The taxonomy of the genus Colletotrichum has undergone tremendous changes over the last decade, with over 200 species being currently recognised and species complexes being informally used to cluster those species. Many of these species are important plant pathogens, some rather polyphagous and others host-specific, but several occur seldomly and some may in fact be ecologically endangered. Based mainly on literature from the past decade, in this work we review the occurrence, geographic distribution and host spectrum of currently recognised Colletotrichum species under phylogenetic, pathological/agronomic and ecological perspectives, providing a list arranged by Colletotrichum species and species complexes. A total of 257 species are listed and grouped into 15 species complexes. In this work we have recorded 1353 unique host species-Colletotrichum species association records from 720 hosts, with the Fabaceae as the family with higher number of hosts (52 host species) but with the Rosaceae as the family with the highest number of host species-Colletotrichum species association records (118 association records). According to occurrence data, 88 species are common in nature, 128 were considered as data deficient and 41 are threatened, some of which are likely extinct from nature and preserved only in culture collections. Several species are relevant plant pathogens, in some cases geographically confined and thus of potential quarantine relevance. Based on the major changes that occurred on Colletotrichum taxonomy over the last decade, this work provides a comprehensive overview of occurrence data of Colletotrichum species, compiling host range and geographical distribution, with relevance for plant pathology and conservation mycology. The current taxonomic framework in Colletotrichum is revealing numerous species but poses challenges to the employment of standard criteria for the evaluation of biological conservation of these fungi. We advocate that conservation mycology and taxonomy should find common routes simultaneously enabling the correct delimitation of species of Colletotrichum and the implementation of feasible criteria for the evaluation of conservation. The employment of new technologies, such whole genome sequencing (WGS), will help and support the description of new species and to gain a better understanding of the genetic bases of speciation processes.

Colletotrichum species and complexes: geographic distribution, host range and conservation status

Two new endophytic species, Colletotrichumjishouensesp. nov. and. C.tongrenensesp. nov. were isolated from Nothapodytespittosporoides in Guizhou and Hunan provinces, China. Detailed descriptions and illustrations of these new taxa are provided and morphological comparisons with similar taxa are explored. Phylogenetic analysis with combined sequence data (ITS, GAPDH, ACT and TUB2) demonstrated that both species formed distinct clades in this genus. This is the first record of Colletotrichum species from N.pittosporoides in China.

Two new endophytic Colletotrichum species from Nothapodytespittosporoides in China.

Strong primer bias for Tulasnellaceae fungi in metabarcoding: Specific primers improve the characterization of the mycorrhizal communities of epiphytic orchids

As one of the largest families of flowering plants, Orchidaceae is well-known for its high diversity and complex life cycles. Interestingly, such exquisite plants originate from minute seeds, going through challenges to germinate and establish in nature. Alternatively, orchid utilization as an economically important plant gradually decreases its natural population, therefore, driving the need for conservation. As with any conservation attempts, broad knowledge is required, including the species’ interaction with other organisms. All orchids establish mycorrhizal symbiosis with certain lineages of fungi to germinate naturally. Since the whole in situ study is considerably complex, in vitro symbiotic germination study is a promising alternative. It serves as a tool for extensive studies at morphophysiological and molecular levels. In addition, it provides insights before reintroduction into its natural habitat. Here we reviewed how mycorrhiza contributes to orchid lifecycles, methods to conduct in vitro study, and how it can be utilized for conservation needs.

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In Vitro Symbiotic Germination: A Revitalized Heuristic Approach for Orchid Species Conservation.

The root mycobiome plays a fundamental role in plant nutrition and protection against biotic and abiotic stresses. In temperate forests or meadows dominated by angiosperms, the numerous fungi involved in root symbioses are often shared between neighboring plants, thus forming complex plant-fungus interaction networks of weak specialization. Whether this weak specialization also holds in rich tropical communities with more phylogenetically diverse sets of plant lineages remains unknown. We collected roots of 30 plant species in semi-natural tropical communities including angiosperms, ferns, and lycophytes, in three different habitat types on La Réunion island: a recent lava flow, a wet thicket, and an ericoid shrubland. We identified root-inhabiting fungi by sequencing both the 18S rRNA and the ITS2 variable regions. We assessed the diversity of mycorrhizal fungal taxa according to plant species and lineages, as well as the structure and specialization of the resulting plant-fungus networks.The 18S and ITS2 datasets are highly complementary at revealing the root mycobiota. According to 18S, Glomeromycotina colonize all plant groups in all habitats forming the least specialized interactions, resulting in nested network structures, while Mucoromycotina (Endogonales) are more abundant in the wetland and show higher specialization and modularity compared to the former. According to ITS2, mycorrhizal fungi of Ericaceae and Orchidaceae, namely Helotiales, Sebacinales, and Cantharellales, also colonize the roots of most plant lineages, confirming that they are frequent endophytes. While Helotiales and Sebacinales present intermediate levels of specialization, Cantharellales are more specialized and more sporadic in their interactions with plants, resulting in highly modular networks.This study of the root mycobiome in tropical environments reinforces the idea that mycorrhizal fungal taxa are locally shared between co-occurring plants, including phylogenetically distant plants (e.g. lycophytes and angiosperms), where they may form functional mycorrhizae or establish endophytic colonization. Yet, we demonstrate that, irrespectively of the environmental variations, the level of specialization significantly varies according to the fungal lineages, probably reflecting the different evolutionary origins of these plant-fungus symbioses. Frequent fungal sharing between plants questions the roles of the different fungi in community functioning and highlights the importance of considering networks of interactions rather than isolated hosts. 

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Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities

Approximately 10% of vascular plants are epiphytes and, even though this has long been ignored in past research, are able to interact with a variety of fungi, including mycorrhizal taxa. However, the structure of fungal communities on bark, as well as their relationship with epiphytic plants, is largely unknown. To fill this gap, we conducted environmental metabarcoding of the ITS-2 region to understand the spatial structure of fungal communities of the bark of tropical trees, with a focus on epiphytic orchid mycorrhizal fungi, and tested the influence of root proximity. For all guilds, including orchid mycorrhizal fungi, fungal communities were more similar when spatially close on bark (i.e. they displayed positive spatial autocorrelation). They also showed distance decay of similarity with respect to epiphytic roots, meaning that their composition on bark increasingly differed, compared to roots, with distance from roots. We first showed that all of the investigated fungal guilds exhibited spatial structure at very small scales. This spatial structure was influenced by the roots of epiphytic plants, suggesting the existence of an epiphytic rhizosphere. Finally, we showed that orchid mycorrhizal fungi were aggregated around them, possibly as a result of reciprocal influence between the mycorrhizal partners.

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A fine-scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids.

The genus Tulasnella often forms mycorrhizas with orchids and has worldwide distribution. Species of this genus are associated with a wide range of orchids, including endangered hosts. Initially, species identification relied mostly on morphological features and few cultures were preserved for later phylogenetic comparisons. In this study, a total of 50 Tulasnella isolates were collected from their natural sites in Minas Gerais, Brazil, cultured, and subjected to a phylogenetic analysis based on alignments of sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal DNA. Our results, based on phylogeny, integrated with nucleotide divergence and morphology, revealed the diversity of isolated Tulasnella species, which included four new species, namely, Tulasnella brigadeiroensis, Tulasnella hadrolaeliae, Tulasnella orchidis and Tulasnella zygopetali. The conservation of these species is important due to their association with endangered orchid hosts and endemic features in the Brazilian Atlantic Forest.

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Diversity of mycorrhizal Tulasnella associated with epiphytic and rupicolous orchids from the Brazilian Atlantic Forest, including four new species.

A new endophytic species of Colletotrichum was isolated from an endangered orchid species, Cattleya jongheana in the Parque Estadual da Serra Negra, from the state of Minas Gerais, Brazil. It is described and illustrated as Colletotrichum serranegrense sp . nov . in this study. Morphology and multi-locus phylogenetic analyses based on combined ITS, ACT, TUB2 and CHS-1 sequence data revealed that these isolates were in the Colletotrichum gigasporum species complex and confirmed differences in this compared to other species in this genus.

Everaldo da Silva Cruz

Papers

A fine-scale spatial analysis of fungal communities on tropical tree bark unveils the epiphytic rhizosphere in orchids.

Diversity of mycorrhizal Tulasnella associated with epiphytic and rupicolous orchids from the Brazilian Atlantic Forest, including four new species.

Colletorichum serranegrense sp. nov. , a new endophytic species from the roots of the endangered Brazilian epiphytic orchid Cattleya jongheana