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Ashrafi S, Wennrich JP, Becker Y, Maciá-Vicente JG, Brißke-Rode A, Daub M, Thünen T, Dababat AA, Finckh MR, Stadler M, Maier W. Polydomus karssenii gen. nov. sp. nov. is a dark septate endophyte with a bifunctional lifestyle parasitising eggs of plant parasitic cyst nematodes (Heterodera spp.). IMA Fungus 2023; 14:6. [PMID: 36998098 PMCID: PMC10064538 DOI: 10.1186/s43008-023-00113-w] [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: 11/25/2022] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.
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Affiliation(s)
- Samad Ashrafi
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104, Brunswick, Germany.
- Institute for Crop and Soil Science, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Bundesallee 58, 38116, Brunswick, Germany.
| | - Jan-Peer Wennrich
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Brunswick, Germany
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104, Brunswick, Germany
| | - Jose G Maciá-Vicente
- Plant Ecology and Nature Conservation, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Anke Brißke-Rode
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104, Brunswick, Germany
| | - Matthias Daub
- Institute for Plant Protection in Field Crops and Grassland, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Dürener Str. 71, 50189, Elsdorf, Germany
| | - Torsten Thünen
- Institute for Crop and Soil Science, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Bundesallee 58, 38116, Brunswick, Germany
| | - Abdelfattah A Dababat
- International Maize and Wheat Improvement Centre (CIMMYT), Emek, P.O. Box 39, 06511, Ankara, Turkey
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Brunswick, Germany
| | - Wolfgang Maier
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104, Brunswick, Germany
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Maria SB, Krystyna P, Monika L, Aleksandra J, Patrycja T, Kornelia K, Aleksandra BB, Joanna Ś, Piotr J, Katarzyna P, Agnieszka K. Natural compounds derived from Brassicaceae plants as an alternative to synthetic fungicides and their influence on soil fungus diversity. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:317-327. [PMID: 35866526 DOI: 10.1002/jsfa.12143] [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: 03/22/2022] [Revised: 06/26/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The study aimed to develop a new formulation based on active substances of natural origin to protect plant seedlings against fungal pathogens, and to evaluate the effect of this formulation on fungal communities in arable soil. RESULTS Coating seeds of common crop plants with a p-coumaric acid (p-CA)-based preparation resulted in a significant reduction in the growth of most of the tested pathogens. When applied to soil, both the p-CA-based formulation and Porter 250 EC had a similar overall effect on soil fungal communities and significantly altered the structure of fungal communities at all of the times examined. Shifts in the fungal community composition concerned less than 2% of the total number of amplicon sequence variants (ASVs). The strongest impact of the formulations on soil microbiota was recorded at the fourth week of treatment. Two ASVs assigned to Botrytis and Chromelosporium, known as plant pathogens, and an unidentified ASV from Diversisporales encompassing the arbuscular mycorrhizal fungi (AMF), were significantly depleted in soil samples treated with p-CA in comparison with Porter 250 EC. CONCLUSION The p-CA-based preparation has the potential to be used as an alternative to synthetic fungicides. It shows a similar effect to Porter 250 EC on the organization of soil communities, determining changes in the character of the communities of fungi in general, at any given time. Moreover, p-CA caused a reduction in ASVs belonging to Botrytis and Chromelosporium (plant pathogens) and ASVs of Diversisporales (containing arbuscular mycorrhizal fungi) in comparison with the commercial compound that was analyzed. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Swiontek Brzezinska Maria
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Pałubicka Krystyna
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Latos Monika
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Janik Aleksandra
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Tarnawska Patrycja
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Krajnik Kornelia
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Burkowska-But Aleksandra
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Świątczak Joanna
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
| | - Jedziniak Piotr
- Department of Pharmacology and Toxicology, National Veterinary Research Institute, Pulawy, Poland
| | - Pietruszka Katarzyna
- Department of Pharmacology and Toxicology, National Veterinary Research Institute, Pulawy, Poland
| | - Kalwasińska Agnieszka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Torun, Torun, 87-100, Poland
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Factors in the Distribution of Mycorrhizal and Soil Fungi. DIVERSITY 2022. [DOI: 10.3390/d14121122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Soil fungi are crucial microorganisms in the functioning of ecosystems. They shape the soil properties, facilitate nutrient circulation, and assist with plant growth. However, their biogeography and distribution studies are limited compared to other groups of organisms. This review aims to provide an overview of the main factors shaping the spatial distribution of soil fungi (with a special focus on mycorrhizal fungi). The review also tries to identify the field frontier where further studies are needed. The main drivers of soil fungal distribution were classified and reviewed into three groups: soil properties, plant interactions, and dispersal vectors. It was apparent that ectomycorrhizal and arbuscular fungi are relatively overrepresented in the body of research, while the other mycorrhiza types and endophytes were grossly omitted. Notwithstanding, soil pH and the share of ectomycorrhizal plants in the plant coverage were repeatedly reported as strong predictors of mycorrhizal fungal distribution. Dispersal potential and vector preferences show more variation among fungi, especially when considering long-distance dispersal. Additionally, special attention was given to the applications of the island biogeography theory to soil fungal assemblages. This theory proves to be a very efficient framework for analyzing and understanding not only the soil fungal communities of real islands but even more effective islands, i.e., isolated habitats, such as patches of trees discontinuous from more enormous forests.
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Dusengemungu L, Gwanama C, Simuchimba G, Mubemba B. Potential of bioaugmentation of heavy metal contaminated soils in the Zambian Copperbelt using autochthonous filamentous fungi. Front Microbiol 2022; 13:1045671. [PMID: 36532421 PMCID: PMC9752026 DOI: 10.3389/fmicb.2022.1045671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2023] Open
Abstract
There is great potential to remediate heavy metal contaminated environments through bioaugmentation with filamentous fungi. However, these fungi have been poorly investigated in most developing countries, such as Zambia. Therefore, the present study aimed at isolating indigenous filamentous fungi from heavy metal contaminated soil and to explore their potential for use in bioaugmentation. The conventional streak plate method was used to isolate fungi from heavy metal-contaminated soil. Filamentous fungal isolates were identified using morphological and molecular techniques. The radial growth diameter technique was used to evaluate heavy metal tolerance of the fungi. The most abundant and highly tolerant fungi, identified as Aspergillus transmontanensis, Cladosporium cladosporioides, and Geotrichum candidum species, were used to bioremediate heavy metal contaminated soil samples with uncontaminated soil sample being employed as a control. A maximum tolerance index (TI) between 0.7 and 11.0 was observed for A. transmontanensis, and G. candidum while C. cladosporioides displayed the TI between 0.2 and 1.2 in the presence of 1,000 ppm of Cu, Co, Fe, Mn, and Zn. The interspecific interaction was analyzed to determine the compatibility among isolates. Our results showed mutual intermingling between the three evaluated fungal species, which confirms their common influence in biomineralization of heavy metals in contaminated soils. Maximum bio-removal capacities after 90 days were 72% for Cu, 99.8% for Co, 60.6% for Fe, 82.2% for Mn, and 100% for both Pb and Zn. This study has demonstrated the potential of highly resistant autochthonous fungal isolates to remediate the heavy metal contamination problem.
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Affiliation(s)
- Leonce Dusengemungu
- School of Mathematics and Natural Sciences, The Copperbelt University, Kitwe, Zambia
- Africa Centre of Excellence for Sustainable Mining, The Copperbelt University, Kitwe, Zambia
| | - Cousins Gwanama
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Grant Simuchimba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
| | - Benjamin Mubemba
- School of Natural Resources, The Copperbelt University, Kitwe, Zambia
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Fox A, Widmer F, Lüscher A. Soil microbial community structures are shaped by agricultural systems revealing little temporal variation. ENVIRONMENTAL RESEARCH 2022; 214:113915. [PMID: 35940233 PMCID: PMC9492858 DOI: 10.1016/j.envres.2022.113915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Many studies in soil microbial ecology are undertaken with a single sampling event, with the influence of temporal progression rarely being considered. Under field conditions, soil samples were taken from different agricultural systems; a sown grassland to maize rotation (MC), an intensively managed permanent grassland (INT), as well as extensively managed permanent grasslands with high (EXT_HP), low to sufficient (EXT_LP) and deficient available P (EXT_DP), six times throughout the 2017 growing season. Thus, this study aimed to determine if any differences in soil microbiome structures between both sharply contrasting (MC - INT - EXT), slightly differing (EXT_HP - EXT_DP) and quite similar (EXT_HP - EXT_LP and EXT_LP - EXT_DP) agricultural systems persist through changing growth conditions within the growing season. For both fungal and bacterial community structure, the influence of agricultural system (CV = 0.256, P < 0.001 and CV = 0.145, P < 0.01, respectively) was much greater than that of temporal progression (√CV = 0.065 and 0.042, respectively, both P < 0.001). Importantly, nearly all agricultural systems persistently harbored significantly distinct fungal community structures across each of the six sampling events (all at least P < 0.05). There were not as many pairwise differences in bacterial community structure between the agricultural systems, but some did persist (MC and EXT_HP ∼ EXT_DP, all P < 0.001). Additionally, persistent indicator fungal OTUs (IndVal >0.7, P ≤ 0.05) associated to each agricultural system (except EXT_LP) were found in each of the six sampling events. These results highlight the temporal stability of pairwise differences in soil microbiome structures between established agricultural systems through changing plant growth conditions, even between those with a comparable management regime. This is a highly relevant finding in informing the sampling strategy of studies in soil microbial ecology as well as for designing efficient soil biodiversity monitoring systems.
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Affiliation(s)
- A Fox
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland; Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - F Widmer
- Molecular Ecology, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - A Lüscher
- Forage Production and Grassland Systems, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
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Salomon MJ, Watts-Williams SJ, McLaughlin MJ, Cavagnaro TR. Spatiotemporal dynamics of soil health in urban agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150224. [PMID: 34818789 DOI: 10.1016/j.scitotenv.2021.150224] [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: 05/10/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
There is a paucity of data on the state of urban agriculture soils. In order to develop efficient management practices, it is necessary to understand the seasonal dynamics of the soil health of these systems. This study sampled two community gardens, and one commercial urban agriculture site on a monthly basis over the span of one year. The dynamic analysis examined soil nutritional, chemical and microbial properties. Plant biodiversity was significantly higher in community gardens compared to commercial sites. Analysis of soil nutrients revealed fluctuations of mineral nitrogen with seasonal conditions and consistently high concentrations of plant-available phosphorus. We identified gradually decreasing soil total nitrogen and carbon concentrations throughout the year. Soils were abundant in arbuscular mycorrhizal fungi spores. Soil metabarcoding using 16S and ITS amplicons revealed a seasonal gradient of the microbial diversity and changes after the application of organic fertilizer. Soil-borne potential human pathogens were also detected in the soils. The results of this study provide relevant information about soil management principles in urban agriculture systems. These principles include mulching and the use of nutrient-balanced composts to counteract decreasing carbon pools and the excessive accumulation of phosphorus.
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Affiliation(s)
- M J Salomon
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064, Australia.
| | - S J Watts-Williams
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064, Australia
| | - M J McLaughlin
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064, Australia
| | - T R Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA 5064, Australia
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Chen X, Zhang Z, Han X, Hao X, Lu X, Yan J, Biswas A, Dunfield K, Zou W. Impacts of land-use changes on the variability of microbiomes in soil profiles. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5056-5066. [PMID: 33570760 DOI: 10.1002/jsfa.11150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The conversion of arable land to grassland and/or forested land is a common strategy of restoration because the development of plant communities can inhibit the erosion of soil, increase biodiversity and improve associated ecosystem services. The vertical profiles of microbial communities, however, have not been well characterized and their variability after land conversion is not well understood. We assessed the effects of the conversion of arable land (AL) to grassland (GL) and forested land (FL) on bacterial communities as old as 29 years in 0-200-cm profiles of a Chinese Mollisol. RESULTS The soil in AL has been a stable ecosystem and changes in the assembly of soil microbiomes tended to be larger in the topsoil. The soil properties and microbial biodiversity of arable land were larger following revegetation and reforestation. The conversion caused a more complex coupling among microbes, and negative interactions and average connectivity were stronger in the 0-20-cm layers in GL and in the 20-60-cm layers in FL. The land use dramatically influenced the assembly of the microbial communities more in GL than AL and FL. The bacterial diversity was an important component of soil multinutrient cycling in the profiles and microbial functions were not as affected by changes in land use. CONCLUSION The spatial variation of the microbiomes provided critical information on below-ground soil ecology and the ability of the soil to provide crucial ecosystem services. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Xu Chen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhiming Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaozeng Han
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiangxiang Hao
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xinchun Lu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Asim Biswas
- School of Environmental Sciences, University of Gulph, Ottawa, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Gulph, Ottawa, Canada
| | - Wenxiu Zou
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Heklau H, Schindler N, Buscot F, Eisenhauer N, Ferlian O, Prada Salcedo LD, Bruelheide H. Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners. Ecol Evol 2021; 11:5424-5440. [PMID: 34026018 PMCID: PMC8131788 DOI: 10.1002/ece3.7437] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/22/2021] [Accepted: 02/26/2021] [Indexed: 11/29/2022] Open
Abstract
Recent studies found that the majority of shrub and tree species are associated with both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungi. However, our knowledge on how different mycorrhizal types interact with each other is still limited. We asked whether the combination of hosts with a preferred association with either AM or EM fungi increases the host tree roots' mycorrhization rate and affects AM and EM fungal richness and community composition.We established a tree diversity experiment, where five tree species of each of the two mycorrhiza types were planted in monocultures, two-species and four-species mixtures. We applied morphological assessment to estimate mycorrhization rates and next-generation molecular sequencing to quantify mycobiont richness.Both the morphological and molecular assessment revealed dual-mycorrhizal colonization in 79% and 100% of the samples, respectively. OTU community composition strongly differed between AM and EM trees. While host tree species richness did not affect mycorrhization rates, we observed significant effects of mixing AM- and EM-associated hosts in AM mycorrhization rate. Glomeromycota richness was larger in monotypic AM tree combinations than in AM-EM mixtures, pointing to a dilution or suppression effect of AM by EM trees. We found a strong match between morphological quantification of AM mycorrhization rate and Glomeromycota richness. Synthesis. We provide evidence that the combination of hosts differing in their preferred mycorrhiza association affects the host's fungal community composition, thus revealing important biotic interactions among trees and their associated fungi.
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Affiliation(s)
- Heike Heklau
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Nicole Schindler
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - François Buscot
- Department of Soil EcologyHelmholtz Centre for Environmental Research – UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Luis D. Prada Salcedo
- Department of Soil EcologyHelmholtz Centre for Environmental Research – UFZHalle (Saale)Germany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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Lumibao CY, Kimbrough ER, Day RH, Conner WH, Krauss KW, Van Bael SA. Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients. FEMS Microbiol Ecol 2020; 96:5860278. [PMID: 32562419 DOI: 10.1093/femsec/fiaa124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Plant roots assemble in two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi, unlike rhizosphere fungi, were correlated with host density and canopy cover, suggesting that hosts can impose selective filters on fungi colonizing their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns, e.g. highest endosphere diversity (hump-shaped) and lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure of the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.
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Affiliation(s)
- Candice Y Lumibao
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Elizabeth R Kimbrough
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Richard H Day
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA, 70506, USA
| | - William H Conner
- Baruch Institute of Coastal Ecology and Forest Science, Clemson University, P.O. Box 596, Georgetown, SC, 29442, USA
| | - Ken W Krauss
- U.S. Geological Survey, Wetland and Aquatic Research Center, 700 Cajundome Blvd., Lafayette, LA, 70506, USA
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
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Legacy Effects Overshadow Tree Diversity Effects on Soil Fungal Communities in Oil Palm-Enrichment Plantations. Microorganisms 2020; 8:microorganisms8101577. [PMID: 33066264 PMCID: PMC7656304 DOI: 10.3390/microorganisms8101577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 11/24/2022] Open
Abstract
Financially profitable large-scale cultivation of oil palm monocultures in previously diverse tropical rain forest areas constitutes a major ecological crisis today. Not only is a large proportion of the aboveground diversity lost, but the belowground soil microbiome, which is important for the sustainability of soil function, is massively altered. Intermixing oil palms with native tree species promotes vegetation biodiversity and stand structural complexity in plantations, but the impact on soil fungi remains unknown. Here, we analyzed the diversity and community composition of soil fungi three years after tree diversity enrichment in an oil palm plantation in Sumatra (Indonesia). We tested the effects of tree diversity, stand structural complexity indices, and soil abiotic conditions on the diversity and community composition of soil fungi. We hypothesized that the enrichment experiment alters the taxonomic and functional community composition, promoting soil fungal diversity. Fungal community composition was affected by soil abiotic conditions (pH, N, and P), but not by tree diversity and stand structural complexity indices. These results suggest that intensive land use and abiotic filters are a legacy to fungal communities, overshadowing the structuring effects of the vegetation, at least in the initial years after enrichment plantings.
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Comparative Toxicity Assessment of Soil Fungi Isolated from Black Sea Coasts. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00745-x] [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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Pecoraro L, Wang X, Venturella G, Gao W, Wen T, Gafforov Y, Gupta VK. Molecular evidence supports simultaneous association of the achlorophyllous orchid Chamaegastrodia inverta with ectomycorrhizal Ceratobasidiaceae and Russulaceae. BMC Microbiol 2020; 20:236. [PMID: 32746782 PMCID: PMC7397628 DOI: 10.1186/s12866-020-01906-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/14/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Achlorophyllous orchids are mycoheterotrophic plants, which lack photosynthetic ability and associate with fungi to acquire carbon from different environmental sources. In tropical latitudes, achlorophyllous forest orchids show a preference to establish mycorrhizal relationships with saprotrophic fungi. However, a few of them have been recently found to associate with ectomycorrhizal fungi and there is still much to be learned about the identity of fungi associated with tropical orchids. The present study focused on mycorrhizal diversity in the achlorophyllous orchid C. inverta, an endangered species, which is endemic to southern China. The aim of this work was to identify the main mycorrhizal partners of C. inverta in different plant life stages, by means of morphological and molecular methods. RESULTS Microscopy showed that the roots of analysed C. inverta samples were extensively colonized by fungal hyphae forming pelotons in root cortical cells. Fungal ITS regions were amplified by polymerase chain reaction, from DNA extracted from fungal mycelia isolated from orchid root samples, as well as from total root DNA. Molecular sequencing and phylogenetic analyses showed that the investigated orchid primarily associated with ectomycorrhizal fungi belonging to a narrow clade within the family Ceratobasidiaceae, which was previously detected in a few fully mycoheterotrophic orchids and was also found to show ectomycorrhizal capability on trees and shrubs. Russulaceae fungal symbionts, showing high similarity with members of the ectomycorrhizal genus Russula, were also identified from the roots of C. inverta, at young seedling stage. Ascomycetous fungi including Chaetomium, Diaporthe, Leptodontidium, and Phomopsis genera, and zygomycetes in the genus Mortierella were obtained from orchid root isolated strains with unclear functional role. CONCLUSIONS This study represents the first assessment of root fungal diversity in the rare, cryptic and narrowly distributed Chinese orchid C. inverta. Our results provide new insights on the spectrum of orchid-fungus symbiosis suggesting an unprecedented mixed association between the studied achlorophyllous forest orchid and ectomycorrhizal fungi belonging to Ceratobasidiaceae and Russulaceae. Ceratobasidioid fungi as dominant associates in the roots of C. inverta represent a new record of the rare association between the identified fungal group and fully mycoheterotrophic orchids in nature.
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Affiliation(s)
- Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
| | - Xiao Wang
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Giuseppe Venturella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Tingchi Wen
- The Engineering Research Center of Southwest Bio-Pharmaceutical Resources, Ministry of Education, Guizhou University, Guiyang, China
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Vijai Kumar Gupta
- AgroBioSciences and Chemical & Biochemical Sciences Department, University Mohammed VI Polytechnic, Hay Moulay Rachid, Ben Guerir, Morocco
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13
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Abstract
Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton–maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini–Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen’s Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70–1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management.
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Gupta P, Vakhlu J, Sharma YP, Imchen M, Kumavath R. Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert. Extremophiles 2020; 24:749-758. [PMID: 32705341 DOI: 10.1007/s00792-020-01191-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.
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Affiliation(s)
- Puja Gupta
- School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
| | - Yash Pal Sharma
- Department of Botany, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Kasaragod, Periya, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Kasaragod, Periya, 671320, India.
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15
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Li X, Wang H, Li X, Li X, Zhang H. Distribution characteristics of fungal communities with depth in paddy fields of three soil types in China. J Microbiol 2020; 58:279-287. [PMID: 32103445 DOI: 10.1007/s12275-020-9409-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/17/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022]
Abstract
Little is known about the distribution of fungal communities with soil depth on relatively large scales. In this study, typical paddy soils in three regions (Hailun, Changshu, and Yingtan) from north to south China were selected to investigate the vertical distribution (0-100 cm) of the fungal community by Illumina MiSeq sequencing, and to identify the main factors influencing the fungal community distribution. The results indicated that the structure of the soil fungal community changed significantly with region and soil depth. Soil fungal taxa such as Zygomycota, Glomeromycota, Saccharomycete, Kazachstania, Mortierella, Massariosphaeria, Hypholoma, and Zopfiella were enriched at depths of 0-20 cm, whereas Dothideomycetes, Microbotryomycetes, Tremellomycetes, Sporobolomyces, Cryptococcus, Rhodotorula, Fusarium, and Pyrenochaetopsis had high relative abundances at 80-100 cm. Variance partitioning analysis indicated that the geographic distance contributed more to the fungal community variation than environmental variables on a large scale. In addition, soil total carbon and nitrogen contents were the main environmental factors driving the vertical distribution of the fungal community in paddy soils.
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Affiliation(s)
- Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China
| | - Huanhuan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.,Graduate University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China.
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, P. R. China
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16
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Upton RN, Checinska Sielaff A, Hofmockel KS, Xu X, Polley HW, Wilsey BJ. Soil depth and grassland origin cooperatively shape microbial community co‐occurrence and function. Ecosphere 2020. [DOI: 10.1002/ecs2.2973] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Racheal N. Upton
- Department of Ecology, Evolution and Organismal Biology Iowa State University Ames Iowa 50011 USA
| | | | - Kirsten S. Hofmockel
- Department of Ecology, Evolution and Organismal Biology Iowa State University Ames Iowa 50011 USA
- Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richmond Washington 99354 USA
| | - Xia Xu
- Department of Ecology, Evolution and Organismal Biology Iowa State University Ames Iowa 50011 USA
| | - H. Wayne Polley
- USDA‐Agricultural Research Service Grassland Soil and Water Research Laboratory Temple Texas 76502 USA
| | - Brian J. Wilsey
- Department of Ecology, Evolution and Organismal Biology Iowa State University Ames Iowa 50011 USA
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17
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Schreiner RP. Depth structures the community of arbuscular mycorrhizal fungi amplified from grapevine (Vitis vinifera L.) roots. MYCORRHIZA 2020; 30:149-160. [PMID: 31993741 DOI: 10.1007/s00572-020-00930-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
The diversity of arbuscular mycorrhizal fungi (AMF) associating with grapevines has been determined previously, yet little is known of how the community in roots is shaped by depth in the soil or where roots occur in different management zones of the vineyard (vine row versus alley). The influence of depth, management zone, and time of year on the community of AMF in grape roots was examined. I also tested the potential influence of the alley vegetation on AMF in grapevines by comparing the taxa amplified from roots of other plants retrieved from the alley surface soil to those from grapevines growing in the same zone. Depth shaped the AMF community in grapevine roots more than the management zone based on dissimilarity among all grapevine samples. Time of the growing season did not, although AMF taxa richness was greater in grapevine roots collected in late summer (veraison) than it was in late spring (bloom). The number of abundant AMF taxa in grapevine roots from the uppermost soil depth in the vine row was substantially lower in late spring than in late summer, and this was related to high soil nitrate in late spring. The alley vegetation comprised primarily grass, and clover plants harbored a different AMF community in roots than did intermingled grapevine roots. The change in the AMF community in a single perennial host (grape) that occurred with depth in this study resulted from a shift among common taxa as opposed to the appearance of unique taxa in the subsoil.
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Affiliation(s)
- R Paul Schreiner
- USDA-ARS, Horticultural Crops Research Laboratory, 3420 NW Orchard Avenue, Corvallis, Oregon, 97330, USA.
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18
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Chen YP, Liaw LL, Kuo JT, Wu HT, Wang GH, Chen XQ, Tsai CF, Young CC. Evaluation of synthetic gene encoding α-galactosidase through metagenomic sequencing of paddy soil. J Biosci Bioeng 2019; 128:274-282. [DOI: 10.1016/j.jbiosc.2019.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/23/2019] [Accepted: 03/09/2019] [Indexed: 12/18/2022]
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19
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Vadkertiová R, Dudášová H, Stratilová E, Balaščáková M. Diversity of yeasts in the soil adjacent to fruit trees of the Rosaceae family. Yeast 2019; 36:617-631. [PMID: 31313345 DOI: 10.1002/yea.3430] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/16/2019] [Accepted: 06/30/2019] [Indexed: 01/01/2023] Open
Abstract
Yeasts are common constituents of different types of soil. Their diversity depends on the season, the type and depth of the soil, the plant species, and the locality. In this study, diversity of yeasts isolated from the soil adjacent to five fruit trees (apple, appricot, peach, pear, and plum) in two localities (in Slovakia) in four sampling periods was examined. Our results demonstrated differences in the species richness and evenness among the yeast populations, which inhabited the soil beneath individual fruit tree species in both localities. Altogether, 32 ascomycetous and 27 basidiomycetous yeast species were discovered. The highest species richness was found in the soil adjacent to the apricot trees. Galactomyces candidum, Metschnikowia pulcherrima, Hanseniaspora uvarum, Schwanniomyces capriottii, and Tausonia pullulans, as well as the genus Apiotrichum, were present in soil samples in all samplings. Two species of the genus Holtermanniella (H. festucosa and H. takashimae) were exclusively isolated during Sampling IV in April. Cyberlindnera spp., Clavispora reshetovae, S. capriottii, and Trichosporon asahii were found only in one of two localities. Ascomycetous yeasts were present more frequently than their basidiomycetous counterparts in the three samplings (one in June and two in October); they formed from 65.6% to 70.8% of the total yeast population, whereas basidiomycetous yeasts prevailed in the April sampling (61.2%).
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Affiliation(s)
- Renáta Vadkertiová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Hana Dudášová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eva Stratilová
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marta Balaščáková
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
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20
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Samet M, Karray F, Mhiri N, Kamoun L, Sayadi S, Gargouri-Bouzid R. Effect of phosphogypsum addition in the composting process on the physico-chemical proprieties and the microbial diversity of the resulting compost tea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:21404-21415. [PMID: 31124074 DOI: 10.1007/s11356-019-05327-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Phosphoric acid production and olive oil production are among the most important economical sectors in Tunisia. However, they generate huge amounts of wastes (phosphogypsum, olive mill waste water, and olive pomace). In a previous study, we used phosphogypsum (PG), in co-composting with organic wastes. Three composts were produced; their PG content was of 0 (AT), 10 (A10), and 30% (A30). In the present study, we focused on their derived compost teas. The physico-chemical characterization of the different compost teas showed that those from A10 and A30 composts presented higher P and Ca contents than that from control one (AT). The microbial characterization using DGGE showed a noticeable microbial diversity in the different compost teas and that the addition of 10% and 30% PG in the compost had different effects on the compost tea microbial diversity. The identification results showed that the addition of 10 and 30% of PG did not affect the presence of PGPR (plant growth-promoting rhizobacteria) and fungal soil antagonists in the compost teas. Two PGPRs were isolated from AT and A30 compost teas, and their effect on the growth of potato plants in vitro was evaluated.
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Affiliation(s)
- Mariem Samet
- Laboratoire d'Amélioration des Plantes et Valorisation des Agro-ressources, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038, Sfax, Tunisia.
| | - Fatma Karray
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Najla Mhiri
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Lotfi Kamoun
- Groupe Chimique Tunisien, Direction de la Recherche Scientifique, Route de Gabes km 3,5, 3000, Sfax, Tunisia
| | - Sami Sayadi
- Laboratoire des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia
| | - Radhia Gargouri-Bouzid
- Laboratoire d'Amélioration des Plantes et Valorisation des Agro-ressources, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, B.P 1173, 3038, Sfax, Tunisia
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21
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Sosa-Hernández MA, Leifheit EF, Ingraffia R, Rillig MC. Subsoil Arbuscular Mycorrhizal Fungi for Sustainability and Climate-Smart Agriculture: A Solution Right Under Our Feet? Front Microbiol 2019; 10:744. [PMID: 31031726 PMCID: PMC6473167 DOI: 10.3389/fmicb.2019.00744] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022] Open
Abstract
With growing populations and climate change, assuring food and nutrition security is an increasingly challenging task. Climate-smart and sustainable agriculture, that is, conceiving agriculture to be resistant and resilient to a changing climate while keeping it viable in the long term, is probably the best solution. The role of soil biota and particularly arbuscular mycorrhizal (AM) fungi in this new agriculture is believed to be of paramount importance. However, the large nutrient pools and the microbiota of subsoils are rarely considered in the equation. Here we explore the potential contributions of subsoil AM fungi to a reduced and more efficient fertilization, carbon sequestration, and reduction of greenhouse gas emissions in agriculture. We discuss the use of crop rotations and cover cropping with deep rooting mycorrhizal plants, and low-disturbance management, as means of fostering subsoil AM communities. Finally, we suggest future research goals that would allow us to maximize these benefits.
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Affiliation(s)
- Moisés A. Sosa-Hernández
- Plant Ecology, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Eva F. Leifheit
- Plant Ecology, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Rosolino Ingraffia
- Department of Agricultural, Food and Forestry Sciences, Università di Palermo, Palermo, Italy
| | - Matthias C. Rillig
- Plant Ecology, Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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22
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Yurkov AM, Kurtzman CP. Three new species of Tremellomycetes isolated from maize and northern wild rice. FEMS Yeast Res 2019; 19:5289409. [DOI: 10.1093/femsyr/foz004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/09/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL, USA
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23
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Al-Sadi AM, Kazerooni EA. Illumina-MiSeq analysis of fungi in acid lime roots reveals dominance of Fusarium and variation in fungal taxa. Sci Rep 2018; 8:17388. [PMID: 30478417 PMCID: PMC6255777 DOI: 10.1038/s41598-018-35404-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/05/2018] [Indexed: 11/08/2022] Open
Abstract
A study was conducted to analyze fungal diversity in the roots of acid lime (Citrus aurantifolia) collected from Oman, a semi-arid country located in the South Eastern part of the Arabian Peninsula. MiSeq analysis showed the Ascomycota and Sordariomycetes were the most abundant phylum and class in acid lime roots, respectively. Glomeromycota, Basidiomycota and Microsporidia were the other fungal phyla, while Glomeromycetes and some other classes belonging to Ascomycota and Basidiomycota were detected at lower frequencies. The genus Fusarium was the most abundant in all samples, making up 46 to 95% of the total reads. Some fungal genera of Arbuscular mycorrhizae and nematophagous fungi were detected in some of the acid lime roots. Analysis of the level of fungal diversity showed that no significant differences exist among groups of root samples (from different locations) in their Chao richness and Shannon diversity levels (P < 0.05). Principle component analysis of fungal communities significantly separated samples according to their locations. This is the first study to evaluate fungal diversity in acid lime roots using high throughput sequencing analysis. The study reveals the presence of various fungal taxa in the roots, dominated by Fusarium species and including some mycorrhizae and nematophagous fungi.
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Affiliation(s)
- Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Oman, PO Box 34, Alkhoud, 123, Oman.
| | - Elham A Kazerooni
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Oman, PO Box 34, Alkhoud, 123, Oman
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24
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Vidal S, Brandt BW, Dettwiler M, Abril C, Bressan J, Greub G, Frey CF, Perreten V, Rodriguez-Campos S. Limited added value of fungal ITS amplicon sequencing in the study of bovine abortion. Heliyon 2018; 4:e00915. [PMID: 30426108 PMCID: PMC6222074 DOI: 10.1016/j.heliyon.2018.e00915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/28/2018] [Accepted: 10/31/2018] [Indexed: 11/29/2022] Open
Abstract
Bovine mycotic abortion is sporadic and caused by different ubiquitous and opportunistic fungi. Recently, a broad spectrum of bacterial opportunists involved in bovine abortion was revealed by 16S rRNA gene amplicon sequencing. We hypothesized that fungal organisms potentially involved in bovine abortion also might remain undetected by conventional culture. In this retrospective study, we therefore applied fungal internal transcribed spacer 2 (ITS2) region amplicon sequencing to 74 cases of bovine abortion submitted to our diagnostic service. The investigation was complemented by fungal culture and, retrospectively, by data from bacteriological, virological and parasitological analyses and histopathological examination of placentas. Fungal DNA was found in both the placentas and abomasal contents, with 92 fungal genera identified. In 18 cases, >75% of the reads belonged to one specific fungal genus: Candida (n = 7), Malassezia (n = 4), Cryptococcus (n = 3), unidentified Capnodiales (n = 3), Actinomucor (n = 1), Cystofilobasidium (n = 1), Penicillium (n = 1), Verticillum (n = 1) and Zymoseptoria (n = 1) with one case harboring two different genera. By culture, in contrast, fungal agents were detected in only 6 cases. Inflammatory and/or necrotizing lesions were found in 27/40 histologically assessed placentas. However, no lesion-associated fungal structures were detected in HE- and PAS-stained specimens. Complementary data revealed the presence of one or more non-fungal possible abortifacient: Chlamydiales, Coxiella burnetii, Leptospira spp., Campylobacter fetus subsp. fetus, Streptococcus uberis, Escherichia coli, Streptococcus pluranimalium, Bacillus licheniformis, Campylobacter fetus subsp. fetus, Serratia marcescens, Trueperella pyogenes, Schmallenbergvirus, Neospora caninum. The mycobiota revealed by sequencing did not differ between cases with or without a possible infectious etiology. Our study suggests that amplicon sequencing of the ITS2 region from DNA isolated from bovine abortion does not provide additional information or new insight into mycotic abortion and without complementary analyses may easily lead to a false interpretation of the role of fungal organisms in bovine abortion.
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Affiliation(s)
- Sara Vidal
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Bernd W. Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, the Netherlands
| | - Martina Dettwiler
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Jenny Bressan
- Department of Neurology, Bern University Hospital and University of Bern, Freiburgstrasse, CH-3010 Bern, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center and University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland
| | - Caroline F. Frey
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
| | - Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, CH-3012 Bern, Switzerland
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Guo Y, Chen X, Wu Y, Zhang L, Cheng J, Wei G, Lin Y. Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:598-606. [PMID: 29679832 DOI: 10.1016/j.scitotenv.2018.04.171] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 05/20/2023]
Abstract
Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems.
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Affiliation(s)
- Yanqing Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaotian Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yuanyuan Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jimin Cheng
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi 712100, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Yanbing Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Hugoni M, Luis P, Guyonnet J, Haichar FEZ. Plant host habitat and root exudates shape fungal diversity. MYCORRHIZA 2018; 28:451-463. [PMID: 30109473 DOI: 10.1007/s00572-018-0857-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/25/2018] [Indexed: 05/06/2023]
Abstract
The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.
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Affiliation(s)
- Mylène Hugoni
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Patricia Luis
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Julien Guyonnet
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Feth El Zahar Haichar
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France.
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Wei Z, Liu Y, Feng K, Li S, Wang S, Jin D, Zhang Y, Chen H, Yin H, Xu M, Deng Y. The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:969-978. [PMID: 30045585 DOI: 10.1016/j.scitotenv.2018.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 05/13/2023]
Abstract
In this study, quantitative PCR (qPCR) and high-throughput sequencing were used to simultaneously examine both bacteria and fungi across temporal and spatial scales in activated sludge from wastewater treatment plants (WWTPs). The ratio of fungi to bacteria was 0.43% on average after accounting for the multicopies in 16S rRNA gene (54.63%), indicating the number of fungi was far lower than bacteria in active sludge. The Miseq sequencing results revealed obvious seasonal and spatial variations in bacterial and fungal distribution patterns in WWTPs. Compared to bacteria, fungi showed a lower divergence in alpha and beta diversity, and exhibited less taxonomic diversity in both abundant and rare subcommunities at the class level, suggesting that the fungal community was less variable in this artificial ecosystem. Such variation of microbial communities was significantly correlated with geographical distance, DO, temperature, HRT, SRT, COD, TN and TP. In activated sludge, the main function of bacteria was chemoheterotrophy, fermentation, and nitrogen cycling processes, while the dominant functional guilds of fungi were saprotroph, animal pathogen, and animal endosymbiont. Moreover, both bacteria and fungi could play important roles in the degradation of toxicants, like hydrocarbon and aromatic compounds.
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Affiliation(s)
- Ziyan Wei
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangying Liu
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuzhen Li
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shang Wang
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongrui Chen
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Zimudzi J, van der Waals JE, Coutinho TA, Cowan DA, Valverde A. Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields. Fungal Biol 2018; 122:928-934. [PMID: 30115327 DOI: 10.1016/j.funbio.2018.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.
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Affiliation(s)
- Josephine Zimudzi
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Teresa A Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa; Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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Osborne SJ, McMillan VE, White R, Hammond-Kosack KE. Elite UK winter wheat cultivars differ in their ability to support the colonization of beneficial root-infecting fungi. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3103-3115. [PMID: 29648609 PMCID: PMC5972604 DOI: 10.1093/jxb/ery136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
In numerous countries, Gaeumannomyces species, within the Magnaporthaceae family, have previously been implicated in the suppression of take-all root disease in wheat. A UK arable isolate collection (n=47) was gathered and shown to contain Gaeumannomyces hyphopodioides and an unnamed Magnaporthaceae species. A novel seedling pot bioassay revealed that both species had a similar ability to colonize cereal roots; however, rye (Secale cereale) was only poorly colonized by the Magnaporthaceae species. To evaluate the ability of 40 elite UK winter wheat cultivars to support soil inoculum of beneficial soil-dwelling fungi, two field experiments were carried out using a naturally infested arable site in south-east England. The elite cultivars grown in the first wheat situation differed in their ability to support G. hyphopodioides inoculum, measured by colonization on Hereward as the subsequent wheat in a seedling soil core bioassay. In addition, the root colonization ability of G. hyphopodioides was influenced by the choice of the second wheat cultivar. Nine cultivars supported the colonization of the beneficial root fungus. Our findings provide evidence of complex host genotype-G. hyphopodioides interactions occurring under field conditions. This new knowledge could provide an additional soil-based crop genetic management strategy to help combat take-all root disease.
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Affiliation(s)
- Sarah-Jane Osborne
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Vanessa E McMillan
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Rodger White
- Department of Computational and Analytical Systems, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
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30
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Schmidt CS, Mrnka L, Frantík T, Lovecká P, Vosátka M. Plant growth promotion of Miscanthus × giganteus by endophytic bacteria and fungi on non-polluted and polluted soils. World J Microbiol Biotechnol 2018. [DOI: 10.1007/s11274-018-2426-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Keiblinger KM, Schneider M, Gorfer M, Paumann M, Deltedesco E, Berger H, Jöchlinger L, Mentler A, Zechmeister-Boltenstern S, Soja G, Zehetner F. Assessment of Cu applications in two contrasting soils-effects on soil microbial activity and the fungal community structure. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:217-233. [PMID: 29297133 PMCID: PMC5847031 DOI: 10.1007/s10646-017-1888-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/12/2017] [Indexed: 05/20/2023]
Abstract
Copper (Cu)-based fungicides have been used in viticulture to prevent downy mildew since the end of the 19th century, and are still used today to reduce fungal diseases. Consequently, Cu has built up in many vineyard soils, and it is still unclear how this affects soil functioning. The present study aimed to assess the short and medium-term effects of Cu contamination on the soil fungal community. Two contrasting agricultural soils, an acidic sandy loam and an alkaline silt loam, were used for an eco-toxicological greenhouse pot experiment. The soils were spiked with a Cu-based fungicide in seven concentrations (0-5000 mg Cu kg-1 soil) and alfalfa was grown in the pots for 3 months. Sampling was conducted at the beginning and at the end of the study period to test Cu toxicity effects on total microbial biomass, basal respiration and enzyme activities. Fungal abundance was analysed by ergosterol at both samplings, and for the second sampling, fungal community structure was evaluated via ITS amplicon sequences. Soil microbial biomass C as well as microbial respiration rate decreased with increasing Cu concentrations, with EC50 ranging from 76 to 187 mg EDTA-extractable Cu kg-1 soil. Oxidative enzymes showed a trend of increasing activity at the first sampling, but a decline in peroxidase activity was observed for the second sampling. We found remarkable Cu-induced changes in fungal community abundance (EC50 ranging from 9.2 to 94 mg EDTA-extractable Cu kg-1 soil) and composition, but not in diversity. A large number of diverse fungi were able to thrive under elevated Cu concentrations, though within the order of Hypocreales several species declined. A remarkable Cu-induced change in the community composition was found, which depended on the soil properties and, hence, on Cu availability.
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Affiliation(s)
- Katharina M Keiblinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Martin Schneider
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Markus Gorfer
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | - Melanie Paumann
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Evi Deltedesco
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Business Unit Bioresources, Tulln, Austria
| | | | - Lisa Jöchlinger
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Axel Mentler
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Gerhard Soja
- AIT Austrian Institute of Technology, Center for Energy, Business Unit Environmental Resources & Technologies, Tulln, Austria
| | - Franz Zehetner
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
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Al-Bulushi IM, Bani-Uraba MS, Guizani NS, Al-Khusaibi MK, Al-Sadi AM. Illumina MiSeq sequencing analysis of fungal diversity in stored dates. BMC Microbiol 2017; 17:72. [PMID: 28347268 PMCID: PMC5369213 DOI: 10.1186/s12866-017-0985-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/17/2017] [Indexed: 12/05/2022] Open
Abstract
Background Date palm has been a major fruit tree in the Middle East over thousands of years, especially in the Arabian Peninsula. Dates are consumed fresh (Rutab) or after partial drying and storage (Tamar) during off-season. The aim of the study was to provide in-depth analysis of fungal communities associated with the skin (outer part) and mesocarp (inner fleshy part) of stored dates (Tamar) of two cultivars (Khenizi and Burny) through the use of Illumina MiSeq sequencing. Results The study revealed the dominance of Ascomycota (94%) in both cultivars, followed by Chytridiomycota (4%) and Zygomycota (2%). Among the classes recovered, Eurotiomycetes, Dothideomycetes, Saccharomycetes and Sordariomycetes were the most dominant. A total of 54 fungal species were detected, with species belonging to Penicillium, Alternaria, Cladosporium and Aspergillus comprising more than 60% of the fungal reads. Some potentially mycotoxin-producing fungi were detected in stored dates, including Aspergillus flavus, A. versicolor and Penicillium citrinum, but their relative abundance was very limited (<0.5%). PerMANOVA analysis revealed the presence of insignificant differences in fungal communities between date parts or date cultivars, indicating that fungal species associated with the skin may also be detected in the mesocarp. It also indicates the possible contamination of dates from different cultivars with similar fungal species, even though if they are obtained from different areas. Conclusion The analysis shows the presence of different fungal species in dates. This appears to be the first study to report 25 new fungal species in Oman and 28 new fungal species from date fruits. The study discusses the sources of fungi on dates and the presence of potentially mycotoxin producing fungi on date skin and mesocarp.
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Affiliation(s)
- Ismail M Al-Bulushi
- Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod, 123, Oman
| | - Muna S Bani-Uraba
- Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod, 123, Oman
| | - Nejib S Guizani
- Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod, 123, Oman
| | - Mohammed K Al-Khusaibi
- Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod, 123, Oman
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, P.O. Box-34, Al-Khod, 123, Oman.
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Soil networks become more connected and take up more carbon as nature restoration progresses. Nat Commun 2017; 8:14349. [PMID: 28176768 PMCID: PMC5309817 DOI: 10.1038/ncomms14349] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 12/19/2016] [Indexed: 11/17/2022] Open
Abstract
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered. Effects of habitat restoration on belowground organisms and ecosystem processes are poorly understood. Morriën and colleagues show that changes in the composition and network interactions of soil biota lead to improved carbon uptake efficiency when formerly cultivated land is restored.
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Kramer S, Dibbern D, Moll J, Huenninghaus M, Koller R, Krueger D, Marhan S, Urich T, Wubet T, Bonkowski M, Buscot F, Lueders T, Kandeler E. Resource Partitioning between Bacteria, Fungi, and Protists in the Detritusphere of an Agricultural Soil. Front Microbiol 2016; 7:1524. [PMID: 27725815 PMCID: PMC5035733 DOI: 10.3389/fmicb.2016.01524] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/12/2016] [Indexed: 01/31/2023] Open
Abstract
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
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Affiliation(s)
- Susanne Kramer
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Dörte Dibbern
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany
| | - Maike Huenninghaus
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Robert Koller
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - Dirk Krueger
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-Halle Halle, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
| | - Tim Urich
- Department of Bacterial Physiology, Institute for Microbiology, Ernst-Moritz-Arndt University of Greifswald Greifswald, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne Köln, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research Leipzig-HalleHalle, Germany; Institute of Biology, University of LeipzigLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv)Leipzig, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim Stuttgart, Germany
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Correction: Spatial Distribution of Fungal Communities in an Arable Soil. PLoS One 2016; 11:e0154290. [PMID: 27101303 PMCID: PMC4839759 DOI: 10.1371/journal.pone.0154290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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