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Aranguren R, Voyron S, Ungaro F, Cañón J, Lumini E. Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia. PLANTS (BASEL, SWITZERLAND) 2023; 12:1126. [PMID: 36903986 PMCID: PMC10005449 DOI: 10.3390/plants12051126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.
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Affiliation(s)
- Raul Aranguren
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Samuele Voyron
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
| | - Fabrizio Ungaro
- Institute for Bio-Economy (IBE), National Research Council (CNR), 50018 Florence, Italy
| | - Julio Cañón
- GAIA Research Group, Universidad de Antioquia, Medellín 050010, Colombia
| | - Erica Lumini
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), 10125 Turin, Italy
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2
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Jamy M, Biwer C, Vaulot D, Obiol A, Jing H, Peura S, Massana R, Burki F. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat Ecol Evol 2022; 6:1458-1470. [PMID: 35927316 PMCID: PMC9525238 DOI: 10.1038/s41559-022-01838-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/23/2022] [Indexed: 12/30/2022]
Abstract
The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
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Affiliation(s)
- Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Daniel Vaulot
- CNRS, UMR7144, Team ECOMAP, Station Biologique, Sorbonne Université, Roscoff, France
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Sari Peura
- Department of Ecology and Genetics (Limnology), Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Effects of Plant Fine Root Functional Traits and Soil Nutrients on the Diversity of Rhizosphere Microbial Communities in Tropical Cloud Forests in a Dry Season. FORESTS 2022. [DOI: 10.3390/f13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The composition and diversity of rhizosphere microbial communities may be due to root–soil–microbial interactions. The fine root functional traits and rhizosphere soil environmental factors of 13 representative plants in the Bawangling tropical cloud forest of Hainan Island were measured, to assess the key factors driving plant rhizosphere microbial communities. Illumina MiSeq sequencing technology was used to sequence the v3-V4 region of the 16SrDNA gene of 13 plant rhizosphere soil bacteria and the ITS1 region of the fungal ITSrDNA gene. Results showed that there were 355 families, 638 genera, and 719 species of rhizosphere soil bacteria as well as 29 families, 31 genera, and 31 species of rhizosphere soil fungi in the tropical cloud forests. The fine root traits, such as root phosphorus content, the specific root length and specific root area, were significantly negatively correlated with the Faith-pd indices of the bacterial community but were not correlated with the diversity of fungi communities. The soil pH was significantly and positively correlated with the Chao1 index, OTUs, Faith-pd and Simpson indices of the bacteria and fungi communities. The soil available phosphorus content was significantly and negatively correlated with the bacteria Simpson and the fungus Faith-pd indices. ABT analysis showed that soil pH and soil available phosphorus were the most important environmental conditions contributing to the rhizosphere bacterial and fungi communities, respectively. Our findings demonstrate that the soil environments had more influence on rhizosphere soil microbial diversity than the fine root functional traits.
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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5
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Kirkman ER, Hilton S, Sethuraman G, Elias DMO, Taylor A, Clarkson J, Soh AC, Bass D, Ooi GT, McNamara NP, Bending GD. Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments. Front Microbiol 2022; 13:792928. [PMID: 35222328 PMCID: PMC8874247 DOI: 10.3389/fmicb.2022.792928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.
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Affiliation(s)
- Eleanor R. Kirkman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gomathy Sethuraman
- Crops for the Future Research Centre, Semenyih, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Dafydd M. O. Elias
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - John Clarkson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aik Chin Soh
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Gin Teng Ooi
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - Niall P. McNamara
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Gary D. Bending,
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6
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Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, Miller AN, Hernández-Restrepo M. Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi. J Fungi (Basel) 2021; 7:1097. [PMID: 34947079 PMCID: PMC8704094 DOI: 10.3390/jof7121097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Jana Nekvindová
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Kamila Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- CEITEC—Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - František Sklenář
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA;
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7
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Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M. Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Mol Ecol Resour 2021; 21:1833-1849. [PMID: 33811446 DOI: 10.1111/1755-0998.13387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023]
Abstract
Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
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Affiliation(s)
- Brendan Furneaux
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Anna Rosling
- Program in Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Fungi Interactions, LEB, University of Parakou, Parakou, Benin
| | - Martin Ryberg
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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8
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Kalsoom Khan F, Kluting K, Tångrot J, Urbina H, Ammunet T, Eshghi Sahraei S, Rydén M, Ryberg M, Rosling A. Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi. IMA Fungus 2020; 11:23. [PMID: 33292867 PMCID: PMC7607712 DOI: 10.1186/s43008-020-00045-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 01/04/2023] Open
Abstract
Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
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Affiliation(s)
- Faheema Kalsoom Khan
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Kerri Kluting
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Jeanette Tångrot
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Umeå University, Umeå, Sweden
| | - Hector Urbina
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, Florida, 32608, USA
| | - Tea Ammunet
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Shadi Eshghi Sahraei
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Rydén
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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9
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Venneman J, De Tender C, Debode J, Audenaert K, Baert G, Vermeir P, Cremelie P, Bekaert B, Landschoot S, Thienpondt B, Djailo BD, Vereecke D, Haesaert G. Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack. FEMS Microbiol Ecol 2020; 95:5524361. [PMID: 31247636 DOI: 10.1093/femsec/fiz101] [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: 05/07/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
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Affiliation(s)
- Jolien Venneman
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281, S9, BE-9000, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Baert
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Laboratory of Chemical Analysis (LCA), Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Bert Thienpondt
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Benoît Dhed'a Djailo
- Faculty of Science and Agriculture, Kisangani University, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
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10
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Kirker GT, Bishell A, Cappellazzi J, Palmer J, Bechle N, Lebow P, Lebow S. Role of Leaf Litter in Above-Ground Wood Decay. Microorganisms 2020; 8:microorganisms8050696. [PMID: 32397554 PMCID: PMC7286020 DOI: 10.3390/microorganisms8050696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
The effects of leaf litter on moisture content and fungal decay development in above-ground wood specimens were assessed. Untreated southern pine specimens were exposed with or without leaf litter contact. Two types of leaf litter were evaluated; aged (decomposed) and young (early stages of decomposition). The moisture content of specimens was monitored, and specimens were periodically removed for visual evaluation of decay development. In addition, amplicon-based sequencing analysis of specimens and associated leaf litter was conducted at two time points. Contact with either type of leaf litter resulted in consistently higher moisture contents than those not in contact with leaf litter. Visually, evident decay developed most rapidly in specimens in contact with the aged leaf litter. Analysis of amplicon-based sequencing revealed that leaf litter contributes a significant amount of the available wood decay fungal community with similar communities found in the litter exposed wood and litter itself, but dissimilar community profiles from unexposed wood. Dominant species and guild composition shifted over time, beginning initially with more leaf saprophytes (ascomycetes) and over time shifting to more wood rotting fungi (basidiomycetes). These results highlight the importance of the contributions of leaf litter to fungal colonization and subsequent decay hazard for above-ground wood.
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Affiliation(s)
- Grant T. Kirker
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
- Correspondence: ; Tel.: +1-608-231-9256
| | - Amy Bishell
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Jed Cappellazzi
- Dept. of Wood Science and Engineering, Oregon State University, Corvallis, OR 97731, USA;
| | - Jonathan Palmer
- Northern Research Station, USDA Forest Service, Madison, WI 53726, USA;
| | - Nathan Bechle
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Patricia Lebow
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
| | - Stan Lebow
- USDA-FS Forest Products Laboratory, Madison, WI 53726, USA; (A.B.); (N.B.); (P.L.); (S.L.)
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Retter A, Nilsson RH, Bourlat SJ. Exploring the taxonomic composition of two fungal communities on the Swedish west coast through metabarcoding. Biodivers Data J 2019; 7:e35332. [PMID: 31871405 PMCID: PMC6739426 DOI: 10.3897/bdj.7.e35332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background Fungi are heterotrophic, unicellular or filamentous organisms that exhibit a wide range of different lifestyles as, e.g., symbionts, parasites, and saprotrophs. Mycologists have traditionally considered fungi to be a nearly exclusively terrestrial group of organisms, but it is now known that fungi have a significant presence in aquatic environments as well. We know little about most fungi in limnic and marine systems, including aspects of their taxonomy, ecology, and geographic distribution. The present study seeks to improve our knowledge of fungi in the marine environment. The fungal communities of two coastal marine environments of the Kattegat sea, Sweden, were explored with metabarcoding techniques using the nuclear ribosomal internal transcribed spacer 2 (ITS2) metabarcode. Our data add new information to the current picture of fungal community composition in benthic and coastal habitats in Northern Europe. New information The dataset describes the number of operational taxonomic units (OTUs) and their taxonomic affiliations in two littoral gradients sampled on the Swedish west coast, Gothenburg municipality. Our data include basic diversity indices as well as chemical and edaphic sediment/soil parameters of the sampling sites. From the sites, 3470 and 4315 fungal OTUs, respectively, were recovered. The number of reads were 673,711 and 779,899, respectively, after quality filtering. Within the benthic sites, more than 80% of the sequences could not be classified taxonomically. The phylum composition of the classifiable sequences was dominated in both localities by Dikarya, which made up around 33% of the OTUs. Within Dikarya, Ascomycota was the dominant phylum. Guild assignment failed for more than half of the classifiable OTUs, with undefined saprotrophs being the most common resolved guild. This guild classification was slightly more common in the ocean sediment samples than in the terrestrial ones. Our metadata indicated that ocean sites contain organisms at a lower trophic level and that there are predominantly endophytic, parasitic, and pathogenic fungi in the marine environments. This hints at the presence of interesting and currently poorly understood fungus-driven ecological processes. It is also clear from our results that a very large number of marine fungi are in urgent need of taxonomic study and formal description.
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Affiliation(s)
- Alice Retter
- University of Vienna, Vienna, Austria University of Vienna Vienna Austria
| | - R Henrik Nilsson
- University of Gothenburg, Göteborg, Sweden University of Gothenburg Göteborg Sweden.,Gothenburg Global Biodiversity Centre, Gothenburg, Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden
| | - Sarah J Bourlat
- Zoological Research Museum Alexander Koenig, Bonn, Germany Zoological Research Museum Alexander Koenig Bonn Germany
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A meta-barcoding analysis of soil mycobiota of the upper Andean Colombian agro-environment. Sci Rep 2019; 9:10085. [PMID: 31300737 PMCID: PMC6625999 DOI: 10.1038/s41598-019-46485-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022] Open
Abstract
Colombia is a country for which one of the highest biodiversity rates is reported, and one of the first in the tropical areas where an effort was made to gather information on indigenous fungi. Nevertheless, mycological data are still scarce and discontinuous, above all on soil fungi. The present study wanted to contribute to unveil the large soil fungal biodiversity in the upper Andean Colombian agro-ecosystems. The studied area is located in the department of Boyacà, considered with a notable economical value, partly devoted to subsistence agriculture. More than 150 described species were revealed in this study, belonging to 5 phyla with Ascomycota representing the dominant taxon. Basidiomycota and Zygomycota are also well represented, dominated by species of the genus Sebacina and Mortierella respectively, mainly distributed in the semi-natural plots (woodland and grassland). Most of the species are reported as first records for Colombia. Some of them are particularly interesting for their conservation significance such as Geoglossum fallax, which is the dominant species in the unimproved grassland plot. The bootstrap-based clustering analysis showed a different distribution of the species in orchards and non-cultivated areas as a possible response of the fungal community to different use of soil in the agro-environment.
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Graphiola fimbriata: the first species of Graphiolaceae (Exobasidiales, Basidiomycota) described only based on its yeast stage. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1450-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Alexandrova AV, Aldobaeva II, Kalashnikova KA, Kuznetsov AN. Influence of Environmental Factors on the Structure of Soil Microfungi of Vietnamese Tropical Forests. CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s1995425518050025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vowles T, Lindwall F, Ekblad A, Bahram M, Furneaux BR, Ryberg M, Björk RG. Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone. Ecol Evol 2018; 8:1019-1030. [PMID: 29375775 PMCID: PMC5773333 DOI: 10.1002/ece3.3657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/17/2017] [Accepted: 11/03/2017] [Indexed: 11/21/2022] Open
Abstract
Mycorrhizal associations are widespread in high-latitude ecosystems and are potentially of great importance for global carbon dynamics. Although large herbivores play a key part in shaping subarctic plant communities, their impact on mycorrhizal dynamics is largely unknown. We measured extramatrical mycelial (EMM) biomass during one growing season in 16-year-old herbivore exclosures and unenclosed control plots (ambient), at three mountain birch forests and two shrub heath sites, in the Scandes forest-tundra ecotone. We also used high-throughput amplicon sequencing for taxonomic identification to investigate differences in fungal species composition. At the birch forest sites, EMM biomass was significantly higher in exclosures (1.36 ± 0.43 g C/m2) than in ambient conditions (0.66 ± 0.17 g C/m2) and was positively influenced by soil thawing degree-days. At the shrub heath sites, there was no significant effect on EMM biomass (exclosures: 0.72 ± 0.09 g C/m2; ambient plots: 1.43 ± 0.94). However, EMM biomass was negatively related to Betula nana abundance, which was greater in exclosures, suggesting that grazing affected EMM biomass positively. We found no significant treatment effects on fungal diversity but the most abundant ectomycorrhizal lineage/cortinarius, showed a near-significant positive effect of herbivore exclusion (p = .08), indicating that herbivory also affects fungal community composition. These results suggest that herbivory can influence fungal biomass in highly context-dependent ways in subarctic ecosystems. Considering the importance of root-associated fungi for ecosystem carbon balance, these findings could have far-reaching implications.
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Affiliation(s)
- Tage Vowles
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Frida Lindwall
- Terrestrial EcologyDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
- Center for PermafrostDepartment of Geoscience and Natural Resource ManagementUniversity of CopenhagenCopenhagenDenmark
| | - Alf Ekblad
- School of Science and TechnologyÖrebro UniversityÖrebroSweden
| | - Mohammad Bahram
- Department of Organismal BiologyUppsala UniversityUppsalaSweden
- Department of BotanyInstitute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Martin Ryberg
- Department of Organismal BiologyUppsala UniversityUppsalaSweden
| | - Robert G. Björk
- Department of Earth SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
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Panelli S, Capelli E, Comandatore F, Landinez-Torres A, Granata MU, Tosi S, Picco AM. A metagenomic-based, cross-seasonal picture of fungal consortia associated with Italian soils subjected to different agricultural managements. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Röhl O, Peršoh D, Mittelbach M, Elbrecht V, Brachmann A, Nuy J, Boenigk J, Leese F, Begerow D. Distinct sensitivity of fungal freshwater guilds to water quality. Mycol Prog 2017. [DOI: 10.1007/s11557-016-1261-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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