil microbial communities following different land use patterns in the Eastern coastal zone of China. Sci Rep 2021; 11:7265. [PMID: 33790383 PMCID: PMC8012362 DOI: 10.1038/s41598-021-86758-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/09/2021] [Indexed: 01/29/2023] Open
Abstract
Coastal reclamation seriously disturbs coastal wetland ecosystems, while its influences on soil microbial communities remain unclear. In this study, we examined the impacts of coastal reclamation on soil microbial communities based on phospholipid fatty acids (PLFA) analysis following the conversion of Phragmites australis wetlands to different land use types. Coastal reclamation enhanced total soil microbial biomass and various species (i.e., gram-positive bacterial, actinomycete, saturated straight-chain, and branched PLFA) following the conversion of P. australis wetland to aquaculture pond, wheat, and oilseed rape fields. In contrast, it greatly decreased total soil microbial biomass and various species following the conversion of P. australis wetland to town construction land. Coastal reclamation reduced fungal:bacterial PLFA, monounsaturated:branched PLFA ratios, whereas increasing gram-positive:gram-negative PLFA ratio following the conversion of P. australis wetland to other land use types. Our study suggested that coastal reclamation shifted soil microbial communities by altering microbial biomass and community composition. These changes were driven primarily by variations in soil nutrient substrates and physiochemical properties. Changes in soil microbial communities following coastal reclamation impacted the decomposition and accumulation of soil carbon and nitrogen, with potential modification of carbon and nitrogen sinks in the ecosystems, with potential feedbacks in response to climate change.
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Affiliation(s)
- Wen Yang
- College of Life Sciences, Shaanxi Normal University, No. 620 West Chang'an St., Chang'an Dist., Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Nasreen Jeelani
- School of Life Sciences and Institute of Wetland Ecology, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Andong Cai
- Key Laboratory for Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 10081, People's Republic of China
| | - Xiaoli Cheng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Shuqing An
- School of Life Sciences and Institute of Wetland Ecology, Nanjing University, Nanjing, 210023, People's Republic of China
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Similarities and Differences among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves. FORESTS 2021. [DOI: 10.3390/f12030353] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unlike the numerous works concerning the effect of management on the forest mycobiome, only a few studies have addressed how fungi from different trophic groups recover from natural and anthropogenic disturbances and develop structural features typical of unmanaged old-growth forests. Our objective is to compare the soil fungal assemblages represented by different functional/trophic groups in protected and managed stands located in European mixed forests dominated by Scots pine. Fungal communities were analyzed using high-throughput Illumina MiSeq sequencing of fungal internal transcribed spacer 1 (ITS1) amplicons. Formerly managed forest reserves (established around 50 years ago) and forests under standard forest management appeared to be similar in terms of total and mean species richness of all fungal operational taxonomic units (OTUs), as well as OTUs assigned to different functional trophic groups. Among the 599 recorded OTUs, 497 (83%) were shared between both management types, whereas 9.5% of taxa were unique to forest reserves and 7.5% were unique to managed stands. Ascomycota and Basidiomycota were the predominant phyla, comprising 88% of all identified fungi. The main functional components of soil fungal assemblages consisted of saprotrophic (42% fungal OTUs; 27% reads) and ectomycorrhizal fungi (16%; 47%). Two-way analysis of similarities (ANOSIM) revealed that both site and management strategy influenced the species composition of soil fungal communities, with site being a primary effect for saprotrophic and ectomycorrhizal fungi. Volume of coarse and very fine woody debris and soil pH significantly influenced the ectomycorrhizal fungal community, whereas saprotrophic fungi were influenced primarily by volume of coarse woody debris and soil nitrate concentration. Among the identified fungal OTUs, 18 red-listed fungal species were identified from both forest reserves and managed forests, comprising two ECM fungi and four saprotrophs from the category of endangered species. Our results suggest that the transformation of fungal diversity after cessation of forest management is rather slow, and that both forest reserves and managed forests help uphold fungal diversity.
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Adamczyk M, Rüthi J, Frey B. Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils. Environ Microbiol 2021; 23:2152-2168. [PMID: 33393203 DOI: 10.1111/1462-2920.15383] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.
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Affiliation(s)
- Magdalene Adamczyk
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Joel Rüthi
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, 8903, Switzerland
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