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Fungal endophyte diversity in coffee plants from Colombia, Hawai’i, Mexico and Puerto Rico. Fungal Ecol 3:122-138

Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
Fungal Ecology (Impact Factor: 2.99). 03/2010; DOI: 10.1016/j.funeco.2009.07.002

ABSTRACT 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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    • "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 · 1.70 Impact Factor
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    • "C. sativa, an important medicinal herb that contains hundreds of medicinally useful compounds (Flores-Sanchez & Verpoorte 2008), was also investigated for endophytic association in the present study and A. niger, A. flavus, P. chrysogenum, Phoma sp., A. alternata, Curvularia, Colltotrichum, Cladosporium and some mycelia setrlia were isolated. The isolation of these fungi is consistent with previous reports (Suryanarayana et al. 2005; Rosa et al. 2009; Gazis & Chaverri 2010; Marquez et al. 2010; Vega et al. 2010; González & Tello 2011; Kusari et al. 2012; Gautam et al. 2013). A. flavus, A. alternata, Cladosproium, Geotrichum and Rhizopus isolated from V. odorata in the present study are not reported frequently earlier, whereas the association of Colletorichum, Phomopsis and A. alternata as endophytes from A. vasica was reported earlier (Molla et al. 2010; Amirita et al. 2012; Dadgale 2012); but the detection of Haplosporium seems to reported for first time to the best of our knowledge. "
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    ABSTRACT: Fungal endophytes were isolated from surface sterilised leaf segments of five medicinal plants collected from Mandi district, Himachal Pradesh, India. A total of 373 fungal strains belonging to 15 fungal genera and 18 species, Aspergillus niger, A. flavus, A. clavatus, A. variecolor, Penicillium chrsogenum, Alternaria alternata, Curvularia lunata, Haplosporium sp., Phoma sp., Nigrospora sp., Colletotrichum sp., Cladosporium sp., Stemphylium sp., Fusarium sp., Geotrichum sp., Phomopsis sp., Trichoderma sp., Rhizopus sp. and some sterile mycelium were isolated from all the plants. The relative frequency, isolation rate and colonisation rates of endophytes were used to study the endophytic diversity. The results showed that the highest colonisation rate (93.05%) was observed in Adhathoda vasica, while it was 91.66% in Ocimum sanctum, 85% in Viola odorata, 82.81% Cannabis sativa and lowest (61.11%) in Withania somnifera. Moreover, reading the richness and diversity of the endophytic fungi, the highest was obtained for O. sanctum, W. somnifera and C. sativa having eight species each, while lowest (6 and 4) was obtained from A. vasica and V. odorata, respectively. As the role of endophytic organisms in defensive mechanisms of plants is now well established, the present study is an important step to find new and interesting endophytes among the medicinal plants.
    Archives of Phytopathology and Plant Protection 03/2014; 47(5). DOI:10.1080/03235408.2013.813678
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