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Zhou J, Liu J, Wang D, Ruan Y, Gong S, Gou J, Zou X. Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes. Appl Microbiol Biotechnol 2024; 108:88. [PMID: 38194134 DOI: 10.1007/s00253-023-12882-w] [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: 06/22/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]
Abstract
Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.
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Affiliation(s)
- Jiaxi Zhou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China
- Postdoctoral Research Workstation of China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jing Liu
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Dongfei Wang
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Yibin Ruan
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Shuang Gong
- China Tobacco Guizhou Industrial Co. Ltd, Guiyang, China
| | - Jianyu Gou
- Guizhou Tobacco Company Zunyi Branch, Zunyi, China
| | - Xiao Zou
- Department of Ecology / Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, China.
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2
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Cao J, Yang X, Guo M, Wu Y, Wang C. Reclamation of abandoned cropland switches fungal community assembly from deterministic to stochastic processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175494. [PMID: 39153623 DOI: 10.1016/j.scitotenv.2024.175494] [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: 06/02/2024] [Revised: 07/28/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024]
Abstract
Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of abandoned agricultural land reclamation on the soil microbe is still poorly understood, especially for the microbial community assembly mechanisms. Here, we investigated the influence of reclamation on the relative importance of stochastic and deterministic processes in shaping microbial community assembly. After reclaiming abandoned cropland for corn and soybean cultivation, the fungal community assembly was shifted to stochastic processes, while bacterial communities remained predominantly influenced by stochastic processes. Our study revealed that reclamation did not significantly affect bacterial diversity, community niche breadth, and community similarity. In contrast, fungal communities exhibited lower alpha diversity, narrower niche breadths, greater niche overlap and higher community similarity in corn and soybean cultivation treatment in response to reclamation. Moreover, soil pH and soil available phosphorus were the most important environmental factors influencing fungal richness, niche breadths, community assembly processes, and community similarity. Together, the reclamation of abandoned cropland promoted the transformation of the fungal community assembly from deterministic process to a stochastic process, leading to decreased fungal diversity and broader ecological niche width, ultimately resulting in greater similarity among fungal communities. This finding provides insight into the varied responses of microbial diversity and ecological process to abandoned cropland reclamation, offering valuable guidance for the conservation and sustainable management of abandoned cropland in future land-use practices.
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Affiliation(s)
- Jia Cao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Xi Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Mengyao Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Yafen Wu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China
| | - Chong Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China; Beijing Key Laboratory of Biodiversity and Organic Farming, PR China; State Key Laboratory of Nutrient Use and Management, PR China.
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3
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Gandhi P, Hebert B, Yun A, Bradley J, Moldoveanu B. Histoplasmosis around the world: A global perspective on the presentation, virulence factors, and treatment of histoplasmosis. Am J Med Sci 2024; 368:287-299. [PMID: 38885929 DOI: 10.1016/j.amjms.2024.06.011] [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: 10/31/2023] [Revised: 04/29/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
Histoplasmosis is a systemic infection caused by an endemic dimorphic fungus, Histoplasma capsulatum. Though prevalent in the eastern United States of America, near the Ohio and Mississippi River Valleys, the evidence underlying the global prevalence of histoplasmosis, especially in immunocompromised populations, is underappreciated. This article highlights the global epidemiology, risk factors, microbiology and pathophysiological characteristics, pulmonary and extrapulmonary manifestations, prevention measures, radiographic patterns, diagnostic techniques, and antifungal treatment approaches for Histoplasma capsulatum.
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Affiliation(s)
- Pooja Gandhi
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Brandon Hebert
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Angelica Yun
- Division of General Internal Medicine, University of Louisville, Louisville, Kentucky, USA
| | - James Bradley
- Division of Pulmonary, Critical Care Medicine, and Sleep Disorders, University of Louisville, Louisville, Kentucky, USA.
| | - Bogdan Moldoveanu
- Division of Pulmonary, Critical Care Medicine, and Sleep Disorders, University of Louisville, Louisville, Kentucky, USA
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Ma C, Zhao T, Baoyin T, Han X, Frey B, Yang J, Dong S. Long-term grazing reduces soil fungal network complexity but enhances plant-soil microbe network connectivity in a semi-arid grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176498. [PMID: 39326755 DOI: 10.1016/j.scitotenv.2024.176498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Grazing plays a significant role in shaping both aboveground vegetation and belowground microbial communities in arid and semi-arid grasslands, which in turn affects ecosystem functions and sustainability. Therefore, it was essential to implement effective grazing management practices to preserve ecological balance and support sustainable development in these delicate environments. To optimize the traditional continuous grazing policy, we conducted a 10-year seasonal grazing experiment with five treatments in a typical grassland in northern China: no grazing (NG), continuous summer grazing (CG), and three seasonal grazing treatments (G57 in May and July, G68 in June and August, and G79 in July and September). Our study found that although grazing reduced plant community biomass, G68 treatment maintained high plant height and community diversity (P < 0.05). Grazing did not affect soil bacterial and archaeal alpha diversity, but CG treatment reduced soil fungal diversity (P < 0.05). CG reduced the archaeal network's vertices (which represent microbial taxa, OTUs) and connections (ecological interactions between taxa), but seasonal grazing increased its complexity. Furthermore, grazing did not change bacterial networks but enhanced cross-domain interactions (relationships between different biological groups) of plant-soil fungi and plant-soil archaea. Overall, we used the Mantel test to find that soil microbial diversity was positively correlated with soil physicochemical properties rather than plant community characteristics after grazing. These findings are beneficial for the optimization of sustainable grassland management policies and the protection of plant and soil biodiversity.
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Affiliation(s)
- Chunhui Ma
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Tianqi Zhao
- Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Taogetao Baoyin
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Xingguo Han
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zurich, Birmensdorf 8903, Switzerland
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zurich, Birmensdorf 8903, Switzerland
| | - Juejie Yang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
| | - Shikui Dong
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China.
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Clark AJ, Masters-Clark E, Moratto E, Junier P, Stanley CE. Visualizing liquid distribution across hyphal networks with cellular resolution. BIOMICROFLUIDICS 2024; 18:054109. [PMID: 39381835 PMCID: PMC11460992 DOI: 10.1063/5.0231656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024]
Abstract
Filamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the fungal-fungal interaction microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular movement of liquid along hyphae can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways.
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Affiliation(s)
- Amelia J. Clark
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Emily Masters-Clark
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Eleonora Moratto
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pilar Junier
- Laboritoire de microbiologie, University of Neuchâtel, Neuchâtel CH-2000, Switzerland
| | - Claire E. Stanley
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
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Hoefle D, Sommer M, Wassermann B, Faticov M, Serra D, Berg G, Tack AJM, Abdelfattah A. Oak seedling microbiome assembly under climate warming and drought. ENVIRONMENTAL MICROBIOME 2024; 19:62. [PMID: 39198873 PMCID: PMC11360865 DOI: 10.1186/s40793-024-00602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024]
Abstract
Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.
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Affiliation(s)
- Daniel Hoefle
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
| | - Milena Sommer
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Maria Faticov
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Demetrio Serra
- Fondazione Mediterranea Terina Onlus, Zona industriale Benedetto XVI, 88046, Ficarella, CZ, Italy
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam OT, Golm, Germany
| | - Ayco J M Tack
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany.
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden.
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Chen L, Yu Z, Zhao M, Kerfahi D, Li N, Shi L, Qi X, Lee CB, Dong K, Lee HI, Lee SS. Elevational Variation in and Environmental Determinants of Fungal Diversity in Forest Ecosystems of Korean Peninsula. J Fungi (Basel) 2024; 10:556. [PMID: 39194882 DOI: 10.3390/jof10080556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/27/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities.
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Affiliation(s)
- Lei Chen
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Zhi Yu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
| | - Mengchen Zhao
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dorsaf Kerfahi
- Department of Biological Sciences, School of Natural Sciences, Keimyung University, Daegu 42601, Republic of Korea
| | - Nan Li
- Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Department of Oceanography, Key Laboratory for Coastal Ocean Variation and Disaster Prediction, College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang 524091, China
| | - Lingling Shi
- Department of Geosciences, Geo-Biosphere Interactions, Faculty of Sciences, University of Tuebingen, 72074 Tuebingen, Germany
| | - Xiwu Qi
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Chang-Bae Lee
- Biodiversity and Ecosystem Functioning Major, Department of Climate Technology Convergence, Forest Carbon Graduate School, Kookmin University, Seoul 02707, Republic of Korea
- Department of Forestry, Environment and Systems, College of Science and Technology, Kookmin University, Seoul 02707, Republic of Korea
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, Suwon 16227, Republic of Korea
| | - Hae-In Lee
- Biodiversity and Ecosystem Functioning Major, Department of Climate Technology Convergence, Forest Carbon Graduate School, Kookmin University, Seoul 02707, Republic of Korea
| | - Sang-Seob Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Martos I, Domínguez-Núñez JA. Soil Fungal Pathogens in Pinus pinaster Mature Reforestation: Silvicultural Treatments Effects. Pathogens 2024; 13:637. [PMID: 39204238 PMCID: PMC11356966 DOI: 10.3390/pathogens13080637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
Soil fungal communities play a key role in multiple functions and ecosystem services within forest ecosystems. Today, forest ecosystems are subject to multiple environmental and anthropogenic disturbances (e.g., fire or forest management) that mainly lead to changes in vegetation as well as in plant-soil interactions. Soil pathogens play an important role in controlling plant diversity, ecosystem functions, and human and animal health. In this work we analyzed the response of soil plant pathogenic fungi to forest management in a Pinus pinaster reforestation. We started from an experimental design, in which forest thinning and gap cutting treatments were applied at different intensities and sizes, respectively. The fungal communities of plant pathogens in spring were described, and the effect of the silvicultural treatments was evaluated 5 years after their application, as were the possible relationships between soil plant pathogenic fungal communities and other environmental factors. Only a strong low thinning treatment (35% basal area) was able to generate homogeneous changes in soil pathogenic diversity. In the gaps, only the central position showed significant changes in the soil plant pathogenic fungi community.
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Affiliation(s)
| | - Jose Alfonso Domínguez-Núñez
- Department of Forest and Environmental Engineering and Management, Universidad Politécnica de Madrid, C/Jose Antonio Novais, 10, 28040 Madrid, Spain
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Cao C, Zhang Y, Cui Z. Response of Soil Fungal Community to Reforestation on Shifting Sand Dune in the Horqin Sandy Land, Northeast China. Microorganisms 2024; 12:1545. [PMID: 39203387 PMCID: PMC11356087 DOI: 10.3390/microorganisms12081545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
Reforestation of native shrub on shifting sand dunes has been widely used for desertification control in semi-arid grassland in Northeast China. Previous studies have confirmed that plantation establishment facilitates fixing sand dunes, restoring vegetation, and improving soil properties, but very few have focused on the response of the soil fungal community. In this study, a chronosequence of Caragana microphylla (CM) shrub sand-fixation plantations (8-, 19-, and 33-year-old), non-vegetated shifting sand dunes (0 years), and adjacent natural CM forests (NCFs; 50-year-old) in the Horqin sandy land were selected as experimental sites. Soil properties including enzymatic activities were determined, and the composition and structure of the soil fungal community were investigated using the Illumina MiSeq sequencing technique based on the internal transcribed spacer (ITS) rDNA. This study aimed to (1) describe the response of the soil fungal community to revegetation onto a moving sand dune by planting a native shrub plantation; (2) determine the main soil factors driving the succession of the fungal community; and (3) discuss whether the soil fungal community can be restored to its original state by reforestation. The reforestation of CM significantly ameliorated soil properties, increased soil fungal diversity, and altered the composition and structure of the soil fungal community. Ascomycota, Basidiomycota, and Zoopagomycota were the dominant phyla in all sites. Ascomycota did not respond to plantation development, whereas the other two dominant phyla linearly increased or decreased with the plantation age. The relative abundance of dominant genera varied with sites and showed a waning and waxing characteristic. The composition and structure of the soil fungal community in the 33-year CM plantation were very close to that of the NCF, indicating the restorability of the soil fungal community. The succession of the soil fungal community was directly driven by soil properties, of which soil moisture, organic matter, total N, urease, and protease were the main affecting factors.
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Affiliation(s)
- Chengyou Cao
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
| | - Ying Zhang
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
| | - Zhenbo Cui
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China; (Y.Z.); (Z.C.)
- Liaoning Province Key Laboratory of Bioresource Research and Development, Northeastern University, Shenyang 110169, China
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10
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Netherway T, Bahram M. Melanized root-associated fungi: key players in plant-soil systems. Trends Microbiol 2024:S0966-842X(24)00169-0. [PMID: 38987052 DOI: 10.1016/j.tim.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024]
Abstract
Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.
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Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Agroecology, Aarhus University, Slagelse, Denmark; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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11
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Trejos-Espeleta JC, Marin-Jaramillo JP, Schmidt SK, Sommers P, Bradley JA, Orsi WD. Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic. Proc Natl Acad Sci U S A 2024; 121:e2402689121. [PMID: 38954550 PMCID: PMC11252988 DOI: 10.1073/pnas.2402689121] [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: 02/07/2024] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
Climate warming is causing widespread deglaciation and pioneer soil formation over glacial deposits. Melting glaciers expose rocky terrain and glacial till sediment that is relatively low in biomass, oligotrophic, and depleted in nutrients. Following initial colonization by microorganisms, glacial till sediments accumulate organic carbon and nutrients over time. However, the mechanisms driving soil nutrient stabilization during early pedogenesis after glacial retreat remain unclear. Here, we traced amino acid uptake by microorganisms in recently deglaciated high-Arctic soils and show that fungi play a critical role in the initial stabilization of the assimilated carbon. Pioneer basidiomycete yeasts were among the predominant taxa responsible for carbon assimilation, which were associated with overall high amino acid use efficiency and reduced respiration. In intermediate- and late-stage soils, lichenized ascomycete fungi were prevalent, but bacteria increasingly dominated amino acid assimilation, with substantially decreased fungal:bacterial amino acid assimilation ratios and increased respiration. Together, these findings demonstrate that fungi are important drivers of pedogenesis in high-Arctic ecosystems that are currently subject to widespread deglaciation from global warming.
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Affiliation(s)
- Juan Carlos Trejos-Espeleta
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Juan P. Marin-Jaramillo
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO80309
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO80309
| | - James A. Bradley
- Aix Marseille University, University of Toulon, Centre national de la recherche scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (MIO), Marseille, France13009
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom, E1 4NS
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany, 80333
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12
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Pérez-Moncada UA, Santander C, Ruiz A, Vidal C, Santos C, Cornejo P. Design of Microbial Consortia Based on Arbuscular Mycorrhizal Fungi, Yeasts, and Bacteria to Improve the Biochemical, Nutritional, and Physiological Status of Strawberry Plants Growing under Water Deficits. PLANTS (BASEL, SWITZERLAND) 2024; 13:1556. [PMID: 38891364 PMCID: PMC11175115 DOI: 10.3390/plants13111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024]
Abstract
Drought affects several plant physiological characteristics such as photosynthesis, carbon metabolism, and chlorophyll content, causing hormonal and nutritional imbalances and reducing nutrient uptake and transport, which inhibit growth and development. The use of bioinoculants based on plant growth-promoting microorganisms such as plant growth-promoting rhizobacteria (PGPR), yeasts, and arbuscular mycorrhizal fungi (AMF) has been proposed as an alternative to help plants tolerate drought. However, most studies have been based on the use of a single type of microorganism, while consortia studies have been scarcely performed. Therefore, the aim of this study was to evaluate different combinations of three PGPR, three AMF, and three yeasts with plant growth-promoting attributes to improve the biochemical, nutritional, and physiological behavior of strawberry plants growing under severe drought. The results showed that the growth and physiological attributes of the non-inoculated plants were significantly reduced by drought. In contrast, plants inoculated with the association of the fungus Claroideoglomus claroideum, the yeast Naganishia albida, and the rhizobacterium Burkholderia caledonica showed a stronger improvement in tolerance to drought. High biomass, relative water content, fruit number, photosynthetic rate, transpiration, stomatal conductance, quantum yield of photosystem II, N concentration, P concentration, K concentration, antioxidant activities, and chlorophyll contents were significantly improved in inoculated plants by up to 16.6%, 12.4%, 81.2%, 80%, 79.4%, 71.0%, 17.8%, 8.3%, 6.6%, 57.3%, 41%, and 22.5%, respectively, compared to stressed non-inoculated plants. Moreover, decreased malondialdehyde levels by up to 32% were registered. Our results demonstrate the feasibility of maximizing the effects of inoculation with beneficial rhizosphere microorganisms based on the prospect of more efficient combinations among different microbial groups, which is of interest to develop bioinoculants oriented to increase the growth of specific plant species in a global scenario of increasing drought stress.
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Affiliation(s)
- Urley A. Pérez-Moncada
- Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4811230, Chile;
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (C.S.); (A.R.); (C.V.)
| | - Christian Santander
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (C.S.); (A.R.); (C.V.)
- Grupo de Ingeniería Ambiental y Biotecnología, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción 4070411, Chile
| | - Antonieta Ruiz
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (C.S.); (A.R.); (C.V.)
| | - Catalina Vidal
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (C.S.); (A.R.); (C.V.)
| | - Cledir Santos
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, P.O. Box 54-D, Temuco 4780000, Chile; (C.S.); (A.R.); (C.V.)
- Centro Regional de Investigación e Innovación para la Sostenibilidad de la Agricultura y los Territorios Rurales, CERES, La Palma, Quillota 2260000, Chile
| | - Pablo Cornejo
- Centro Regional de Investigación e Innovación para la Sostenibilidad de la Agricultura y los Territorios Rurales, CERES, La Palma, Quillota 2260000, Chile
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile
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Feng Y, Xu T, Wang W, Sun S, Zhang M, Song F. Nitrogen addition changed soil fungal community structure and increased the biomass of functional fungi in Korean pine plantations in temperate northeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172349. [PMID: 38615770 DOI: 10.1016/j.scitotenv.2024.172349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Nitrogen (N) deposition is a global environmental issue that can have significant impacts on the community structure and function in ecosystems. Fungi play a key role in soil biogeochemical cycles and their community structures are tightly linked to the health and productivity of forest ecosystems. Based on high-throughput sequencing and ergosterol extraction, we examined the changes in community structure, composition, and biomass of soil ectomycorrhizal (ECM) and saprophytic (SAP) fungi in 0-10 cm soil layer after 8 years of continuous N addition and their driving factors in a temperate Korean pine plantation in northeast China. Our results showed that N addition increased fungal community richness, with the highest richness and Chao1 index under the low N treatment (LN: 20 kg N ha-1 yr-1). Based on the FUN Guild database, we found that the relative abundance of ECM and SAP fungi increased first and then decreased with increasing N deposition concentration. The molecular ecological network analysis showed that the interaction between ECM and SAP fungi was enhanced by N addition, and the interaction was mainly positive in the ECM fungal network. N addition increased fungal biomass, and the total fungal biomass (TFB) was the highest under the MN treatment (6.05 ± 0.3 mg g-1). Overall, we concluded that N addition changed soil biochemical parameters, increased fungal activity, and enhanced functional fungal interactions in the Korean pine plantation over an 8-year simulated N addition. We need to consider the effects of complex soil conditions on soil fungi and emphasize the importance of regulating soil fungal community structure and biomass for managing forest ecosystems. These findings could deepen our understanding of the effects of increased N deposition on soil fungi in temperate forests in northern China, which can provide the theoretical basis for reducing the effects of increased N deposition on forest soil.
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Affiliation(s)
- Yuhan Feng
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Tianle Xu
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Wei Wang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Simiao Sun
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China; Heilongjiang Academy of Black Soil Conservation & Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Mengmeng Zhang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Fuqiang Song
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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14
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Wang C, Shi Z, Li A, Geng T, Liu L, Liu W. Long-term nitrogen input reduces soil bacterial network complexity by shifts in life history strategy in temperate grassland. IMETA 2024; 3:e194. [PMID: 38898994 PMCID: PMC11183191 DOI: 10.1002/imt2.194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 06/21/2024]
Abstract
We investigated soil bacterial and fungal communities, constructed co-occurrence networks, and estimated bacterial traits along a gradient of nitrogen (N) input. The results showed that soil bacterial co-occurrence networks complexity decreased with increasing N input. The ratio of negative to positive cohesion decreased with increasing N input, suggesting the declined competitive but strengthened cooperative interactions. However, soil fungal network complexity did not change under N enrichment. In addition, N input stimulated the copiotroph/oligotroph ratio, ribosomal RNA operon (rrn) copy number, and guanine-cytosine (GC) content of soil bacteria, shifting bacterial life history strategy toward copiotroph with increased r-/K-strategy ratio. Piecewise structural equation modeling results further revealed that the reduction in bacterial co-occurrence network complexity was directly regulated by the increased bacterial r-/K-strategy ratio, rather than reduced bacterial richness. Our study reveals the mechanisms through which microbial traits regulate interactions and shape co-occurrence networks under global changes.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi‐Arid Arable Land in Northern China, Hulunber Grassland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Ziyue Shi
- State Key Laboratory of Efficient Utilization of Arid and Semi‐Arid Arable Land in Northern China, Hulunber Grassland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Aogui Li
- State Key Laboratory of Efficient Utilization of Arid and Semi‐Arid Arable Land in Northern China, Hulunber Grassland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Tianyi Geng
- State Key Laboratory of Efficient Utilization of Arid and Semi‐Arid Arable Land in Northern China, Hulunber Grassland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Lingli Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Weixing Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi‐Arid Arable Land in Northern China, Hulunber Grassland Ecosystem National Observation and Research Station, Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
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15
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Rähn E, Lutter R, Riit T, Tullus T, Tullus A, Tedersoo L, Drenkhan R, Tullus H. Soil mycobiomes in native European aspen forests and hybrid aspen plantations have a similar fungal richness but different compositions, mainly driven by edaphic and floristic factors. Front Microbiol 2024; 15:1372938. [PMID: 38774505 PMCID: PMC11106484 DOI: 10.3389/fmicb.2024.1372938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/02/2024] [Indexed: 05/24/2024] Open
Abstract
Background The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied. Methods The goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17-18-year-old plantations) and native aspen stands of three age classes (8-29, 30-55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages. Results Native aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30-55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands. Conclusion We conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective.
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Affiliation(s)
- Elisabeth Rähn
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Reimo Lutter
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Taavi Riit
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Tea Tullus
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Arvo Tullus
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Rein Drenkhan
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Hardi Tullus
- Chair of Silviculture and Forest Ecology, Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
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16
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Mateos DM, Bhatnagar JM. Restoring ecological complexity in a changing environment. Curr Biol 2024; 34:R365-R371. [PMID: 38714167 DOI: 10.1016/j.cub.2024.03.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
As land use leaves massive tracts of land vacant for recovery, restoration must undergo a substantial shift to incorporate a complexity perspective beyond the traditional community, biodiversity or functional views. With an interaction-function perspective, we may be able to achieve ecosystems with better chances to adapt to current environmental changes and, especially, to climate change. We explore combined approaches that include still unused and underexplored techniques that will soon go mainstream and produce massive amounts of information to address the complexity gap. As we understand how complexity reassembles after the end of agriculture, we will be able to design actions to restore or enhance it at unprecedented spatial scales while increasing its adaptability to environmental changes.
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Affiliation(s)
- David Moreno Mateos
- School of Geography and the Environment, University of Oxford, Oxford OX1 3QY, UK; Basque Centre for Climate Change (BC3), Leioa 48940, Spain; Ikerbasque Foundation, Bilbao 48009, Spain.
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17
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Auer L, Buée M, Fauchery L, Lombard V, Barry KW, Clum A, Copeland A, Daum C, Foster B, LaButti K, Singan V, Yoshinaga Y, Martineau C, Alfaro M, Castillo FJ, Imbert JB, Ramírez L, Castanera R, Pisabarro AG, Finlay R, Lindahl B, Olson A, Séguin A, Kohler A, Henrissat B, Grigoriev IV, Martin FM. Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems. THE NEW PHYTOLOGIST 2024; 242:1676-1690. [PMID: 38148573 DOI: 10.1111/nph.19471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023]
Abstract
Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.
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Affiliation(s)
- Lucas Auer
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Laure Fauchery
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, Marseille, 13288, France
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, 13009, France
| | - Kerry W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chris Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christine Martineau
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Federico J Castillo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - J Bosco Imbert
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Lucia Ramírez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), Pamplona, 31006, Spain
| | - Roger Finlay
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Björn Lindahl
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Ake Olson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Armand Séguin
- Laurentian Forestry Centre, Natural Resources Canada, Canadian Forest Service, Quebec, G1V4C7, QC, Canada
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
| | - Bernard Henrissat
- DTU Bioengineering, Denmarks Tekniske Universitet, Copenhagen, 2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Francis M Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres-Microorganismes, Nancy, F-54000, France
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18
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Camenzind T, Aguilar-Trigueros CA, Hempel S, Lehmann A, Bielcik M, Andrade-Linares DR, Bergmann J, Dela Cruz J, Gawronski J, Golubeva P, Haslwimmer H, Lartey L, Leifheit E, Maaß S, Marhan S, Pinek L, Powell JR, Roy J, Veresoglou SD, Wang D, Wulf A, Zheng W, Rillig MC. Towards establishing a fungal economics spectrum in soil saprobic fungi. Nat Commun 2024; 15:3321. [PMID: 38637578 PMCID: PMC11026409 DOI: 10.1038/s41467-024-47705-7] [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: 02/02/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Trait-based frameworks are promising tools to understand the functional consequences of community shifts in response to environmental change. The applicability of these tools to soil microbes is limited by a lack of functional trait data and a focus on categorical traits. To address this gap for an important group of soil microorganisms, we identify trade-offs underlying a fungal economics spectrum based on a large trait collection in 28 saprobic fungal isolates, derived from a common grassland soil and grown in culture plates. In this dataset, ecologically relevant trait variation is best captured by a three-dimensional fungal economics space. The primary explanatory axis represents a dense-fast continuum, resembling dominant life-history trade-offs in other taxa. A second significant axis reflects mycelial flexibility, and a third one carbon acquisition traits. All three axes correlate with traits involved in soil carbon cycling. Since stress tolerance and fundamental niche gradients are primarily related to the dense-fast continuum, traits of the 2nd (carbon-use efficiency) and especially the 3rd (decomposition) orthogonal axes are independent of tested environmental stressors. These findings suggest a fungal economics space which can now be tested at broader scales.
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Affiliation(s)
- Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany.
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
| | - Carlos A Aguilar-Trigueros
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Stefan Hempel
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Milos Bielcik
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Diana R Andrade-Linares
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, 85764, Neuherberg, Germany
| | - Joana Bergmann
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374, Müncheberg, Germany
| | - Jeane Dela Cruz
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jessie Gawronski
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Polina Golubeva
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Heike Haslwimmer
- Institute of Soil Science and Land Evaluation, Soil Biology department, University of Hohenheim, Emil-Wolff-Str. 27, 70599, Stuttgart, Germany
| | - Linda Lartey
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Eva Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefanie Maaß
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology department, University of Hohenheim, Emil-Wolff-Str. 27, 70599, Stuttgart, Germany
| | - Liliana Pinek
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Julien Roy
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stavros D Veresoglou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Dongwei Wang
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Anja Wulf
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Weishuang Zheng
- Marine Institute for Bioresources and Environment, Peking University Shenzhen Institute, Shenzhen, 518057, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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19
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Leifheit EF, Camenzind T, Lehmann A, Andrade-Linares DR, Fussan M, Westhusen S, Wineberger TM, Rillig MC. Fungal traits help to understand the decomposition of simple and complex plant litter. FEMS Microbiol Ecol 2024; 100:fiae033. [PMID: 38486354 PMCID: PMC11022653 DOI: 10.1093/femsec/fiae033] [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: 12/12/2022] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/18/2024] Open
Abstract
Litter decomposition is a key ecosystem process, relevant for the release and storage of nutrients and carbon in soil. Soil fungi are one of the dominant drivers of organic matter decomposition, but fungal taxa differ substantially in their functional ability to decompose plant litter. Knowledge is mostly based on observational data and subsequent molecular analyses and in vitro studies have been limited to forest ecosystems. In order to better understand functional traits of saprotrophic soil fungi in grassland ecosystems, we isolated 31 fungi from a natural grassland and performed several in vitro studies testing for i) leaf and wood litter decomposition, ii) the ability to use carbon sources of differing complexity, iii) the enzyme repertoire. Decomposition strongly varied among phyla and isolates, with Ascomycota decomposing the most and Mucoromycota decomposing the least. The phylogeny of the fungi and their ability to use complex carbon were the most important predictors for decomposition. Our findings show that it is crucial to understand the role of individual members and functional groups within the microbial community. This is an important way forward to understand the role of microbial community composition for the prediction of litter decomposition and subsequent potential carbon storage in grassland soils.
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Affiliation(s)
- Eva F Leifheit
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Anika Lehmann
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Diana R Andrade-Linares
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit for Comparative Microbiome Analyses – COMI, 85764 Neuherberg, Germany
| | - Max Fussan
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
| | - Sophia Westhusen
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Till M Wineberger
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin 14195, Germany
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20
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Gadd GM, Fomina M, Pinzari F. Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation. Microbiol Mol Biol Rev 2024; 88:e0020022. [PMID: 38179930 PMCID: PMC10966957 DOI: 10.1128/mmbr.00200-22] [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: 05/30/2023] [Accepted: 09/11/2023] [Indexed: 01/06/2024] Open
Abstract
SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.
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Affiliation(s)
- Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, Beijing, China
| | - Marina Fomina
- Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National Reserve “Sophia of Kyiv”, Kyiv, Ukraine
| | - Flavia Pinzari
- Institute for Biological Systems (ISB), Council of National Research of Italy (CNR), Monterotondo (RM), Italy
- Natural History Museum, London, United Kingdom
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21
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Fu Q, Qiu Y, Zhao J, Li J, Xie S, Liao Q, Fu X, Huang Y, Yao Z, Dai Z, Qiu Y, Yang Y, Li F, Chen H. Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169351. [PMID: 38123079 DOI: 10.1016/j.scitotenv.2023.169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siqi Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Furong Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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22
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Gacura MD, Zak DR, Blackwood CB. From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition. FEMS Microbiol Ecol 2024; 100:fiae016. [PMID: 38373845 PMCID: PMC10913062 DOI: 10.1093/femsec/fiae016] [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: 09/01/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Biology Department, Gannon University, 109 University Square, Erie, PA 16541, United States
| | - Donald R Zak
- School for Environment and Sustainability, University of Michigan, 440 Church St., Ann Arbor, MI 48109, United States
| | - Christopher B Blackwood
- Department of Biological Sciences, Kent State University, 800 E. Summit St., Kent, OH 44242, United States
- Department of Plant, Soil, and Microbial Sciences and Department of Plant Biology, Michigan State University, 1066 Bogue St., East Lansing, MI 48842, United States
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23
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Pellitier PT, Van Nuland M, Salamov A, Grigoriev IV, Peay KG. Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient. ISME COMMUNICATIONS 2024; 4:ycae031. [PMID: 38524763 PMCID: PMC10960952 DOI: 10.1093/ismeco/ycae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024]
Abstract
Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.
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Affiliation(s)
- Peter T Pellitier
- Department of Biology, Stanford University, Stanford CA 94305, United States
- Department of Earth System Science, Stanford University, Stanford CA 94305, United States
| | - Michael Van Nuland
- Department of Biology, Stanford University, Stanford CA 94305, United States
- Society for the Protection of Underground Networks, SPUN, Dover, DE 19901, United States
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 United States
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, United States
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford CA 94305, United States
- Department of Earth System Science, Stanford University, Stanford CA 94305, United States
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24
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Błońska E, Jankowiak R, Lasota J, Krzemińska N, Zbyryt A, Ciach M. The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:2583-2594. [PMID: 38066283 PMCID: PMC10791925 DOI: 10.1007/s11356-023-31383-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
Organic debris accumulated in bird nests creates a unique environment for organisms, including microbes. Built from various plant materials that are typically enriched by animal residues, bird nest favours the development of various fungal groups. The aim of this study was to investigate the chemical properties of the material deposited in the white stork Ciconia ciconia nests and the link between extracellular enzyme activity and the diversity and composition of culturable fungi. Our findings revealed low C/P and N/P ratio values in the nest materials, which indicate a high P availability. Nest material C/N/P ratio ranged from 67/8/1 to 438/33/1. Enzymatic activity strongly correlated with the content of carbon, nitrogen, and pH of the material deposited in the nests. A total of 2726 fungal isolates were obtained from the nests, from which 82 taxa were identified based on morphology and DNA sequence data. The study indicates that white stork nests are microhabitat characterised by diverse chemical and biochemical properties. We found relationship between the fungal richness and diversity and the C/P and N/P ratios of materials from the nests. Our study showed that culturable fungi occurred frequently in materials with high levels of C, N, and P, as well as high concentrations of base alkaline elements (Ca, Mg, and K).
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Affiliation(s)
- Ewa Błońska
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Krakow, Poland.
| | - Robert Jankowiak
- Department of Forest Ecosystem Protection, University of Agriculture, 29 Listopada 46, 31-425, Krakow, Poland
| | - Jarosław Lasota
- Department of Ecology and Silviculture, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Krakow, Poland
| | - Natalia Krzemińska
- Department of Forest Ecosystem Protection, University of Agriculture, 29 Listopada 46, 31-425, Krakow, Poland
| | - Adam Zbyryt
- Faculty of Biology, University of Białystok, Ciołkowskiego 1J, 15-245, Białystok, Poland
| | - Michał Ciach
- Department of Forest Biodiversity, Faculty of Forestry, University of Agriculture, Al. 29 Listopada 46, 31-425, Krakow, Poland
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25
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Perkins AK, Rose AL, Grossart HP, Schulz KG, Neubauer D, Tonge MP, Rosentreter JA, Eyre BD, Rojas-Jimenez K, Deschaseaux E, Oakes JM. Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166957. [PMID: 37704140 DOI: 10.1016/j.scitotenv.2023.166957] [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: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.
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Affiliation(s)
- Anita K Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia.
| | - Andrew L Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Kai G Schulz
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Darshan Neubauer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Matthew P Tonge
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Judith A Rosentreter
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | | | - Elisabeth Deschaseaux
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Joanne M Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
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26
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Awad A, Pena R. An improved method for extraction of soil fungal mycelium. MethodsX 2023; 11:102477. [PMID: 38023315 PMCID: PMC10679939 DOI: 10.1016/j.mex.2023.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.
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27
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Van Nuland ME, Daws SC, Bailey JK, Schweitzer JA, Busby PE, Peay KG. Above- and belowground fungal biodiversity of Populus trees on a continental scale. Nat Microbiol 2023; 8:2406-2419. [PMID: 37973868 DOI: 10.1038/s41564-023-01514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023]
Abstract
Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.
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Affiliation(s)
- Michael E Van Nuland
- Department of Biology, Stanford University, Stanford, CA, USA.
- Society for the Protection of Underground Networks, SPUN, Dover, DE, USA.
| | - S Caroline Daws
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joseph K Bailey
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Jennifer A Schweitzer
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Earth System Science, Stanford University, Stanford, CA, USA
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28
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Wang L, Guo J, Liu X, Li K, Ma L, Tian Y, Wang J, Zhang Q, Tian Y, Li C, Lu M. Assessment of soil quality in an arid and barren mountainous of Shandong province, China. Sci Rep 2023; 13:19966. [PMID: 37968306 PMCID: PMC10652006 DOI: 10.1038/s41598-023-46136-6] [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: 07/07/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Forest soils are important components of forest ecosystems, and soil quality assessment as a decision-making tool to understand forest soil quality and maintain soil productivity is essential. Various methods of soil quality assessment have been developed, which have occasionally generated inconsistent assessment results between soil types. We assessed the soil quality of five communities (herb, shrub, Quercus acutissima, Pinus thunbergii, and Q. acutissima-P. thunbergii mixed plantation) using two common methods of dry and barren mountains in the Yimeng Mountain area, China. Sixteen soil physical, chemical and biological properties were analysed. The soil quality index was determined using the established minimum data set based on the selection results of principal component analysis and Pearson analysis. Silt, soil total phosphorus (P), soil total nitrogen (N), L-leucine aminopeptidase, acid phosphatase and vector length were identified as the most representative indicators for the minimum data set. Linear regression analysis showed that the minimum data set can adequately represent the total data set to quantify the impact of different communities on soil quality (P < 0.001). The results of linear and non-linear methods of soil quality assessment showed that the higher soil quality index was Pinus forest (0.59 and 0.54), and the soil quality index of mixed plantation (0.41 and 0.45) was lower, which was similar to the herb community (0.37 and 0.44). Soil quality was mostly affected by soil chemical properties and extracellular enzyme activities of different communities, and the different reasons for the low soil quality of mixed plantations were affected by soil organic carbon (C) and total C. Overall, we demonstrate that the soil quality index based on the minimum data set method could be a useful tool to indicate the soil quality of forest systems. Mixed plantations can improve soil quality by increasing soil C, which is crucial in ecosystem balance.
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Affiliation(s)
- Lu Wang
- Landscape Architecture Research Center, Shandong Jianzhu University, Jinan, 250101, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Jianyao Guo
- Shandong Forestry Protection and Development Service Center, Jinan, 250000, Shandong, China
| | - Xiumei Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
- Shanghai Environment College, Shanghai, 200135, China
| | - Kun Li
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Liang Ma
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Yehan Tian
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Jinming Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Qingdong Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Yaozhen Tian
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China
| | - Chuanrong Li
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, 271018, Shandong, China.
| | - Min Lu
- Landscape Architecture Research Center, Shandong Jianzhu University, Jinan, 250101, Shandong, China.
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Ren Z, Ye S, Li H, Huang X, Chen L, Cao S, Chen T. Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2023; 86:2756-2769. [PMID: 37542537 DOI: 10.1007/s00248-023-02280-0] [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: 03/26/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.
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Affiliation(s)
- Ze Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 Beijing East Road, Nanjing, 210008, China.
- Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, 519087, China.
| | - Shudan Ye
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Hongxuan Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Xilei Huang
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Luyao Chen
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China
| | - Shengkui Cao
- School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Tao Chen
- Center for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, 768 Jiayuguan W Road, Lanzhou, 730020, China.
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30
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Hassan S, Syun-ichi U, Shabeer S, Wu CF, Moriyama H, Coutts RHA, Kotta-Loizou I, Jamal A. Molecular and biological characterization of a partitivirus from Paecilomyces variotii. J Gen Virol 2023; 104:001925. [PMID: 38015047 PMCID: PMC10768695 DOI: 10.1099/jgv.0.001925] [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: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Paeciliomyces variotii is a thermo-tolerant, ubiquitous fungus commonly found in food products, indoor environments, soil and clinical samples. It is a well-known biocontrol agent used against phytopathogenic fungi and its metabolites have many industrial applications. Rare reports of P. variotii-related human infections have been found in the medical literature. In this study, we report for the first time the infection of P. variotii isolated from a soil sample collected in a rice field with a double-stranded RNA virus, Paeciliomyces variotii partitivirus 1 (PvPV-1) in the family Partitiviridae. P. variotii harboured icosahedral virus particles 30 nm in diameter with two dsRNA segments 1758 and 1356 bp long. Both dsRNA1 and dsRNA2 have a single open reading frame encoding proteins of 63 and 40 kDa, respectively. These proteins have significant similarity to the RNA-dependent RNA polymerase and capsid protein encoded by the genomic segments of several viruses from the family Partitiviridae. Phylogenetic analysis revealed that PvPV-1 belongs to the family Partitiviridae but in an unclassified group/genus, tentatively nominated Zetapartitivirus. PvPV-1 was found to increase the growth rate of the host fungus, as indicated by time course experiments performed on a range of different media for virus-infected and virus-free isogenic lines. Further, dual-culture assays performed for both isogenic lines confirmed the antagonistic potential of P. variotii against other phytopathogenic fungi. The findings of this study assist us in understanding P. variotii as a potential biocontrol agent, together with plant-fungus-virus interactions.
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Affiliation(s)
- Sidra Hassan
- Department of Plant and Environmental Protection, PARC Institute of Advanced Studies in Agriculture (Affiliated with Quaid-i-Azam University), National Agricultural Research Centre, Islamabad, 45500, Pakistan
| | - Urayama Syun-ichi
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Saba Shabeer
- Department of Bioscience, COMSATS University, Islamabad, 44000, Pakistan
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Chien-Fu Wu
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8, Saiwaicho, Fuchu, Tokyo 184-8509, Japan
| | - Robert H. A. Coutts
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Ioly Kotta-Loizou
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Atif Jamal
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
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31
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Mason CN, Shahar S, Beals KK, Kelley ST, Lipson DA, Swingley WD, Barber NA. Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils. FEMS Microbiol Ecol 2023; 99:fiad120. [PMID: 37791391 DOI: 10.1093/femsec/fiad120] [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: 06/08/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.
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Affiliation(s)
- Cayla N Mason
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Shayla Shahar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Kendall K Beals
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - David A Lipson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Nicholas A Barber
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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32
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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [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: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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Dong H, Sun H, Chen C, Zhang M, Ma D. Compositional Shifts and Assembly in Rhizosphere-Associated Fungal Microbiota Throughout the Life Cycle of Japonica Rice Under Increased Nitrogen Fertilization. RICE (NEW YORK, N.Y.) 2023; 16:34. [PMID: 37526797 PMCID: PMC10393908 DOI: 10.1186/s12284-023-00651-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Soil fungal microbiomes facilitate a range of beneficial functions for their host plants, and rhizosphere fungal community composition, richness, and diversity affect plant growth and development, and crop yield. Therefore, exploring the community structure and assembly of the rhizosphere fungal microbiome and its relationship with soil biochemical properties are fundamental to elucidating how rice plants benefit from their fungal symbionts. In this study, soil samples were collected at seedling, tillering, heading, and ripening stages of rice subjected to three levels of nitrogen fertilization. Plant growth demonstrates a substantial influence on fungal community composition and diversity. From the tillering to the ripening stage, the fungal communities were governed by homogenizing dispersal and dispersal limitation. The prevalence of Glomeromycota, the beneficial fungi, was considerably higher during the heading stage compared to the three other growth stages. This increase in abundance was strongly associated with increased levels of soil nutrients and enhanced activity of nitrogen acquisition enzymes. This may be a strategy developed by rice grown in flooded soil to recruit beneficial fungi in the rhizosphere to meet high nitrogen demands. Our study findings contribute to elucidating the influence of plant development and nitrogen fertilization on the structure and composition of the fungal community as well as its relationship with soil key soil nutrient content and nitrogen-related enzyme activities. They also illustrate how a shift in the fungal community mediates and reflects the effects of nitrogen fertilization input in rice agroecosystems. These findings provide new insights into the effects of changes in nitrogen application in rice rhizosphere at different growth stages on fungal communities and soil biochemical characteristics.
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Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Conglin Chen
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Mingyu Zhang
- Key Laboratory of Northeast Rice Biology and Breeding, Rice Research Institute, Shenyang Agricultural University, Shenyang, China
- Agronomy College, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Agronomy College, Liaodong University, Dandong, China.
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34
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Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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35
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Grishkan I, Kidron GJ, Rodriguez-Berbel N, Miralles I, Ortega R. Altitudinal Gradient and Soil Depth as Sources of Variations in Fungal Communities Revealed by Culture-Dependent and Culture-Independent Methods in the Negev Desert, Israel. Microorganisms 2023; 11:1761. [PMID: 37512933 PMCID: PMC10383159 DOI: 10.3390/microorganisms11071761] [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: 06/08/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
We examined fungal communities in soil profiles of 0-10 cm depth along the altitudinal gradient of 250-530-990 m.a.s.l. at the Central Negev Desert, Israel, which benefit from similar annual precipitation (95 mm). In the soil samples collected in the summer of 2020, a mycobiota accounting for 169 species was revealed by both culture-dependent and culture-independent (DNA-based) methodologies. The impact of soil depth on the variations in fungal communities was stronger than the impact of altitude. Both methodologies displayed a similar tendency in the composition of fungal communities: the prevalence of melanin-containing species with many-celled large spores (mainly Alternaria spp.) in the uppermost layers and the depth-wise increase in the proportion of light-colored species producing a high amount of small one-celled spores. The culturable and the DNA-based fungal communities had only 13 species in common. The differences were attributed to the pros and cons of each method. Nevertheless, despite the drawbacks, the employment of both methodologies has an advantage in providing a more comprehensive picture of fungal diversity in soils.
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Affiliation(s)
- Isabella Grishkan
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa 3498838, Israel
| | - Giora J Kidron
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel
| | - Natalia Rodriguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Isabel Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Raúl Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
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36
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Lee H, Cho YJ, Cho A, Kim OS. Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats. J Microbiol 2023; 61:663-672. [PMID: 37615929 DOI: 10.1007/s12275-023-00068-y] [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: 06/21/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/25/2023]
Abstract
Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.
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Affiliation(s)
- Hanbyul Lee
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yong-Joon Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ahnna Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ok-Sun Kim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
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37
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Schlatter DC, Gamble JD, Castle S, Rogers J, Wilson M. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Appl Environ Microbiol 2023; 89:e0193122. [PMID: 37212685 PMCID: PMC10304672 DOI: 10.1128/aem.01931-22] [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: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.
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Affiliation(s)
| | - Joshua D. Gamble
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Sarah Castle
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Julia Rogers
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Melissa Wilson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
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38
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Yu J, Lai J, Neal BM, White BJ, Banik MT, Dai SY. Genomic Diversity and Phenotypic Variation in Fungal Decomposers Involved in Bioremediation of Persistent Organic Pollutants. J Fungi (Basel) 2023; 9:418. [PMID: 37108874 PMCID: PMC10145412 DOI: 10.3390/jof9040418] [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: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Fungi work as decomposers to break down organic carbon, deposit recalcitrant carbon, and transform other elements such as nitrogen. The decomposition of biomass is a key function of wood-decaying basidiomycetes and ascomycetes, which have the potential for the bioremediation of hazardous chemicals present in the environment. Due to their adaptation to different environments, fungal strains have a diverse set of phenotypic traits. This study evaluated 320 basidiomycetes isolates across 74 species for their rate and efficiency of degrading organic dye. We found that dye-decolorization capacity varies among and within species. Among the top rapid dye-decolorizing fungi isolates, we further performed genome-wide gene family analysis and investigated the genomic mechanism for their most capable dye-degradation capacity. Class II peroxidase and DyP-type peroxidase were enriched in the fast-decomposer genomes. Gene families including lignin decomposition genes, reduction-oxidation genes, hydrophobin, and secreted peptidases were expanded in the fast-decomposer species. This work provides new insights into persistent organic pollutant removal by fungal isolates at both phenotypic and genotypic levels.
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Affiliation(s)
- Jiali Yu
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Jingru Lai
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Brian M. Neal
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Bert J. White
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
| | - Mark T. Banik
- USDA Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, WI 53726, USA
| | - Susie Y. Dai
- Systems and Synthetic Biology Innovation Hub, Texas A&M University, College Station, TX 77843, USA; (J.Y.)
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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39
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Itani A, Masuo S, Yamamoto R, Serizawa T, Fukasawa Y, Takaya N, Toyota M, Betsuyaku S, Takeshita N. Local calcium signal transmission in mycelial network exhibits decentralized stress responses. PNAS NEXUS 2023; 2:pgad012. [PMID: 36896124 PMCID: PMC9991499 DOI: 10.1093/pnasnexus/pgad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/03/2023] [Accepted: 01/18/2023] [Indexed: 03/09/2023]
Abstract
Many fungi live as mycelia, which are networks of hyphae. Mycelial networks are suited for the widespread distribution of nutrients and water. The logistical capabilities are critical for the extension of fungal survival areas, nutrient cycling in ecosystems, mycorrhizal symbioses, and virulence. In addition, signal transduction in mycelial networks is predicted to be vital for mycelial function and robustness. A lot of cell biological studies have elucidated protein and membrane trafficking and signal transduction in fungal hyphae; however, there are no reports visualizing signal transduction in mycelia. This paper, by using the fluorescent Ca2+ biosensor, visualized for the first time how calcium signaling is conducted inside the mycelial network in response to localized stimuli in the model fungus Aspergillus nidulans. The wavy propagation of the calcium signal inside the mycelium or the signal blinking in the hyphae varies depending on the type of stress and proximity to the stress. The signals, however, only extended around 1,500 μm, suggesting that the mycelium has a localized response. The mycelium showed growth delay only in the stressed areas. Local stress caused arrest and resumption of mycelial growth through reorganization of the actin cytoskeleton and membrane trafficking. To elucidate the downstream of calcium signaling, calmodulin, and calmodulin-dependent protein kinases, the principal intracellular Ca2+ receptors were immunoprecipitated and their downstream targets were identified by mass spectrometry analyses. Our data provide evidence that the mycelial network, which lacks a brain or nervous system, exhibits decentralized response through locally activated calcium signaling in response to local stress.
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Affiliation(s)
- Ayaka Itani
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Shunsuke Masuo
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Riho Yamamoto
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Tomoko Serizawa
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Yu Fukasawa
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko, Osaki, Miyagi, 989-6711, Japan
| | - Naoki Takaya
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
| | - Masatsugu Toyota
- Department of Biochemistry and Molecular Biology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
- Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), Kyoto, Japan
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Shigeyuki Betsuyaku
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194Japan
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, 305-8572, Japan
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Li W, Li Z, Liu Y, Nie X, Zheng H, Zhang G, Wang S, Ma Y. Soil nutrients shape the composition and function of fungal communities in abandoned ancient rice terraces. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 329:117064. [PMID: 36535145 DOI: 10.1016/j.jenvman.2022.117064] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In recent decades, terraces abandonment has been prevalent in the hilly areas of China. Soil fungi play an important role in clarifying soil ecosystematic feedback after ancient rice terraces abandonment, but how their community composition and function shift remains unclear. Soil profiles of 0-120 cm were excavated in ancient rice terraces, dry land, and forest land (formed from ancient rice terraces abandonment), respectively. The 13C NMR and high-throughput sequencing were used to determine soil organic carbon chemical groups and fungal community, respectively, and FUNGuild was used to predict functional groups. The results showed that the soil fungal community changed from Ascomycota to Basidiomycota after ancient rice terraces abandonment. The trophic modes of dry land and forest land were transformed into pathotrophic fungi and symbiotrophic fungi, respectively. The number of nodes and edges of fungal co-occurrence networks increased by 83.8% and 644.1% in dry land, and 81.3% and 431.2% in forest land, respectively. Moreover, soil nutrients (especially DOC, TN, and TP) can more affected the variation of fungal community composition and function than soil organic carbon chemical groups. These findings indicate that soil fungal community shifts in different directions in response to ancient rice terraces abandonment, which is related to the adaptive strategies for environmental changes and may be more conducive to the acquisition and turnover of soil nutrients.
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Affiliation(s)
- Wenqing Li
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
| | - Zhongwu Li
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China.
| | - Yaojun Liu
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
| | - Xiaodong Nie
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
| | - Han Zheng
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China
| | - Guangye Zhang
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
| | - Shuyuan Wang
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
| | - Yichun Ma
- School of Geographic Sciences, Hunan Normal University, Changsha, 410081, PR China; Key Laboratory of Subtropical Ecology and Environmental Change, Hunan Normal University, Changsha, 410081, PR China
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Wan P, Zhang N, Li Y, Li S, Li FM, Cui Z, Zhang F. Reducing plant pathogens could increase crop yields after plastic film mulching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160615. [PMID: 36464048 DOI: 10.1016/j.scitotenv.2022.160615] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi are closely associated with crop growth in agricultural ecosystems through processes such as nutrient uptake and pathogenesis. Plastic film mulching (PM) plays a dominant role in increasing crop yields in dryland agriculture worldwide. The functional guilds of soil fungi under PM and their effects on crops remain unclear. In this study, we explored the absolute abundance, diversity, community composition, and functional guilds of soil fungi after short-term (2 years) and long-term (10 years) mulching experiments. Short-term mulching caused a 37 %-51 % decrease in absolute fungal abundance owing to abrupt changes in the microenvironment. The response of the fungal community to PM varied with sites, with the effect being more pronounced under poor hydrothermal conditions (314 mm). The abundance of potential fungal pathogens decreased under PM; for example, Gibberella (maize ear rot) abundance was 45 % and 72 % lower under short- and long-term mulching, respectively, when compared with that in control. In contrast, the abundance of plant biocontrol fungi increased under PM; for instance, Glomeromycota abundance increased twofold under long-term mulching. Although PM did not alter the complexity and stability of fungal co-occurrence network, competition among fungi increased in the absence of sufficient carbon (C) sources. Long-term mulching reduced phytopathogen guilds by 12 %-77 % and increased arbuscular mycorrhizal fungi (AMF) guilds by 89 %-94 %. Structural equation modeling suggested that PM altered fungal functional guilds mainly by shaping the structure of the fungal community, and fungal pathogens decreased with increased AMF functional guilds, inducing higher maize yields. These results showed for the first time, from a microbial perspective, that pathogens reduction owing to PM could explain 4.4 % of maize yield variation, providing theoretical guidance to accomplish sustainability of continuous maize mulching.
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Affiliation(s)
- Pingxing Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ningning Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yufei Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Yangling 712100, China
| | - Feng-Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China; College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zengtuan Cui
- General Station of Gansu Cultivated Land Quality Construction and Protection, Lanzhou, Gansu 730000, China.
| | - Feng Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China.
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Grishkan I, Temina M. Composition and diversity of endolichenic microfungal communities from saxicolous lichens at Nahal Boker, the central Negev Desert, Israel. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Vivelo S, Alsairafi B, Walsh JT, Bhatnagar JM. Intrinsic growth rate and cellobiohydrolase activity underlie the phylogenetic signal to fungal decomposer succession. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Nie C, Geng X, Ouyang H, Wang L, Li Z, Wang M, Sun X, Wu Y, Qin Y, Xu Y, Tang X, Chen J. Abundant bacteria and fungi attached to airborne particulates in vegetable plastic greenhouses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159507. [PMID: 36257421 DOI: 10.1016/j.scitotenv.2022.159507] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/12/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The proliferation of modern vegetable plastic greenhouses (VPGS) supplies more and more vegetables for food all over the world. The airborne bacteria and fungi induce more exposure opportunities for workers toiling in confined plastic greenhouses. Culture-independent approaches by qPCR and high-throughput sequencing technology were used to study the airborne particulates microbiota in typic VPGS in Shandong, a large base of vegetables in China. The result revealed the mean airborne bacteria concentrations reached 1.67 × 103 cells/m3 (PM2.5) and 2.38 × 103 cells/m3 (PM10), and the mean airborne fungal concentrations achieved 1.49 × 102 cells/m3 (PM2.5) and 3.19 × 102 cells/m3 (PM10) in VPGS. The predominant bacteria in VPGS included Ralstonia, Alcanivorax, Pseudomonas, Bacillus, and Acinetobacter. Botrytis, Alternaria, Fusarium, Sporobolomyces, and Cladosporium were frequently detected fungal genera in VPGS. A higher Chao1 of bacteria in PM10 was significantly different from PM2.5 in VPGS. The potential pathogens in VPGS include Raltonia picketti, Acinetobacter lwoffii, Bacillus anthracis, Botrytis cinerea, and Cladosporium sphaerospermum. The network analysis indicated that airborne microbiota was associated with soil microbiota which was affected by anthropologic activities. The predicted gene functions revealed that bacterial function mainly involved metabolism, neurodegenerative diseases, and fungal trophic mode dominated by Pathotroph-Saprotroph in VPGS. These findings unveiled airborne microbiomes in VPGS so that a strategy for improving air quality can be applied to safeguard health and vegetation.
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Affiliation(s)
- Changliang Nie
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Xueyun Geng
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Huiling Ouyang
- IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Lina Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; Institute of Eco-Chongming (IEC), Shanghai 200062, China
| | - Zongzhen Li
- Weifang University of Science and Technology, Weifang 262700, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaomin Sun
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Yan Wu
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Yunhan Qin
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Youxin Xu
- Weifang University of Science and Technology, Weifang 262700, China; School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xu Tang
- IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China; Institute of Eco-Chongming (IEC), Shanghai 200062, China.
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Li C, Xu Y, Wang Z, Zhu W, Du A. Mixing planting with native tree species reshapes soil fungal community diversity and structure in multi-generational eucalypt plantations in southern China. Front Microbiol 2023; 14:1132875. [PMID: 36910166 PMCID: PMC9994620 DOI: 10.3389/fmicb.2023.1132875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
The continuous planting pattern of eucalypt plantations negatively affects soil quality. A mixed planting pattern using native species implanted in pure plantations has been considered a preferable measure for this problem. However, the impact of this approachon the structure and function of fungal communities is not clear. Here, harvesting sites that had undergone two generations of eucalypt plantations were selected to investigate soil fungal community structure and the co-occurrence network characteristics in response to two silvicultural patterns involving the third generation of eucalypt plantations (E) and mixed plantations of Eucalyptus. urograndis × Cinnamomum. camphora (EC) and E. urograndis × Castanopsis. hystrix (EH). Compared with the first generation of eucalypt plantations (CK), E markedly weakened enzyme activities associated with carbon-, nitrogen-. and phosphorus-cycling. Reduced soil fungal alpha diversity, and elevated the relative abundance of Basidiomycota while decreasing the abundance of Ascomycota. In contrast, EC and EH not only enhanced fungal alpha diversity, but also reshaped fungal composition. At the class level, E caused an enrichment of oligotrophic Agaricomycetes fungi, classified into symbiotroph guild, while EC markedly decreased the abundance of those fungi and increased the abundances of Sordariomycetes, Dothideomycetes, Eurotiomycetes, and Tremellomycetes fungi, which were classified into saprotroph or pathotroph guild. Moreover, fungal network complexity and robustness topological attributes were higher or significantly higher in mixed plantations soils compared with those of pure eucalypt plantation E. Furthermore, fungal diversity, structure, and functional taxa were significantly affected by soil organic matter, pH, total nitrogen, and nitrate nitrogen.
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Affiliation(s)
- Chao Li
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Yuxing Xu
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Zhichao Wang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Wankuan Zhu
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
| | - Apeng Du
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, Zhanjiang, Guangdong, China
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Ghignone S, Zampieri E, Tinti F, Torti V, Giacoma C, Mello A. Fungal Patterns from Soils in Madagascar: an Insight from Maromizaha Forest (Evergreen Humid Forest) to Outside (Deciduous Forest). MICROBIAL ECOLOGY 2023; 85:184-196. [PMID: 34907449 DOI: 10.1007/s00248-021-01887-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/29/2021] [Indexed: 05/25/2023]
Abstract
Soil fungal diversity was studied by next-generation sequencing and compared in two different Malagasy ecosystems, the first a New Protected Area (Maromizaha NAP) that is a rich humid evergreen forest and the second a degraded and declined deciduous forest (Andaravina) whose area has been also eroded. Both areas, however, have comparable annual rainfalls and soil pH values. So it was of interest to examine the soil fungal diversity in each system and compare them. We detected 1,817,658 reads representing Ascomycota, which were dominant in both habitats (55.9%), followed by unidentified fungi (21.5%), Basidiomycota (12.7%) and Mortierellomycota (6.7%), with Mucoromycota, Chytridiomycota, Glomeromycota and other phyla accounting for less than 5% in total. In detail, 1,142 OTUs out of 1,368 constitute the common core shared by both sampling areas, which are characterized by tropical climate, whereas 185 are Maromizaha specific and 41 Andaravina specific. The most represented guilds involve fungi related to saprotrophic behaviour, with a greater tendency towards pathotrophic mode. A significant variability in terms of richness and abundance is present within Maromizaha, which is a heterogeneous environment for fungi but also for plant composition, as it emerged from the vegetational survey of the investigated sites. A few fungal sequences match taxa from Madagascar, highlighting the scarce representativeness of fungi from this island in the fungal databases and their still low knowledge. Enlarging studies in Madagascar will help not only to unravel its largely unknown fungal biodiversity but also to give a contribution for studies on the reconstruction of the diversity of soil fungi worldwide.
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Affiliation(s)
- Stefano Ghignone
- Institute for Sustainable Plant Protection - Turin Unit, C.N.R., Viale P.A. Mattioli 25, 10125, Torino, Italy
| | - Elisa Zampieri
- Institute for Sustainable Plant Protection, C.N.R., Strada delle Cacce 73, 10135, Torino, Italy
| | - Fabio Tinti
- Athénée Saint Joseph Antsirabe, Antsohihy, Madagascar
| | - Valeria Torti
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Cristina Giacoma
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection - Turin Unit, C.N.R., Viale P.A. Mattioli 25, 10125, Torino, Italy.
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Micheluz A, Pinzari F, Rivera-Valentín EG, Manente S, Hallsworth JE. Biophysical Manipulation of the Extracellular Environment by Eurotium halophilicum. Pathogens 2022; 11:1462. [PMID: 36558795 PMCID: PMC9781259 DOI: 10.3390/pathogens11121462] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Eurotium halophilicum is psychrotolerant, halophilic, and one of the most-extreme xerophiles in Earth's biosphere. We already know that this ascomycete grows close to 0 °C, at high NaCl, and-under some conditions-down to 0.651 water-activity. However, there is a paucity of information about how it achieves this extreme stress tolerance given the dynamic water regimes of the surface habitats on which it commonly occurs. Here, against the backdrop of global climate change, we investigated the biophysical interactions of E. halophilicum with its extracellular environment using samples taken from the surfaces of library books. The specific aims were to examine its morphology and extracellular environment (using scanning electron microscopy for visualisation and energy-dispersive X-ray spectrometry to identify chemical elements) and investigate interactions with water, ions, and minerals (including analyses of temperature and relative humidity conditions and determinations of salt deliquescence and water activity of extracellular brine). We observed crystals identified as eugsterite (Na4Ca(SO4)3·2H2O) and mirabilite (Na2SO4·10H2O) embedded within extracellular polymeric substances and provide evidence that E. halophilicum uses salt deliquescence to maintain conditions consistent with its water-activity window for growth. In addition, it utilizes a covering of hair-like microfilaments that likely absorb water and maintain a layer of humid air adjacent to the hyphae. We believe that, along with compatible solutes used for osmotic adjustment, these adaptations allow the fungus to maintain hydration in both space and time. We discuss these findings in relation to the conservation of books and other artifacts within the built environment, spoilage of foods and feeds, the ecology of E. halophilicum in natural habitats, and the current episode of climate change.
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Affiliation(s)
- Anna Micheluz
- Conservation Science Department, Deutsches Museum, Museumsinsel 1, 80538 Munich, Germany
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy, Area della Ricerca di Roma 1, Via Salaria Km 29,300, 00015 Monterotondo, Italy
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Sabrina Manente
- Department of Molecular Sciences and Nanosystems, Scientific Campus, Ca’ Foscari University of Venice, Via Torino, 30170 Venice, Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
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Qu ZL, Braima A, Liu B, Ma Y, Sun H. Soil Fungal Community Structure and Function Shift during a Disease-Driven Forest Succession. Microbiol Spectr 2022; 10:e0079522. [PMID: 36073819 PMCID: PMC9602832 DOI: 10.1128/spectrum.00795-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/05/2022] [Indexed: 12/30/2022] Open
Abstract
Forest succession is important for sustainable forest management in terrestrial ecosystems. However, knowledge about the response of soil microbes to forest disease-driven succession is limited. In this study, we investigated the soil fungal biomass, soil enzyme activity, and fungal community structure and function in forests suffering succession processes produced by pine wilt disease from conifer to broadleaved forests using Illumina Miseq sequencing coupled with FUNGuild analysis. The results showed that the broadleaved forest had the highest fungal biomass and soil enzyme activities in C, N, and S cycles, whereas the conifer forest had the highest enzyme activity in the P cycle. Along the succession, the fungal diversity and richness significantly increased (P < 0.05). The fungal communities were dominated by Ascomycota (42.0%), Basidiomycota (38.0%), and Mortierellomycota (9.5%), among which the abundance of Ascomycota significantly increased (P < 0.05), whereas that of Basidiomycota and Mortierellomycota decreased (P < 0.05). The abundance of species Mortierella humilis, Lactarius salmonicolor, and Russula sanguinea decreased, whereas that of Mortierella minutissima increased (P < 0.05). The forests in different succession stages formed distinct fungal communities and functional structures (P < 0.05). Functionally, the saprotrophs, symbiotrophs, and pathotrophs were the dominant groups in the conifer, mixed, and broadleaved forests, respectively. Soil pH and soil organic carbon were the key factors influencing the fungal community and functional structures during the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease. IMPORTANCE The studies on soil fungal communities in disease-driven forest succession are rare. This study showed that during the disease-driven forest succession, the soil enzyme activity, soil fungal diversity, and biomass increased along succession. The disease-driven forest succession changed the soil fungal community structure and function, in which the symbiotrophs were the most dominant group along the succession. These findings provide useful information for better understanding the plant-microbe interaction during forest succession caused by forest disease.
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Affiliation(s)
- Zhao-lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ahmed Braima
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Yangzhou Polytechnic College, Yangzhou, China
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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49
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Watershed-scale Variation in Potential Fungal Community Contributions to Ectomycorrhizal Biogeochemical Syndromes. Ecosystems 2022. [DOI: 10.1007/s10021-022-00788-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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50
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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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