Plant Fungal Communities Research Articles

Soil mycobiome and forest endophytic fungi: Is there a relationship between them?

Fungi are important ecological agents in forests that contribute to increase the resilience of the whole ecosystem against environmental challenges. Mediterranean forests rank among the habitats most threatened by climate change and the spread of pests and diseases, which ultimately lead them into a spiral of decline. As such, changes in the composition of soil and trees’ mycobiota might correlate with health status of the forest and has been scarcely addressed in Mediterranean tree species. In this work, rhizosphere and bark-wood samples from declining Spanish forests of Castanea sativa Mill. (chestnut), Quercus ilex L. (holm oak), Q. suber L. (cork oak) and Q. pyrenaica Willd. (Pyrenean oak) were compared. Fungal communities were characterised by means of ITS metabarcoding. Higher diversity in terms of richness was found in soil, with 674 genera belonging to 15 phyla in soil vs 420 genera and 6 phyla in trees. Fungal genera exclusive to declining forests’ soils and trees didn’t include pathogenic organisms, thus preventing the association of certain genera with forest decline. Alpha diversity didn’t correlate with health status or sample type either, as it only increased in soils of asymptomatic chestnuts and not in any of the other analysed tree species. Some differentially abundant genera found in asymptomatic trees, such as Metarhizium, Aspergillus, Russula, Chaetomium, Mortierella or Cladophialophora, may be related to the biological control of decline-contributing pathogens. Finally, no relationship was found between health status and the primary lifestyles of fungi in soil and bark, which can be interpreted as a sign of resilience against adversities following cross-talk between soil and plant fungal communities.

Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.

Dynamic preferential allocation to arbuscular mycorrhizal fungi explains fungal succession and coexistence.

Evidence accumulates about the role of arbuscular mycorrhizal (AM) fungi in shaping plant communities, but little is known about the factors determining the biomass and coexistence of several types of AM fungi in a plant community. Here, using a consumer-resource framework that treats the relationship between plants and fungi as simultaneous, reciprocal exploitation, we investigated what patterns of dynamic preferential plant carbon allocation to empirically-defined fungal types (on-going partner choice) would be optimal for plants, and how these patterns depend on successional dynamics. We found that ruderal AM fungi can dominate under low steady-state nutrient availability, and competitor AM fungi can dominate at higher steady-state nutrient availability; these are conditions characteristic of early and late succession, respectively. We also found that dynamic preferential allocation alone can maintain a diversity of mutualists, suggesting that on-going partner choice is a new coexistence mechanism for mutualists. Our model can therefore explain both mutualist coexistence and successional strategy, providing a powerful tool to derive testable predictions.

The microscopic pathogenic fungi of the Łęczna-Włodawa Lake District. I. The occurrence of pathogenic fungi in plant communities and theirs phenology

The paper presents the results of the studies on tbe occurrence and phenology of puthogenic fungi in plant communities of the Łęczna-Włodawa Lake District in 1981-1984. The taxonomic list of collected fungi species will be published in another paper.

Environmental barcoding of the ectomycorrhizal fungal genus Cortinarius

Understanding the role of ectomycorrhizal fungi in plant communities is hampered by a lack of knowledge about fungal diversity. DNA barcoding of the ectomycorrhizal fungal genus Cortinarius was used to compare fungal diversity in soil from four plant communities: (i) Nothofagus forest (where Cortinarius is common and diverse), (ii) Kunzea forest (where Cortinarius is present but with low diversity), (iii) a Pinus radiata plantation (Cortinarius is not thought to be present) and (iv) a sub-Antarctic island (where known ectomycorrhizal hosts are absent). PCR primers specific for the ITS region of Cortinarius species were developed. Specificity was tested in vitro and in silico against DNA from basidiocarps of Cortinarius and non-Cortinarius species. The primers were tested for their ability to amplify Cortinarius DNA in soil from forests of the three ectomycorrhizal forest communities and a range of soils from the ectomycorrhiza-free subantarctic Campbell Island. High diversity of Cortinarius was associated with soil of all three ectomycorrhizal communities, despite Cortinarius being previously unrecorded from Pinus. Soil from all three communities share some ectomycorrhizal fungi (including fungi shared between native and exotic hosts), having implications for community succession, introduction of exotic fungi and biodiversity assessment. No Cortinarius was detected from Campbell Island samples. The validated molecular protocol assessed species diversity in a rapid and cost effective way. Baseline biodiversity assessment based on DNA barcoding is more effective at detecting diversity than traditional methods, but requires careful consideration of the difference between ectomycorrhizal fungal diversity in soil versus root-tips.

Perspectives on ICOM 6 “beyond the roots”

From August 9 to 14, 2009, the Sixth International Conference on mycorrhizas brought together 290 participants from 41 countries to learn first-hand the latest information on mycorrhizal research. All activities and the housing for most participants were centered at the Ouro Minas Palace Hotel in the city of Belo Horizonte, Brazil. ICOM 6 was organized by the Microbiology Department of the Federal University of Vicosa and the International Mycorrhiza Society (IMS). The conference was organized around 11 topic areas covered in workshops, symposia, and poster sessions held on each of 4 days which gave time for informal debate and discussion outside formal sessions. One day midconference was devoted to tours to various scenic areas in the state of Minas Gerais. Topics were genome structure and evolution, cell biology and development, signal perception and metabolism, population structure, community diversity, plant–fungal community interactions, nutritional interactions, mycorrhizosphere interactions, stress tolerance, mycoheterotrophic interactions, and systematics of glomeromycetes. Of the presentations, 72 were oral and 218 were posters. Almost 72% of these concerned arbuscular mycorrhizal (AM) fungi, 25% involved ectomycorrhizal (ECM) fungi, and nearly 3% reported on coevolution, conservation potential, and diversity of fungi forming symbiosis with orchids. In this report, we can highlight the content of only a few of the excellent presentations and posters at ICOM 6, and we apologize to colleagues whose interesting work is not mentioned. Jose Siqueira spoke at the opening ceremony and discussed the three decades of research on mycorrhizal symbioses conducted in Brazil. It was clear from his talk that the projects are as eclectic as the habitats spanning this large country. Even though some work done in the tropics was reported, considerable potential exists to accomplish much more in such an expansive natural laboratory. A stimulating keynote lecture started each day. George Kowalchuk provided a broad overview of the application of genomics and metagenomics to elucidating community dynamics and processes occurring in soil microbes. All other keynote talks focused on AM fungi. Sally Smith provided insights into new ways of interpreting positive and negative consequences of phosphorus responses in mycorrhizal plants based on partitioning of P transfer pathways in the plant versus fungal symbiont. Paola Bonfante discussed recent developments in fungus–plant interactions at the cellular level, some of which were depicted in a breathtaking video. This and other reports provide striking evidence of the depth and breadth of AM fungus–plant coevolution. Lastly, Peter Young discussed progress on the Glomus intraradices genome project. While problems and challenges have plagued this project, valuable information is being obtained. Most notably, genome size is considerably larger than previously estimated, as is gene variability and organization. This species is a model organism, justified in part because of its ubiquity worldwide. The diversity of haplotypes, the ability to anastomose among populations, suggestions of putative recombination, and other interactions likely will not translate to other lineages, even within J. Morton Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506-6108, USA

Effects of long-term fungicide applications on microbial properties in tallgrass prairie soil

Several studies investigating the role of arbuscular mycorrhizal (AM) fungi in plant communities have included manipulations of AM fungal symbiosis using the fungicide benomyl. The objectives of this study were to evaluate the potential non-target effects of benomyl on soil biota and nutrient cycling in tallgrass prairie and to determine how mycorrhizae may influence these belowground properties. To accomplish these objectives, soil samples were collected during the 1996–1997 growing seasons from long-term benomyl-treated plots established on tallgrass prairie (Manhattan, KS) in 1991, and the following measurements were made: total bacterial and fungal biomass; abundance of nematodes; microbial biomass carbon and nitrogen; substrate-induced respiration; and potentially mineralizable C and N. Long-term benomyl applications resulted in an 80% reduction in mycorrhizal root colonization. By reducing root colonization, benomyl applications resulted in significant decreases in total bacterial biomass and abundance of fungal-feeding and predatory nematodes (20, 12 and 33% reductions compared to control, respectively). Total microbial potential activity (i.e., substrate-induced respiration) increased by 10% with benomyl treatment, whereas the relative contribution of fungi to total microbial activity decreased significantly with benomyl applications. In addition, microbial biomass C increased from 1364 (± 51.2 SE) to 1485 (± 51.2 SE) with benomyl treatment, and total carbon increased significantly (∼8%) only in annually burned soils treated with benomyl. The magnitude of benomyl effects on soil components and processes were small (<33% change with benomyl) relative to effects on mycorrhizal root colonization (80% decrease with benomyl). These results indicate that rather than having large non-target effects, benomyl applications principally affect mycorrhizal root colonization, thereby indirectly influencing soil biota and nutrient availability. Results also indicate that mycorrhizal fungi play an important role in altering the availability and flow of carbon in prairie soil and may influence the composition and abundance of groups of some soil biota. Changes in soil organisms and nutrient availability associated with altered mycorrhizal symbiosis may influence aboveground plant species responses to mycorrhizal suppression, but further research is needed to understand these potential effects.