Fungal endophyte diversity in coffee plants from Colombia, Hawai’i, Mexico and Puerto Rico

Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
Fungal Ecology (Impact Factor: 2.93). 03/2010; DOI: 10.1016/j.funeco.2009.07.002


Coffee (Coffea arabica) plant tissues were surface-sterilized and fungal endophytes isolated using standard techniques, followed by DNA extraction and sequencing of the internal transcribed spacer region (ITS). A total of 843 fungal isolates were recovered and sequenced (Colombia, 267; Hawai'i, 393; Mexico, 109; Puerto Rico, 74) yielding 257 unique ITS genotypes (Colombia, 113; Hawai'i, 126; Mexico, 32; Puerto Rico, 40). The most abundant taxa were Colletotrichum, Fusarium, Penicillium, and Xylariaceae. Overall, 220 genotypes were detected in only one of the countries sampled; only two genotypes were found in all four countries. Endophytes were also isolated from Coffea canephora, Coffea congensis, Coffea liberica, Coffea macrocarpa, Coffea racemosa, and Coffea stenophylla in Hawai'i. The high biodiversity of fungal endophytes in coffee plants may indicate that most of these are “accidental tourists” with no role in the plant, in contrast to endophytes that could be defined as “influential passengers” and whose role in the plant has been elucidated. This study, the most comprehensive analysis of fungal endophytes associated with a single host species, demonstrates that coffee plants serve as a reservoir for a wide variety of fungal endophytes that can be isolated from various plant tissues, including the seed, and illustrates the different fungal communities encountered by C. arabica in different coffee-growing regions of the world.

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    • "Plants growing in different geographical regions are confronted with different environmental challenges (Arnold 2007). These environmental cues, in combinatorial effect with host genotype, may shape the endophytic diversity harbored by the host plants (Vega et al. 2010). The diversity of endophytes associated with the plants varies not only temporally but spatially as well (Herrera et al. 2010; Ek-Ramos et al. 2013). "
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    ABSTRACT: Endophytism is the phenomenon of mutualistic association of a plant with a microorganism wherein the microbe lives within the tissues of the plant without causing any symptoms of disease. In addition to being a treasured biological resource, endophytes play diverse indispensable functions in nature for plant growth, development, stress tolerance and adaptation. Our understanding of endophytism and its ecological aspects are overtly limited and we have only recently started to appreciate its essence. Endophytes may impact plant biology through the production of diverse chemical entities including, but not limited to, plant growth hormones, and by modulating the gene expression of defense and other secondary metabolic pathways of the host. Studies have shown differential recruitment of endophytes in endophytic populations of plants growing in the same locations, indicating host specificity and that endophytes evolve in a coordinated fashion with the host plants. Endophytic technology can be employed for the efficient production of agricultural and economically important plants and plant products. The rational application of endophytes to manipulate the microbiota, intimately associated with plants, can help in enhancement of production of agricultural produce, increased production of key metabolites in medicinal and aromatic plants as well as adaption to new bio-geographic regions through tolerance to various biotic and abiotic conditions. However, the potential of endophytic biology can be judiciously harnessed only when we obtain insight into the molecular mechanism of this unique mutualistic relationship. In this paper, we present a discussion on endophytes, endophytism, their significance and diverse functions in nature as unraveled by the latest research to understand this universal natural phenomenon.
    Applied Microbiology and Biotechnology 02/2015; 99(7). DOI:10.1007/s00253-015-6487-3 · 3.34 Impact Factor
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    • "Other studies on the foliar endophytic fungi (EF) associated with coffee plants have been conducted in abandoned coffee plantations in Puerto Rico [15]; in various locations in Colombia, Hawai'i, Mexico, and Puerto Rico [16]; and in plantations in the center of Veracruz [17]. However, no studies have been conducted to investigate the effects of the different coffee agroforestry systems on the diversity of EF found on coffee leaves. "
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    ABSTRACT: Over the past 20 years, the biodiversity associated with shaded coffee plantations and the role of diverse agroforestry types in biodiversity conservation and environmental services have been topics of debate. Endophytic fungi, which are microorganisms that inhabit plant tissues in an asymptomatic manner, form a part of the biodiversity associated with coffee plants. Studies on the endophytic fungi communities of cultivable host plants have shown variability among farming regions; however, the variability in fungal endophytic communities of coffee plants among different coffee agroforestry systems is still poorly understood. As such, we analyzed the diversity and communities of foliar endophytic fungi inhabiting Coffea arabica plants growing in the rustic plantations and simple polycultures of two regions in the center of Veracruz, Mexico. The endophytic fungi isolates were identified by their morphological traits, and the majority of identified species correspond to species of fungi previously reported as endophytes of coffee leaves. We analyzed and compared the colonization rates, diversity, and communities of endophytes found in the different agroforestry systems and in the different regions. Although the endophytic diversity was not fully recovered, we found differences in the abundance and diversity of endophytes among the coffee regions and differences in richness between the two different agroforestry systems of each region. No consistent pattern of community similarity was found between the coffee agroforestry systems, but we found that rustic plantations shared the highest number of morphospecies. The results suggest that endophyte abundance, richness, diversity, and communities may be influenced predominantly by coffee region, and to a lesser extent, by the agroforestry system. Our results contribute to the knowledge of the relationships between agroforestry systems and biodiversity conservation and provide information regarding some endophytic fungi and their communities as potential management tools against coffee plant pests and pathogens.
    PLoS ONE 06/2014; 9(6):e98454. DOI:10.1371/journal.pone.0098454 · 3.23 Impact Factor
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    • "A 99 % threshold level was used for xylariaceous isolates based on Okane et al. (2008). The sequences of the OTUs were compared with the GenBank database using BLAST (Altschul et al. 1997) to assign their genera by referring to the first 100 BLAST matches and the distance trees produced by the BLAST-generated pairwise alignments (Vega et al. 2010). The nearest match reported for each OTU was the first BLAST match with detailed descriptions of taxa and multiple hits, rather than the top BLAST match. "
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    ABSTRACT: The diversity, composition, and host recurrence of endophytic fungi in the Xylariaceae were compared in subtropical (ST), cool temperate (CT), and subboreal forests (SB) in Japan based on the 28S ribosomal DNA sequences from fungal isolates. A total of 610 isolates were obtained from the leaves of 167 tree species in three sites, which were classified into 42 operational taxonomic units (OTUs) at the 99 % similarity level of the 28S rDNA sequence. ST, CT, and SB yielded 31, 13, and three OTUs, respectively. The OTU richness, diversity, and evenness of fungal communities were in the order: ST > CT > SB. The 42 OTUs were assigned to nine genera in the Xylariaceae: Xylaria, Annulohypoxylon, Anthostomella, Biscogniauxia, Nemania, Hypoxylon, Muscodor, Daldinia, and Rosellinia. Xylarioid isolates in the subfamily Xylarioideae outnumbered Hypoxyloid isolates in the subfamily Hypoxyloideae in ST and CT, whereas the opposite was found in SB. Sørensen’s quotient of similarity was generally low between the three sites. Host recurrence of fungal OTUs was evaluated with the degree of specialization of interaction network between xylariaceous endophytes and plant species and compared between the three sites. We found that the networks in the three sites showed a significantly higher degree of specialization than simulated networks, where partners were associated randomly. Permutational multivariate analyses of variance indicated that plant family and leaf trait significantly affected the OTU composition in ST, which can account for the specialization of interaction network and host recurrence of xylariaceous endophytes.
    Population Ecology 04/2014; 56(2). DOI:10.1007/s10144-013-0412-3 · 1.57 Impact Factor
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