rMyCoPortal - an R package to interface with the Mycology Collections Portal

Using aggregated field collection data and the novel r package fungarium to investigate fungal fire association

Understanding which fungi exhibit certain ecological traits, such as habitat, host, or substrate associations, and knowing how these traits change across space and time can provide invaluable insight into the roles fungi play in their respective ecosystems. Archived sporocarp data, such as the collection and observation records accessible through the Mycology Collections Portal (MyCoPortal), are well suited for trait investigations, since these records circumvent the need for field work, are geographically and temporally diverse, and often have detailed and trait-relevant environmental metadata. However, there are inefficiencies and inadequacies in the MyCoPortal online interface that affect data set generation and trait searching, and many of the available records have outdated or misspelled taxon names as well as misspelled location names. Thus, we created the r package fungarium, which enables the efficient download of complete MyCoPortal data sets from within the R environment, enhances the identification of trait-relevant records, confirms or updates taxon names while also accounting for spelling errors, and fixes misspelled location names. Utilizing this package and MyCoPortal data, we demonstrated methods for analyzing taxonomic, geographic, and temporal patterns in ecological traits, using fire association as an example. We found that fire association, which was quantified via fire-associated enrichment factors (fire-associated records/total records), differed substantially between taxa, and these differences were qualitatively supported by existing literature, as hypothesized. Sampling bias within the MyCoPortal data and limitations of the burned acreage data set used (i.e., Monitoring Trends in Burn Severity) were identified as confounding factors in our geographic and temporal analyses, as evidenced by the unexpected lack of correlation between fire association and burned acreage on county and year bases. However, both confounding factors likely depend on the trait analyzed and external data set used. Overall, the fungarium package and associated methods presented here effectively enable the use of archived sporocarp data for future ecological trait studies.

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration

Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.