Unveiling fungal diversity associated with coffee trees in China using a polyphasic approach and a global review of coffee saprobic fungi

Karimi M., Mehrabi-Koushki M., Farokhinejad R., Beigi S.

Xenodidymella species have a wide range of hosts and can be found as pathogens and saprobes. In this study, two new species of Xenodidymella were found from leaf diseases of three pasture-medicinal plants in Ilam Province, in the west of Iran, and proposed here as X. ilamica and X. scandicis spp. nov. These species were identified based on morphological features and phylogenetic analyses of the internal transcribed spacer regions 1 & 2 and 5.8S nrDNA (ITS), partial beta-tubulin gene (tub2), and partial RNA polymerase II second largest subunit (rpb2) gene. The four Xenodidymella strains isolated in this study were delimited into two sister clades, with the two isolates of X. ilamica from the leaf spot of Colchicum speciosum and Ficaria kochii and two isolates of X. scandicis from leaf blight of Scandix pecten-veneris. Morphologically, X. scandicis produces larger, ostiolate or poroid pycnidia in vitro, while pycnidia in the cultures of X. ilamica are non-ostiolate and smaller. Some pycnidia in old cultures of X. scandicis produce a neck, but a distinct neck in X. ilamica has not been observed. Moreover, three plants under study are new hosts for the genus Xenodidymella.

Rathnayaka A.R., Tennakoon D.S., Jones G.E., Wanasinghe D.N., Bhat D.J., Priyashantha A.K., Stephenson S.L., Tibpromma S., Karunarathna S.C.

Freitas V.V., Borges L.L., Vidigal M.C., dos Santos M.H., Stringheta P.C.

Coffee is a culture of great economic importance on the global stage. In the international market, the term "specialty coffee" describes a beverage of exceptional quality, distinguished by its unique flavors and characteristics. This superior quality becomes a key factor in accessing markets where consumers are willing to pay an added value for the product. Numerous factors, from cultivation to consumer preferences, play an essential role in determining the final quality of coffee. Understanding of these factors is essential for effectively managing coffee processing and beneficiation procedures. The review unveiled innovative findings that underscore the crucial influence of specific environmental variables on coffee quality, opening new perspectives enhance further the production and flavor of this highly valued crop. Additionally, the research addressed health-related aspects, providing insights into the potential benefits and impacts of coffee consumption on human health, expanding the understanding of this widely cherished beverage globally and individually. This comprehensive review explores various aspects of the coffee post-harvest process, encompassing its production, consumption, and the factors influencing its quality. Special emphasis will be given to the entire quality process involving coffee, with a discussion based on the available scientific literature. The quality of coffee beans is deeply influenced by various factors, including harvesting methods, geographical location, climate, and genetic characteristics. Additionally, post-harvest processing plays a crucial role, significantly impacting coffee's chemical composition and sensory attributes. The intrinsic complexity of coffee, composed of caffeine, chlorogenic acids, sugars, lipids, amino acids, minerals, and vitamins, makes it essential to understand these interconnected elements. Consumption of coffee offers a variety of health benefits when consumed in moderation. Studies indicate that coffee contains antioxidants that can help combat diseases such as type 2 diabetes, Parkinson's, and Alzheimer's. Additionally, the caffeine in coffee can improve alertness, concentration, and even athletic performance when consumed appropriately. Coffee can also promote sociability, providing a meeting point and a pause in the daily routine for many people worldwide. The review innovatively addresses the interaction of these factors, highlighting the influence of harvesting and processing on coffee quality. The complexity involved in production is emphasized, underscoring the importance of considering all stages, from cultivation to processing. This holistic approach aims to optimize coffee production, maximizing the value of its distinct characteristics. The focus is on the rich chemical composition of coffee, emphasizing the presence of individual components and the synergistic interaction between them. This interconnection is crucial for understanding how different production stages can influence the formation of unique sensory attributes in coffee. Furthermore, the review highlights the importance of sensory quality and the potential health benefits associated with coffee consumption. This comprehensive approach underscores how a deep understanding of these elements can guide the production of high-quality coffee. Consolidating this knowledge can serve as a foundation for developing of harmonized production procedures. This, in turn, not only elevates the quality of produced coffee but also contributes to creating prosperous market, where consumers can fully appreciate and value this beloved beverage's inherent nuances and benefits.

Kraisitudomsook N., Ahrendt S., Riley R., LaButti K., Lipzen A., Daum C., Barry K., Grigoriev I.V., Rämä T., Martin F., Smith M.E.

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.

Liu S., Zhao P., Cai L., Shen S., Wei H., Na Q., Han M., Wei R., Ge Y., Ma H., Karunarathna S.C., Tibprommab S., Zhang B., Dai D., Lin L., et. al.

LU L., KARUNARATHNA S.C., LIU Y., ELGORBAN A.M., TIBPROMMA S., JAYAWARDENA R.S.

During a survey of saprobic fungi on coffee samples in Yunnan Province, China, in 2020 and 2022, fungal fruiting bodies on decaying Liberian coffee twigs were collected and isolated. Maximum likelihood and Bayesian analyses of combined ITS, LSU, and RPB2 genes showed that the two isolated fungal strains belonged to a distinct species in Coniocessiaceae and were well separated from closely related genera with 73% ML and 0.92 PP statistical support. Morphologically, this distinct species can be differentiated from other genera in Coniocessiaceae by aseptate hamathecium, 4–8-spored asci with a flat apical ring, and fusiform ascospores, conical at the lower end. Based on morphology and phylogenetic analyses, the two fungal strains are described as a distinct new genus Pseudoconiocessia, within Coniocessiaceae. Pseudoconiocessia is introduced here with Pseudoconiocessia xishuangbannaensis as the type species.

Wanasinghe D.N., Nimalrathna T.S., Qin Xian L., Faraj T.K., Xu J., Mortimer P.E.

Whilst conducting surveys of lignicolous microfungi in Yunnan Province, we collected a large number of taxa that resemble Montagnula (Didymosphaeriaceae, Pleosporales). Our phylogenetic study on Montagnula involved analysing sequence data from ribosomal RNA genes (nc18S, nc28S, ITS) and protein-coding genes (rpb2, tef1-α). We present a biphasic approach (morphological and molecular phylogenetic evidence) that supports the recognition of four new species in Montagnula viz., M. lijiangensis, M. menglaensis, M. shangrilana and M. thevetiae. The global diversity of Montagnula is also inferred from metabarcoding data and published records based on field observations. Metabarcoding data from GlobalFungi and field observations provided insights into the global diversity and distribution patterns of Montagnula. Studies conducted in Asia, Australia, Europe, and North America revealed a concentration of Montagnula species, suggesting regional variations in ecological preferences and distribution. Montagnula species were found on various substrates, with sediments yielding a high number of sequences. Poaceae emerged as a significant contributor, indicating a potential association between Montagnula species and grasses. Culture-based investigations from previously published data revealed Montagnula species associations with 105 plant genera (in 45 plant families), across 55 countries, highlighting their wide ecological range and adaptability. This study enhances our understanding of the taxonomy, distribution, and ecological preferences of Montagnula species. It emphasizes their role in the decomposition of organic matter in grasslands and savannah systems and suggests further investigation into their functional roles in ecosystem processes. The global distribution patterns and ecological interactions of Montagnula species underscore the need for continued research and conservation efforts.

Adugna G.

Coffee berry disease (CBD), anthracnose of green berries of Arabica coffee, chronicles 100 years in 2022. The disease was detected for the first time in Kenya in 1922, and its causal pathogen was designated Colletotrichum coffeanum Noack (renamed C. kahawae). CBD has been causing substantial yield losses (ca. 80%) in susceptible varieties, and there has not been a coffee disease with a remarkable economic impact as CBD resulting in a sharp decline in total Arabica exports from Africa. During the past 100 years, a considerable amount of scientific knowledge on the biology, epidemiology, and management of coffee berry disease has been documented. The use of resistant varieties is the most empirical and effective CBD management practices in East Africa. The disease is still of great concern to Arabica producers and exporters around the world. There are unresolved issues that require the due attention of scientists and coffee communities. The nomenclature and taxonomic position of the fungus (C. coffeanum, C. kahawae, C. kahawae subsp. kahawae, and C. kahawae subsp. cigarro) confuse pathologists in identifying the actual cause of anthracnose in coffee berries and other hosts. The host resistance is consistently long-lasting. However, the nature of resistance and its inheritance mechanisms remained a major point of debate (oligogenic vs. polygenic), implicating that genetics of CBD resistance needs further in-depth analysis. This comprehensive review examines published information during the past 100 years that shows success stories; pinpoint contrasting research gaps that motivate scientists and sensitize coffee industries to the impact of coffee berry disease in Africa and beyond.

De Oliveira S.A., Barbosa F.R., De Andrade E.A., Bonaldo S.M.

Fungi play a pivotal role as nature's primary decomposers, thriving in diverse environments, particularly in soil and decaying organic matter. They contribute significantly to the renewal and recycling of materials, making a substantial impact on sustainable development. While research on saprophytic fungi in tropical regions has predominantly centered around South America, there is necessary to intensify studies in the Amazon region. This area remains relatively unexplored and is believed to harbor a greater biodiversity of species compared to temperate regions. Of notable importance agronomic field is the potential for saprophytic fungi to serve as novel biocontrol agents and resistance inducers. This study aimed to assess the capabilities of saprophytic fungi native to southern Amazonia in vitro, specifically in their ability to combat phytopathogens like Colletotrichum truncatum (LU2), Colletotrichum musae, Fusarium solani, Fusarium sp., Aspergillus clavatus, Sclerotinia sclerotiorum, and Rhizoctonia solani. The evaluation encompassed direct confrontation, sporulation, quantification of sclerodes and microsclerodes, the mycelial growth rate index (MGRI), and the percentage of inhibition. The saprophytic fungi employed in the study, Beltrania rhombica, Brachysporiella sp., Dictyochaeta sp., and Gonytrichum sp., demonstrated a significant impact in direct confrontation. These fungi exhibited varying degrees of growth inhibition against A. clavatus, C. truncatum (LU2), C. musae, and F. udum, with notes from 1 to 2. The results underscore their efficiency as promising antagonists to phytopathogens. In conclusion, the saprophytic fungi under investigation exhibit substantial potential in the control of these plant pathogens.

Niskanen T., Lücking R., Dahlberg A., Gaya E., Suz L.M., Mikryukov V., Liimatainen K., Druzhinina I., Westrip J.R., Mueller G.M., Martins-Cunha K., Kirk P., Tedersoo L., Antonelli A.

Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2–3 million fungal species with a “best estimate” at 2.5 million. To name the unknown >90% of these by the end of this century, we propose recognition of species known only from DNA data and call for large-scale sampling campaigns. We present an updated global map of fungal richness, highlighting tropical and temperate ecoregions of high diversity. We call for further Red List assessments and enhanced management guidelines to aid fungal conservation. Given that fungi play an inseparable role in our lives and in all ecosystems, and considering the fascinating questions remaining to be answered, we argue that fungi constitute the next frontier of biodiversity research. Expected final online publication date for the Annual Review of Environment and Resources, Volume 48 is October 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Hyde K., Norphanphoun C., Ma J., Yang H., Zhang J., Du T., Gao Y., Gomes de Farias A., He S., He Y., Li C., Li J., Liu X., Lu L., Su H., et. al.

Lu L., Karunarathna S.C., Dai D., Jayawardena R.S., Suwannarach N., Tibpromma S.

Coffee is one of the most important cash crops in Yunnan Province, China. Yunnan is ranked as the biggest producer of high-quality coffee in China. During surveys of microfungi from coffee plantations in Yunnan, six fungal strains that resemble Nigrogranaceae were collected. Multi-gene analyses of a combined SSU-LSU-ITS-rpb2-tef1-α sequence data matrix were used to infer the phylogenetic position of the new species in Nigrograna while morphological characteristics were used to deduce the taxonomic position of the new species. Six fungal strains isolated from decaying branches of Coffea arabica represent three new saprobic species in Nigrograna. The three new species, N. asexualis, N. coffeae, and N. puerensis, are described with full (macro and micro characteristics) descriptions, illustrations, and a phylogenetic tree that shows the phylogenetic position of new taxa.

Yang T., Tedersoo L., Soltis P.S., Soltis D.E., Sun M., Ma Y., Ni Y., Liu X., Fu X., Shi Y., Lin H., Zhao Y., Fu C., Dai C., Gilbert J.A., et. al.

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.

Lu L., Karunarathna S.C., Dai D., Xiong Y., Suwannarach N., Stephenson S.L., Elgorban A.M., Al-Rejaie S., Jayawardena R.S., Tibpromma S.

In Yunnan Province, the coffee-growing regions are mainly distributed in Pu’er and Xishuangbanna. During the surveys of microfungi associated with coffee in Yunnan Province, seven taxa were isolated from coffee samples. Based on molecular phylogenetic analyses of combined ITS, LSU, SSU, rpb2, and tef1-α sequence data and morphological characteristics, four new species viz. Deniquelata yunnanensis, Paraconiothyrium yunnanensis, Pseudocoleophoma puerensis, and Pse. yunnanensis, and three new records viz. Austropleospora keteleeriae, Montagnula thailandica, and Xenocamarosporium acaciae in Pleosporales are introduced. In addition, Paracamarosporium fungicola was transferred back to Paraconiothyrium based on taxonomy and DNA sequences. Full descriptions, illustrations, and phylogenetic trees to show the placement of new and known taxa are provided. In addition, the morphological comparisons of new taxa with closely related taxa are given.

Yu X., Zhang S., Liu J.

Pleosporales is the largest and most morphologically diverse order in Dothideomycetes, including a large proportion of saprobic fungi. During the investigation of microfungi from decaying wood in Sichuan Province, several novel fungal taxa of asexual and sexual morphs were collected, identified, and well-described. Phylogenetic analyses based on SSU, ITS, LSU, RPB2 and TEF1α gene sequences suggested that these new taxa were related to Pleosporales and distributed in five families, viz. Amorosiaceae, Bambusicolaceae, Lophiostomataceae, Occultibambusaceae and Tetraplosphaeriaceae. The morphological comparison and molecular phylogeny evidence justify the establishment of six new taxa, namely Bambusicola guttulata sp. nov., Flabellascoma sichuanense sp. nov., Neoangustimassarina sichuanensis gen. et sp. nov., Occultibambusa sichuanensis sp. nov. and Pseudotetraploa bambusicola sp. nov. Among them, Neoangustimassarina was introduced as the second sexual morph genus in Amorosiaceae; Bambusicola guttulata, O. sichuanensis and P. bambusicola were isolated from bamboos, which contributed to the diversity of bambusicolous fungi. The detailed, illustrated descriptions and notes for each new taxon are provided, as well as a brief note for each family. The potential richness of fungal diversity in Sichuan Province is also discussed.