Special Issue "Ecology and Genomics of Forest Fungi and their Interactions"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 30 November 2019

Special Issue Editor

Guest Editor
Prof. Dr. Fred O. Asiegbu

Department of Forest Sciences, University of Helsinki, Helsinki, Finland
Website | E-Mail
Fax: +358- (0) 294158109
Interests: forest fungi; tree–microbe interactions; fungal genomics; ecogenomics; molecular pathobiology; interspecific fungal interactions; mycobiome; comparative fungal genomics; symbiosis; biocontrol

Special Issue Information

Dear Colleagues,

Our interest for this Special Issue stems from the fact that there have been very scanty literature reports on the impact of genomics and molecular biology on the mechanistic understanding of life styles of forest fungi and their interactions (pathogenic, saprotrophic, endophytic, mutualistic) with direct relevance to forest ecosystems. There are several reasons for the paucity of information on the mechanistic understanding of life styles and phenotypic plasticity on fungi associated with forest biome. An underlying factor is that the genomics and molecular ecology of forest fungi and their associated interactions have for a long time lagged behind parallel studies on microbes associated with agricultural crops or human health. The recent novel technological advances in -omics and bioinformatics have remarkably contributed to the perceived progress in this field. The field of fungal genomics is expanding rapidly, as new fungal genomes are currently being produced at an exponential rate. The availability of genome sequences of hundreds of fungal species occupying diverse ecological niches and representing various taxonomic groups provides unmatched opportunities for comparative genomics analysis. At the same time, the application of next-generation sequencing (NGS) and transcriptomics has facilitated the accumulation of an enormous amount of data on forest trees and soil microbiome, as well as their molecular interactions. Studies on communities of mycobiome colonizing different forest tree tissues (endophere, rhizosphere, phyllosphere) are also of interest.

Prof. Dr. Fred O. Asiegbu
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

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  • forest fungi
  • tree–microbe interactions
  • fungal genomics
  • ecogenomics
  • molecular pathobiology
  • interspecific fungal interactions
  • mycobiome
  • comparative fungal genomics
  • symbiosis
  • biocontrol

Published Papers (1 paper)

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Open AccessArticle New R-Based Methodology to Optimize the Identification of Root Endophytes against Heterobasidion parviporum
Microorganisms 2019, 7(4), 102; https://doi.org/10.3390/microorganisms7040102
Received: 12 March 2019 / Revised: 2 April 2019 / Accepted: 4 April 2019 / Published: 6 April 2019
PDF Full-text (2217 KB) | HTML Full-text | XML Full-text | Supplementary Files
Many root fungal endophytes inhabiting forest trees have potential impact on the health and disease progression of certain tree species. Hence, the screening of root endophytes for their biocontrol abilities is relevant for their potential to protect their hosts against invaders. The aim [...] Read more.
Many root fungal endophytes inhabiting forest trees have potential impact on the health and disease progression of certain tree species. Hence, the screening of root endophytes for their biocontrol abilities is relevant for their potential to protect their hosts against invaders. The aim of this research is to screen for the potential inhibitory effects of selected conifer root endophytes during interaction, in vitro, with the root rot pathogen, Heterobasidion parviporum. Here, we introduce a guideline that facilitates the use of root fungal endophytes as biocontrol agents. We isolated fungal root endophytes from eight different conifers. These root fungal endophytes were evaluated for their antagonism against the root rot pathogen, H. parviporum, by means of paired-culture antagonism assays. We determined the antagonism of the isolated root fungal endophytes to elucidate potential biocontrol applications. For the analysis, a software package in R was developed. Endophyte candidates with antagonistic potential were identified. Full article
(This article belongs to the Special Issue Ecology and Genomics of Forest Fungi and their Interactions)

Figure 1

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Fungal and bacterial communities exhibit spatial but not temporal response to reversal of soil acidification
Authors: Sarah R. Carrino-Kykera a,b, Kate P. Coyle b,c, Laurel A. Klubera a,b, and David J. Burkea a,b
Affiliations:  The Holden Arboretum, Kirtland, OH, USA a; Case Western Reserve University, Department of Biology, Cleveland, OH, USA b; North Carolina State University, Department of Biological Sciences, Raleigh, NC, USA c
Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that soil organisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial community structure changes with soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies. However, this remains largely unexplored. In this study, we examined fungal and bacterial community structure in an ecosystem level manipulative experiment where pH and/or P availability were elevated in temperate forests of northern Ohio. Tag-encoded pyrosequencing was used to examine fungal and bacterial community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time of sampling on fungal and bacterial communities in soil. However, we found no interaction between treatments and time of sampling, suggesting that microbial community structure responses to soil pH are independent of plant phenological stage. These results suggest that the taxonomic make-up of below-ground communities consistently respond to changes in soil pH regardless of plant C allocation.

Title: Seed endophytes exhibit stronger ecological interactions than needle endophtyes in Pinus monticola
Authors: Maria Marlin 1,* Jos Houbraken 2, Posy E. Busby 3 and George Newcombe 1
Affiliations: 1 Department of Forest, Rangelands and Fire Sciences, 875 Perimeter Dr. MS 1133, University of Idaho, Moscow, ID 83844-1133, USA; 2 Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3509 AD Utrecht, The Netherlands; 3 Botany and Plant Pathology Department, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis OR 97331
Abstract: Endophytes can antagonize pathogens and could thus be used as disease-reducing inoculants in agriculture and forestry. However, identifying robust endophytic antagonists that are bioactive against a diverse group of microbes remains a challenge. Exclusionary interactions between endophytes have been reported for the seed microbiome but not the foliar microbiome, suggesting that seed endophytes may be stronger antagonists than foliar endophytes. We used seed and foliar (needle) endophytes of Pinus monticola to test this hypothesis. Eight fungal needle endophytes, eight bacterial seed endophytes, and eight fungal seed endophytes were selected and tested in all 576 possible pair-wise combinations in a replicated in agaro experiment where interactions were identified as growth inhibitory (i.e., antagonism), stimulatory (i.e., facilitation), or neutral. Seed bacteria (Bacillus spp.) were the strongest antagonists, with a mean interaction strength 2.8 times greater than seed fungi and 3.2 times greater than needle fungi.  Needle fungi, including its dominant member, Lophodermium nitens, were the least antagonistic, and were themselves antagonized the most. Some stimulatory activity (about 2/3 of all possible pair-wise combinations) occurred, with seed bacteria being the strongest interactors, in this case as stimulators, and seed fungi the most stimulated. Hierarchal clustering separated most microbes into their communities of origin based on their in agaro interactions alone. Overall, our results support the hypothesis that seed endophytes are more antagonistic toward other microbes than needle endophytes.

Title: Ectomycorrhizal fungal communities associated to Pinus hartwegii sky-islands: the highest alpine forest at tropical latitudes
Authors: Dora Trejo Aguilar et al.
: Alpine ecosystems are highly vulnerable to global warming. Pinus hartwegii is the only ectomycorrhizal host that distributes higher than 4000 m above sea level in the Neotropical ecozone. It forms monospecific "sky island" forests at the upper vegetation limit of the Trans-Mexican Volcanic Belt. Ectomycorrhizal (ECM) fungi favor the establishment, growth, and survival of such pines. In this work, we studied the ECM community associated with P. hartwegii from three sites in the tree limit of Cofre de Perote National Park, Veracruz, Mexico. We identified ectomycorrhizal fungi by internal transcribed spacer ribosomal DNA sequence analyses. These fungal communities are characterized by low alpha diversity (richness less than ten species per site) and high beta diversity (only two species shared between sites). The genera with the highest number of species were Cortinarius (5) and Piloderma (4). These forests constitute Holarctic sky-island refuges in the Neotropic where several endemic ECM species have evolved. Up to 46% of its species have a wide distribution in Holarctic alpine and boreal forests; while 30% species are endemic and like Gautieria sp1, can be dominant in some places. This study suggests that in isolated alpine ecosystems, the environmental variations and the biogeographic history of sites strongly determine the diversity and composition of the mycorrhizal community.

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