Little is known about the diversity patterns of plant pathogens and how they change with land use at a broad scale. We employed DNA metabarcoding to describe the diversity and composition of putative plant pathogen communities in three substrates (soil, roots, and leaves) across five major land uses at a national scale. Almost all plant pathogen communities (fungi, oomycetes, and bacteria) showed strong responses to land use and substrate type. Land use category could explain up to 24% of the variance in composition between communities. Alpha-diversity (richness) of plant pathogens was consistently lower in natural forests than in agricultural systems. In planted forests, there was also generally low pathogen alpha-diversity in soil and roots, but alpha-diversity in leaves was high compared with most other land uses. In contrast to alpha-diversity, differences in within-land use beta-diversity of plant pathogens (the predictability of plant pathogen communities within land use) were subtle. Our results show that large-scale patterns and distributions of putative plant pathogens can be determined using metabarcoding, allowing some of the first landscape level insights into these critically important communities.

Land use is a determinant of plant pathogen alpha- but not beta-diversity.

The collection of papers in this special issue examines the nature of some of the ecosystemand environmental interactions involving fungi in the tropics and the biodiversity of certainof these tropical fungal guilds in an effort to provide improved estimates to answer thequestion of just how much undescribed tropical fungal diversity remains to be discovered.Fungi are ubiquitously found in all tropical environments where they are essential forecosystem processes. For example, in interactions with plants, fungi facilitate nutrientuptake (as mycorrhizas), provide protection against phytopathogens (as endophytes,phylloplane constituents or mycoparasites), breakdown and recycle the nutrients otherwiselocked in cell wall compounds (as wood and litter decomposers), and act as agents ofdisease. They cover a broad range of life-forms and life-histories from microscopic yeaststo those having large and conspicuous sporocarps or genets covering many hectares.Tropical regions are incredibly species rich, harbouring the majority of terrestrial biodi-versity as well as a broad variety of often unusual interactions between species. Yet despiteincreasing interest, our understanding of the mycobiota and its roles in tropical ecosystemsis woefully incomplete.The question of how many fungal species there are is indisputably important. Currentestimates of these numbers range from 611,000 (Mora et al. 2011) to nearly ten million(Cannon 1997). However, Hawksworth’s (1991) estimate of 1.5 million species remains,for most, the benchmark. One of the several caveats of the Hawksworth (1991) study wasthe dearth of information with regard to fungal biodiversity within tropical ecosystems and

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Tropical fungal diversity: closing the gap between species estimates and species discovery

In order to document the species richness of plants and fungi in a tropical area, a trail of 500 m in tropical lowlands in the Chiriqui province, on the Pacific side of western Panama, was sampled each month during 2 years with 2 h dedicated to plants and 2 h dedicated to fungi, each by two botanists or mycologists respectively. The 24 sampling events yielded approximately 4,000 records of plants corresponding to 311 species as well as 1,614 records of fungi corresponding to approximately 567 species. Lists of more or less certain names of plants and fungi as well as voucher specimens are provided. The randomized species accumulation curve for plants approaches an asymptote and estimators yield stable values of 310–318 predicted plant species in the area of investigation. The curve for records of fungal species, however, did not saturate and all applied estimator functions failed to predict the total richness of fungi for the area convincingly. Two plant collections correspond to new records for Panama and 54 species and infraspecific taxa are new for the Chiriqui province. The identification of fungi is still in process and yielded two species probably new to science as well as 17 new records of species for Panama to date. In order to assess biodiversity patterns (e.g. fungi to plant ratios) of tropical fungi more accurately, it is necessary to repeat such investigations in other areas and to improve the tools for taxonomic identification of these highly diverse but mostly microscopic organisms.

Species richness of plants and fungi in western Panama: towards a fungal inventory in the tropics

Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. As such, reliably and cost effectively detecting, identifying and monitoring these fungi at large scales is important to industry, government and research institutions. Metabarcoding is one approach, based on next-generation sequencing, that could be used for this purpose. However, metabarcoding has not been widely applied for the monitoring of rust fungi. This is in part due to uncertainties of the new approach, mainly concerning the ability to detect rare species and reliability of measuring species abundances (quantification). Furthermore, outcomes might differ between sequencing platforms, although this aspect has not been well examined. In this chapter, I investigated possible differences in (1) detection ability and (2) quantification of rust fungi from environmental DNA (eDNA) samples between two metabarcoding approaches and traditional DNA cloning. I then analysed (3) the causes of these differences. I used two fundamentally different next-generation sequencing technologies (Illumina MiSeq and Ion Torrent), and cloning followed by Sanger sequencing. I found strong biases between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) across different methods. However, there was no significant difference in abundance of OTUs that all methods were capable of detecting. Therefore, differences between the methods were mainly driven by the method’s ability to detect specific OTUs. The difference in detection could be explained by a phylogenetic bias of the methods. This bias was very likely caused by base pair mismatches of the metabarcoding

Characterising plant pathogen communities and their environmental drivers at a national scale

Biodiversity of Tropical Microfungi.Kevin D. Hyde

The occurrence of rust fungi (Basidiomycota) infecting vascular plants on 14 sites in western Panama differing in altitude, climate, and vegetation type was analyzed. Three vegetation-types are investigated: (1) Disturbed sites where Asteraceae, Fabaceae, and Poaceae are most speciose, (2) slightly disturbed high canopy forests with sparse herbaceous undergrowth and no dominant plant family, and (3) relatively undisturbed forests with rich herbaceous undergrowth where Orchidaceae and ferns are most speciose. The majority of species of Pucciniales were found in disturbed sites on Asteraceae, Cyperaceae, Fabaceae, and Poaceae, whereas high canopy forests with sparse herbaceous layers yielded only few species of Pucciniales that were not common on any specific plant family. In undisturbed forests, a higher number of Pucciniales was found infecting mostly pteridophytes and Orchidaceae. Generally, undisturbed sites yielded a lower number of Pucciniales in relation to the number of plant species of which several species have a wide host range within the same site, and a low percentage of samples containing teliospores. Disturbed sites yielded a high number of Pucciniales in relation to the number of plant species, many rusts having a wide geographical distribution and a wide host range outside the sites, and a higher percentage of samples containing teliospores.

O. Perdomo-Sánchez

Papers

Correlation of diversity of rust fungi and their host plants with disturbance and conservation of vegetation in western Panama