Leho Tedersoo

and 17 more

Fungi are a key component of tropical biodiversity. Due to their inconspicuous and largely subterranean nature, they are however usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomies) emerges as the strongest factor in explaining fungal community composition. Naturally open areas – campinas – are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi–plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short-reads can suffice for diversity and community comparison, long-reads add taxonomic precision and have the potential to reveal population diversity.

Kalev Adamson

and 18 more

Diplodia sapinea is a cosmopolitan endophyte and opportunistic pathogen occurring on several conifer species in Europe for at least 200 years. In Europe, disease outbreaks have increased on several Pinus spp. in the last few decades. In this study, the genetic structure of the European D. sapinea population was investigated using thirteen microsatellite markers. In total, 425 isolates from 15 countries were analysed. A high clonal fraction and low genetic distance between most populations was found. One single haplotype dominates the European population, being represented by 44% of all isolates and found in nearly all investigated countries. Three genetically distinct subpopulations were found: Central/North European, Italian and Georgian. The recently detected populations of D. sapinea in northern Europe (Latvia, Estonia and Finland) share several haplotypes with the German population, suggesting introduction from Central Europe. The northern European populations show similar genetic diversity to those in Central Europe suggesting either that the fungus has existed in the North in an asymptomatic mode for a long time or that it has spread recently by multiple introductions. Although this fungus reproduces predominantly asexually, considerable genetic diversity was found even among isolates of a single tree. According to currently published allelic patterns, D. sapinea most likely originates from North America. In order to enable the detection of endophytic or latent infections of planting stock by D. sapinea, new species-specific PCR primers were designed. During the search for Diplodia isolates, we identified D. africana in California, USA, which is the first record of this species in North America.

Melinda Greenfield

and 6 more

In recent decades, multipartite mutualisms involving microorganisms such as fungi have been discovered in associations traditionally thought of as bipartite. Ant-plant mutualisms were long thought to be bipartite despite fungi being noticed in an epiphytic ant-plant over 100 years ago. We sequenced fungal DNA from the three distinct domatium chambers of the epiphytic ant-plant Myrmecodia beccarii Hook.f. to establish if fungal communities differ by chamber type across five locations spanning 675 km. The three chamber types serve different ant-associated functions including: ‘waste’ chambers, where ant workers deposit waste; ‘nursery’ chambers, where the brood are kept; and ‘ventilation’ chambers, that allow air into the domatium. Overall, fungi from the order Chaetothyriales dominated the chambers in terms of the proportion of OTUs (13.4%) and sequence abundances of OTUs (28% of the total), however a large portion of OTUs (28%) were unidentified at the order level. Notably, the fungal community in the waste chambers differed consistently from the nursery and ventilation chambers across all five locations. We identified 13 fungal OTUs as ‘common’ in the waste chambers that were rare or in very low sequence abundance in the other two chambers. Fungal communities in the nursery and ventilation chambers were also significantly different, but variation between these chambers was less pronounced. Differences in dominance of the common OTUs drive the observed patterns in the fungal communities for each of the chamber types. This suggests a multipartite mutualism involving fungi exists in this ant-plant and that the role of fungi differs among chamber types.