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Seasonality affects the community of endophytic fungi in coconut (Cocos nucifera) crop leaves

ABSTRACT

The diversity of endophytic fungi in healthy coconut palm leaves (Cocos nucifera) was assessed by analyzing fungal isolates from three coconut cultivars (yellow dwarf, green dwarf, and a hybrid cultivar PB121) used agriculturally in Brazil. The influence of season (rainy or dry) on the endophytic fungal community was also analyzed. Overall, 318 fungal isolates were obtained from 972 coconut leaf fragments. The rDNA ITS region was sequenced from representative species of the isolated endophytic fungi and the most common species identified were Nigrospora oryzae, Pestalotiopsis sp., and Zasmidium musae. The alpha diversity of the endophytic fungi was also calculated. Nonmetric multidimensional scaling (NMDS) ordination and permutational analysis of variance (PERMANOVA) revealed significant seasonal effects on the composition of the endophyte community. However, practically no influence was observed on the fungal communities for the different cultivars of coconut.

Keywords:
Arecaceae; coconut palm; Cocos nucifera; endophytic fungi; internal transcribed

Introdution

Coconut (Cocos nucifera) belongs to the palm family Arecaceae and is one of the most important tropical crops in the world (Lamdande et al. 2018Lamdande AG, Prakash M, KSMS R. 2018. Storage study and quality evaluation of fresh coconut grating. Journal of Food Processing and Preservation 42: e13350. doi: 10.1111/jfpp.13350
https://doi.org/10.1111/jfpp.13350...
). It is commonly used to produce coconut oil, husk, fiber, and water, but it also has non-food uses in various industries, such as for brick, furniture, and coir production, as well as in the adsorption industry (Roopan & Elango2015Roopan SM, Elango G. 2015. Exploitation of Cocos nucifera a non-food toward the biological and nanobiotechnology field. Industrial Crops and Products 67: 130-136.). Additionally, coconuts are important for health promotion and disease prevention (DebMandal & Mandal 2011DebMandal M, Mandal S. 2011. Coconut (Cocos nucifera L.: Arecaceae): in health promotion and disease prevention. Asian Pacific Journal of Tropical Medicine 4: 241-247.), and they have been studied for their potential to prevent and treat Alzheimer’s disease (Fernando et al. 2015Fernando WMADB, Martins IJ, Goozee KG, Brennan CS, Jayasena V, Martins RN. 2015. The role of dietary coconut for the prevention and treatment of Alzheimer's disease: potential mechanisms of action. British Journal of Nutrition 114: 1-14.), as well as for their anti-inflammatory activity (Silva 2013Silva RR, Silva DO, Fontes HR, Alviano CS, Fernandes PD, Alviano DS. 2013. Anti-inflammatory, antioxidant, and antimicrobial activities of Cocos nucifera var. typica. BMC complementary and alternative medicine 13: 1-8.).

Endophytic fungi are microorganisms that inhabit plant tissues without causing disease symptoms (Azevedo & Araujo 2007Azevedo JL, Araujo WL. 2007. Diversity and applications of endophytic fungi isolated from tropical palnts. In: Ganguli BN, Deshmukh SK. (eds.) Fungi: multifaceted microbes. Boca Raton p, Chemical Rubber Company Press. p. 189-207.). They are helpful to many different plants by acting as biocontrol agents (Mejía et al. 2008Mejía LC, Rojas EI, Maynard Z, et al. 2008. Endophytic fungi as biocontrol agents of Theobroma cacao pathogens. Biological Control 46: 4-14.; Larran et al. 2016Larran S, Simon MR, Moreno MV, Siurana MS, Perelló A. 2016. Endophytes from wheat as biocontrol agents against tan spot disease. Biological Control 92: 17-23.; Saad et al. 2019Saad MM, Ghareeb RY, Saeed AA. 2019. The potential of endophytic fungi as bio-control agents against the cotton leafworm, Spodoptera littoralis (Boisd.) (Lepidoptera: Noctuidae). Egyptian Journal of Biological Pest Control 29: 7. doi: 10.1186/s41938-019-0108-x
https://doi.org/10.1186/s41938-019-0108-...
; NI Silva et al. 2019Silva NI, Brooks S, Lumyong S, Hyde KD. 2019. Use of endophytes as biocontrol agents. Fungal Biology Reviews 33: 133-148.), promoters of antimicrobial activity (Malhadas et al. 2017Malhadas C, Malheiro R, Pereira JA, Pinho PG, Baptista P. 2017. Antimicrobial activity of endophytic fungi from olive tree leaves. World Journal of Microbiology and Biotechnology 33: 46. doi: 10.1007/s11274-017-2216-7
https://doi.org/10.1007/s11274-017-2216-...
), and contributing to abiotic stress tolerance (Hubbard et al. 2014Hubbard M, Germida JJ, Vujanovic V. 2014. Fungal endophytes enhance wheat heat and drought tolerance in terms of grain yield and second‐generation seed viability. Journal of Applied Microbiology 116: 109-122.).

Several new species of endophytic fungi have been described (Bezerra et al. 2017 a Bezerra JDP, Sandoval-Denis M, Paiva LM, et al. 2017a. New endophytic Toxicocladosporium species from cacti in Brazil, and description of Neocladosporium gen. nov. International Mycological Association Fungus 8: 77-97.; bBezerra JDP, Oliveira RJV, Paiva LM, et al. 2017b. Bezerromycetales and Wiesneriomycetales ord. nov. (class Dothideomycetes), with two novel genera to accommodate endophytic fungi from Brazilian cactus. Mycological Progress 16: 297-309.; 2018Bezerra JDP, Machado AR, Firmino AL, et al. 2018. Mycological Diversity Description I. Acta Botanica Brasilica 32: 656-666.; Oliveira et al. 2016Oliveira RJV, Bezerra JL, Lima TEF, Silva GA, Cavalcanti MADQ. 2016. Phaeosphaeria nodulispora, a new endophytic coelomycete isolated from tropical palm (Cocos nucifera) in Brazil. Nova Hedwigia 185-192.; Silva et al. 2019 a Silva RMF, Soares AM, Pádua APSL, et al. 2019a. Mycological Diversity Description II. Acta Botanica Brasilica 33: 163-173.; bSilva RMF, Oliveira RJV, Bezerra JDP, Bezerra JL, Souza-Motta CM, Silva GA. 2019b. Bifusisporella sorghi gen. et sp. nov. (Magnaporthaceae) to accommodate an endophytic fungus from Brazil. Mycological Progress 18: 847-854.) and many studies have been carried out on the endophytic fungal communities of important crop plants, such as coffee, rice, grapes, and soybeans (Pimentel et al. 2006Pimentel IC, Glienke-Blanco C, Gabardo J, Stuart RM, Azevedo JL. 2006. Identification and colonization of endophytic fungi from soybean (Glycine max (L.) Merril) under different environmental conditions. Brazilian Archives of Biology and Technology 49: 705-711. ; Sette et al. 2006Sette LD, Passarini MRZ, Delarmelina C, Salati F, Duarte MCT. 2006. Molecular characterization and antimicrobial activity of endophytic fungi from coffee plants. World Journal of Microbiology and Biotechnology 22: 1185-1195.; Naik et al. 2009Naik BS, Shashikala J, Krishnamurthy YL. 2009. Study on the diversity of endophytic communities from rice (Oryza sativa L.) and their antagonistic activities in vitro. Microbiological Research 164: 290-296.; Lima et al. 2014Lima TEF, Oliveira RJV, Bezerra JL, Cavalcanti MDQ. 2014. Endophytic fungi from leaves and roots of Vitis labrusca cv. Isabel in Pernambuco/Brazil. Sydowia 66: 115-128. ; Oliveira et al. 2014aOliveira R, Souza R, Lima T, Cavalcanti M. 2014a. Endophytic fungal diversity in coffee leaves (Coffea arabica) cultivated using organic and conventional crop management systems. Mycosphere 5: 523-530.; Vaz et al. 2014Vaz AB, Fontenla S, Rocha FS, et al. 2014. Fungal endophyte β-diversity associated with Myrtaceae species in an Andean Patagonian forest (Argentina) and an Atlantic forest (Brazil). Fungal Ecology 8: 28-36.; Varanda et al. 2016Varanda CMR, Oliveira M, Materatski P, Landum M, Clara MIE, Rosário FM. 2016. Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management. Fungal Biology 120: 1525-1536.). Initial studies of endophytic fungi in palm species (Arecaceae) were carried out by Rodrigues & Samuels (1990Rodrigues KF, Samuels GJ. 1990. Preliminary study of endophytic fungi in a tropical palm. Mycological Research 94: 827-830.) in Australia, who isolated fungi from the leaves of Licuala ramsayi. Further studies were performed by Taylor et al. (1999Taylor JE, Hyde KD, Jones EBG. 1999. Endophytic associated with the temperate palm Trachycarpus fortunei within and outside its natural geographical range. New Phytologist 142: 335-346.), who characterized the endophytic mycobiota of Trachycarpus fortunei; Rodrigues (1994)Rodrigues KF. 1994. The foliar fungal endophytes of the Amazonian palm Euterpe oleracea. Mycologia 86: 376-385., who isolated endophytic fungi from the Amazonian palm (Euterpe oleracea); and Mariano et al. (1997Mariano RLR, Lira RVI, Silveira EB, Menezes M. 1997. Levantamento de fungos endofíticos e epifíticos em folhas de coqueiro no Nordeste do Brasil. I. Frequência da população fúngica e efeito da hospedeira. Agrotópica 9: 127-134.), who compared the epiphytic and endophytic communities of Cocos nucifera. In addition, other studies on endophytic fungal isolates from palm species have been carried out on the Bermudian palmetto (Sabal bermudana), the Chinese fan palm (Livistona chinensis), and Wallichia caryotoides (Southcott & Johnson 1997Southcott KA, Johnson JA. 1997. Isolation of endophytes from two species of palm from Bermuda. Canadian Journal of Microbiology 43: 789-792.; Lumyong et al. 2009Lumyong S, Techa W, Lumyong P, McKenzie EHC, Hyde KD. 2009. Endophytic fungi from Calamus kerrianus and Wallichia caryotoides (Arecaceae) at Doi Suthep-Pui National Park, Thailand. Chiang Mai Journal Science 36: 158-167.). Many studies have already investigated the influence of seasonality on endophytic fungal communities (Arnold & Lutzoni 2007Arnold AE, Lutzoni F. 2007. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88: 541-549.; Mishra et al. 2012Mishra A, Gond SK, Kumar A, Sharma VK, Verma SK, Kharwar RN, Sieber TN. 2012. Season and tissue type affect fungal endophyte communities of the Indian medicinal plant Tinospora cordifolia more strongly than geographic location. Microbial Ecology 64: 388-398.; U’Ren et al. 2012U'Ren JM, Lutzoni F, Miadlikowska J, Laetsch AD, Arnold AE. 2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany 99: 898-914.; Ek-Ramos et al. 2013Ek-Ramos MJ, Zhou W, Valencia CU, et al. 2013. Spatial and temporal variation in fungal endophyte communities isolated from cultivated cotton (Gossypium hirsutum). PLOS ONE 8: e66049. doi: 10.1371/journal.pone.0066049
https://doi.org/10.1371/journal.pone.006...
; Yadav et al. 2016Yadav M, Yadav A, Kumar S, Yadav JP. 2016. Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains. BMC Microbiology 16: 44. doi: 10.1186/s12866-016-0664-0
https://doi.org/10.1186/s12866-016-0664-...
). However, little is known about the influence of seasonality on endophytic fungi in species of palm crops (such as coconut).

Studies on the composition of endophytic fungal communities, in relation to the influence of seasonality and the differences between plant cultivars of the same species, are poorly understood, especially in palm crops. We hypothesize that the endophytic fungal communities of different cultivars of Cocos nucifera are influenced by both seasonal factors and cultivar type. The aim of the present study was to evaluate the influence of both seasonality and coconut cultivar on the community of endophytic fungi in healthy leaves of plants cultivated in Northeastern Brazil.

Materials and methods

Sampling area

The study was conducted in three coconut crops located in the Instituto Agronômico de Pernambuco (IPA) in Goiana, Pernambuco state, Northeastern Brazil (7°33'45" S, 35°0'0" W). The precipitation and temperature for the area are shown in Figure 1.

Figure 1
Climatic characteristics (precipitation and temperature) of the collecting area located in Pernambuco, Brazil. The collection dates are represented by circles and triangles (source: http://www. inmet.gov.br).

Leaf sampling

Between May 2012 and April 2013, six leaf collections were performed (three in the dry season, September to March, and three in the rainy season, April to August). Samples were collected from three subareas, each of which corresponded to the location of a specific coconut cultivar. The cultivars used were as follows: 1. Yellow dwarf, 2. Green dwarf, and 3. A hybrid cultivar (PB121). In each subarea, three random points were delimited. Three individuals of coconut were chosen at each point, from which three leaves were collected, giving a total of 27 leaves from each subarea. Eighty-one leaves were obtained per collection from across all of the subareas, giving an overall total of 486 leaves for the study (243 leaves from the dry season and 243 from the rainy season). The samples were processed within a maximum of 24 h from collection.

Isolation of endophytic fungi

In the laboratory, the collected leaves were first washed carefully with running water and soap. Leaf discs (6 mm diameter) were then cut at random from all parts of the leaves. The discs were then decontaminated with 70 % ethanol for 1 min and 2 % sodium hypochlorite (NaOCl) for 2.5 min. Finally, they were washed again with 70 % alcohol for 30 s to remove excess hypochlorite. To complete the sterilization process, the material was rinsed with sterilized distilled water (Araújo et al. 2002Araújo WL, Lima ADS, Azevedo JLD, Marcon J, Sobral JK, Lacava PT. 2002. Manual: isolamento de microrganismos endofíticos. Piracicaba, Centro Acadêmico "Luiz de Queiroz".).

The leaves from each collection point were mixed to create composite samples. In total, 972 leaf fragments were obtained (equating to 324 fragments per cultivar or 486 fragments per season). Six leaf discs were transferred to each of three Malt Extract Agar (MEA) Petri dishes supplemented with chloramphenicol (50 mg L-1), which were incubated at room temperature (28 ± 2 °C) and observed daily for 15 days to record the development of fungal colonies from each sample. As an aseptic control, 50 µL of the final rinsing water was plated on MEA as evidence of surface disinfection (Pereira et al. 1993Pereira JO, Azevedo JL, Petrini O. 1993. Endophytic fungi of Stylosanthes. Mycologia 85: 362-364. ). Isolates were first grouped into morphotypes based on morphological characteristics, and then confirmed by DNA sequencing.

Extraction, amplification, and sequencing of rDNA

Biomass was obtained from cultures grown on MEA after 7 days at 25 °C. DNA was extracted using the cetyltrimethylammonium bromide (CTAB) method based on the protocol described by Oliveira et al. (2016Oliveira RJV, Bezerra JL, Lima TEF, Silva GA, Cavalcanti MADQ. 2016. Phaeosphaeria nodulispora, a new endophytic coelomycete isolated from tropical palm (Cocos nucifera) in Brazil. Nova Hedwigia 185-192.). To amplify the internal transcribed spacer (ITS) sequence of nuclear rDNA, the primer pair ITS1/ITS4 (White et al. 1990 White TJ, Bruns T, Lee SJWT, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: a Guide to Methods and Applications 18: 315-322.) were used, following the PCR protocol described by Oliveira et al. (2014b)Oliveira RJV, Lima TE, Cunha IB, Coimbra VR, Silva GA, Bezerra JL, Cavalcanti MA. 2014b Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil. Phytotaxa 178: 197-204.. Sequencing was performed by the Plataforma Multiusuária de Sequenciamento de DNA, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil. The sequences obtained were deposited in the National Center for Biotechnology Information (NCBI), under accession numbers MK508790 to MK508819, and were compared by percentual of identity, with homologous sequences of several fungi taxa (by BLASTn) already deposited in the NCBI (Tab. 1). Species sequences with multiple coincidences or ambiguous results were only classified to the genus level. Cladosporium dominicanum (KJ000287) and Phaeosphaeria nodulispora (KR092904) were identified from previous studies (Oliveira et al. 2014cOliveira RJV, Lima TE, Cunha IB, Coimbra VR, Silva GA, Bezerra JL, Cavalcanti MA. 2014b Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil. Phytotaxa 178: 197-204.; Oliveira et al. 2016Oliveira RJV, Bezerra JL, Lima TEF, Silva GA, Cavalcanti MADQ. 2016. Phaeosphaeria nodulispora, a new endophytic coelomycete isolated from tropical palm (Cocos nucifera) in Brazil. Nova Hedwigia 185-192.).

Table 1
Endophytic fungi isolated from three cultivars of coconut crop in Brazil.

Data analysis

The sampling efficacy was assessed using individual-based rarefaction (interpolation) and extrapolation analyses with 95 % unconditional confidence intervals in the iNEXT R software package (Hsieh et al. 2016Hsieh TC, Ma KH, Chao A. 2016. iNEXT: an R package for rarefaction and extrapolation of species diversity (H ill numbers). Methods in Ecology and Evolution 7: 1451-1456.). The rarefied and extrapolated alpha diversities of taxa were displayed in relation to the sample unit. The general linear model (GLM) was used to test for significant differences in fungal endophyte diversity (alpha diversity and effective alpha diversity as the exponential of the Shannon index) for each cultivar and season (Jost 2006Jost L. 2006. Entropy and diversity. Oikos 113: 363-375.). A general linear mixed model (GLMM) was used to test for cultivar specificity of endophytic species abundance, with plant species as fixed factors and plots as random factors, using the lme4 software package (Bates et al. 2014Bates D, Mächler M, Bolker B, Walker S. 2014. Fitting linear mixed-effects models using lme4. Journal of Statistical Software 67. https://arxiv.org/pdf/1406.5823.pdf.
https://arxiv.org/pdf/1406.5823.pdf...
). The generalized additive model (GAM) was used to test for the influence of sampling time on endophytic species diversity, using the mgcv R software package (Wood 2017Wood S. 2017. R Package mgcv: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation. https://CRAN.R-project.org/package=mgcv . 21 Oct. 2017.
https://CRAN.R-project.org/package=mgcv...
). Post hoc multiple comparison tests were conducted using the agricolae software package with the Bonferroni-adjusted kruskal function (Mendiburu 2016Mendiburu F. 2016. Package agricolae: Statistic procedure for agricultural research. https://CRAN.R-project.org/package=agricolae. 21 Oct. 2017.
https://CRAN.R-project.org/package=agric...
). The diversity and overlap of endophytic taxa across the three cultivars were visualized by assembling a bipartite network, implemented with the bipartite package in R (Dormann et al. 2008Dormann C, Gruber B, Fründ J. 2008. Introducing the bipartite package: analysing ecological networks. R News 8: 8-11.).

The endophytic community data were standardized according to the Hellinger method, using the decostand function of the vegan R software package, to avoid variable sampling intensity due to variation in the number of species. A variety of other statistical tests were also performed using various functions of the vegan software package, as described below. The variation in endophytic fungal communities between host cultivars was determined using multivariate analysis (Oksanen et al. 2015Oksanen J, Blanchet F, Kindt R, et al. 2015. vegan: community ecology package. R package v.2.2-1. http://CRAN.R-project.org/package=vegan. 21 Oct. 2017.
http://CRAN.R-project.org/package=vegan...
), and differences in fungal community composition between the samples were calculated using the Bray-Curtis dissimilarity method. Nonmetric multidimensional scaling (NMDS) was used to graphically visualize the organization of the samples in two-dimensional space using the metaMDS function. To test the overall effects of host identity and seasonality on the endophytic fungal community, permutational multivariate analysis of variance (PERMANOVA) (Anderson 2001Anderson MJ. 2001. A new method for non‐parametric multivariate analysis of variance. Austral Ecology 26: 32-46. ; McArdle & Anderson 2001McArdle BH, Anderson MJ. 2001. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82: 290- 297.) was performed using the adonis function (9,999 permutations). The turnover of species composition among communities (beta diversity) was evaluated using the betadisper function to perform analyses of multivariate homogeneity of group dispersion (Anderson 2006Anderson MJ. 2006. Distance‐based tests for homogeneity of multivariate dispersions. Biometrics 62: 245-253.). Post hoc pairwise PERMANOVA analyses were used to test for significant differences in each of the factors.

Results

Composition of fungal endophytes

In the 972 leaf fragments, 318 fungal endophyte specimens were found, with an isolation frequency of 32.7 %. Overall, 32 species belonging to 14 orders were identified. The rDNA ITS region was sequenced from representatives of each endophytic fungal species isolated from Cocos nucifera, except for Syncephalastrum racemosum and Xylaria sp. (for which it was not possible to amplify the ITS region). The maximum identity of each species was then calculated using the BLASTn program from the NCBI platform (Tab. 1).

Variation in the diversity of endophytic fungi between cultivars

The abundance of endophytic species differed between the cultivars (X 2 = 7.39, P = 0.02), with the highest number of species found in the PB121 hybrid cultivar (Fig. S1A in the supplementary material). The most abundant taxa were Cladosporium sp., Pestalotiopsis sp., Nigrospora oryzae, and Zasmidium musae, which presented similar distribution patterns in the different coconut cultivars throughout the sampling period (Fig. S1B in the supplementary material). The alpha diversity and effective number of species (exponential of Shannon index) of endophytic fungi were similar in the three cultivars (X 2 = 0.40, P = 0.81 and X 2 = 0.56, P = 0.75, respectively) (Fig. S2 in the supplementary material). The endophytic fungi rarefaction curves indicated that the overall number of endophytic fungi was higher in the yellow dwarf cultivar (mean and SE per plot; 2.74 ± 0.39), followed by the green dwarf (2.56 ± 0.33) and the PB121 hybrid (2.5 ± 0.25) (Fig. S3 in the supplementary material). The extrapolation curves suggest that additional sampling may allow the detection of more endophytic fungi.

The alpha diversity of endophytic fungi varied significantly with the sampling season (edf = 5, F = 2.67, P = 0.03). The alpha diversity of endophytic fungi associated with the green dwarf cultivar was lower (X 2 = 11.3, P = 0.04) at the end of both the rainy and dry seasons, while the alpha diversity of the yellow dwarf (X 2 = 3.2, P = 0.66) and PB121 hybrid cultivars (X 2 = 1.53, P = 0.9) did not differ over time (Fig. 2). Only six fungal taxa were common to the three cultivars, with the highest number of shared taxa (eight) found between the yellow and green dwarf cultivars (Fig. S4 in the supplementary material). According to a network analysis, the PB121 hybrid presented the highest specificity index (0.29), followed by green dwarf (0.25), with yellow dwarf (0.24) being the most generalist host among the coconut cultivars.

Figure 2
The alpha diversity of endophytic fungi associated with the three coconut cultivars throughout the sampling timeframe. The letters compare the alpha diversity of endophytic fungi associated with a host (mean ± SE) at different sampling times. Different letters represent significant differences identified using the generalized additive model (GAM) and post hoc Kruskal-Wallis test for multiple comparisons (p<0.05).

Occurrence and community composition of endophytic fungi according to season

NMDS ordination and PERMANOVA analyses revealed significant effects of the season on endophytic fungal community composition (Pseudo-F = 4.38, R 2 = 0.08, P = 0.003). The standardized deviation ellipses showed clear separation of the fungal communities between the rainy and dry seasons (Fig. 3). In the dry season, 21 taxa from 10 orders were recorded, compared to 22 species from 11 orders in the rainy season. The greatest number of orders was associated with the yellow dwarf cultivar (12), followed by the green dwarf (11) and PB121 hybrid (10) cultivars. Capnodiales and Tricosphaeriales were the richest orders found in the three cultivars. The order Mucorales occurred only in the yellow dwarf cultivar. The order Amphisphaeriales was mostly present during the rainy season, with the highest abundance at the beginning of the season in all the cultivars. Cystobasidiales was present only in the yellow dwarf and green dwarf cultivars, and only two isolates of this order occurred during the dry season. Conversely, the order Ustilaginales occurred only during the rainy season (Tab. 1).

Figure 3
Nonmetric multidimensional scaling (NMDS) ordination plot of the endophytic fungal communities associated with the three coconut cultivars based on Bray-Curtis dissimilarities between samples. Ellipses represent confidence regions based on the SD from the centroid for each ecological unit.

Discussion

The isolation frequency (32.7 %) of endophytic fungi was similar to that found in other studies of the Arecaceae family. Rodrigues (1994Rodrigues KF. 1994. The foliar fungal endophytes of the Amazonian palm Euterpe oleracea. Mycologia 86: 376-385.) isolated endophytic fungi from Euterpe oleracea, obtaining a 21-30 % isolation rate, and Southcott & Johnson (1997Southcott KA, Johnson JA. 1997. Isolation of endophytes from two species of palm from Bermuda. Canadian Journal of Microbiology 43: 789-792.) reported an isolation frequency of 20.3 % in two species of palm (Sabal bermudana and Livistona chinensis). However, Taylor et al. (1999Taylor JE, Hyde KD, Jones EBG. 1999. Endophytic associated with the temperate palm Trachycarpus fortunei within and outside its natural geographical range. New Phytologist 142: 335-346.) and Lumyong et al. (2009Lumyong S, Techa W, Lumyong P, McKenzie EHC, Hyde KD. 2009. Endophytic fungi from Calamus kerrianus and Wallichia caryotoides (Arecaceae) at Doi Suthep-Pui National Park, Thailand. Chiang Mai Journal Science 36: 158-167.) reported higher isolation frequencies of endophytic fungi, of 60.9 % and 68.7 %, from Trachycarpus fortunei and Wallichia caryotoides.

In this study, we found that alpha diversity was similar between the three cultivars, and the most abundant taxa were the same for all the cultivars. The genetic and physiological differences between the coconut cultivars are insufficient to greatly influence the species richness of the endophytic fungal communities. Mariano et al. (1997Mariano RLR, Lira RVI, Silveira EB, Menezes M. 1997. Levantamento de fungos endofíticos e epifíticos em folhas de coqueiro no Nordeste do Brasil. I. Frequência da população fúngica e efeito da hospedeira. Agrotópica 9: 127-134.), also working with Cocos nucifera, similarly reported that very common species were not specific to any cultivar. Pancher et al. (2012Pancher M, Ceol M, Corneo PE, et al. 2012. Fungal endophytic communities in grapevines (Vitis vinifera L.) respond to crop management. Applied and Environmental Microbiology 78: 4308-4317.) suggested that differences between grape cultivars (Merlot and Chardonnay) may drive only a minor shift in endophyte composition when compared to crop management. In addition, the composition of the endophytic fungal communities was not found to be significantly different between the Syrah, Cabernet Sauvignon, and Aragonez grape cultivars (Varanda et al. 2016Varanda CMR, Oliveira M, Materatski P, Landum M, Clara MIE, Rosário FM. 2016. Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management. Fungal Biology 120: 1525-1536.). On the other hand, the endophytic communities were found to be statistically different between two cultivars of pepper (at the seedling stage) in open field and greenhouse trials (Halász et al. 2016Halász K, Borbély C, Pós V, Gáspár L, Haddadderafshi N, Winter Z, Lukács N. 2016. Effect of crop management and cultivar on colonization of Capsicum annuum L. by Endophytic Fungi. Acta Universitatis Sapientiae, Agriculture and Environment 8: 5-15.). In olive cultivars, endophytic fungi richness and diversity are influenced by changes in season, site, and cultivar (Materatski et al. 2019Materatski P, Varanda C, Carvalho T, et al. 2019. Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars. Fungal Biology 123: 66-76.). The reports above suggest that the differences in endophytic fungal community composition between cultivars depend on the host species.

Although the endophytic fungal community composition was not significantly different between cultivars, NMDS ordination and PERMANOVA analyses revealed significant effects of the season on the fungal community composition. This suggests that environmental factors can influence the fungal community more than the choice of cultivar. It is possible that differences in the environmental humidity favor some groups of endophytic fungi, or that, depending on the season, the plant physiology changes to give an advantage to some taxa of fungi over others. In Eugenia jambolana, the diversity of fungal species was different in summer compared to winter (Yadav et al. 2016Yadav M, Yadav A, Kumar S, Yadav JP. 2016. Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains. BMC Microbiology 16: 44. doi: 10.1186/s12866-016-0664-0
https://doi.org/10.1186/s12866-016-0664-...
). According to Martins et al. (2016Martins F, Pereira JA, Bota P, Bento A, Baptista P. 2016. Fungal endophyte communities in above-and belowground olive tree organs and the effect of season and geographic location on their structures. Fungal Ecology 20: 193-201.), seasonal differences in the endophytic fungal communities were detected in the olive tree, but other factors, such as different tissues of the host, are also important. The fungal communities in the Indian medicinal plant Tinospora cordifolia were more strongly affected by season when compared to geographic location (Mishra et al. 2012Mishra A, Gond SK, Kumar A, Sharma VK, Verma SK, Kharwar RN, Sieber TN. 2012. Season and tissue type affect fungal endophyte communities of the Indian medicinal plant Tinospora cordifolia more strongly than geographic location. Microbial Ecology 64: 388-398.). Similarly, according to Yadav et al. (2016)Yadav M, Yadav A, Kumar S, Yadav JP. 2016. Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains. BMC Microbiology 16: 44. doi: 10.1186/s12866-016-0664-0
https://doi.org/10.1186/s12866-016-0664-...
, the diversity and colonization frequency of endophytic populations are more influenced by factors such as season.

In the present study, some species were detected only in the rainy season, while others were present only in the dry season. The order Cystobasidiales, for example, was present only during the dry season, while Ustilaginales occurred only during the rainy season. According to Sadeghi et al. (2019Sadeghi F, Samsampour D, Seyahooei M A, Bagheri A, Soltani J. 2019. Diversity and spatiotemporal distribution of fungal endophytes associated with Citrus reticulata cv. Siyahoo. Current Microbiology 76: 279-289.), the species richness of endophytic fungi in mandarin trees is probably higher in the autumn than in the spring, due to the higher rainfall. Factors such as precipitation and temperature can impact the release of inoculum and the germination of fungal spores, subsequently influencing the establishment of the fungi. Under favorable conditions (depending on the season), a greater number of fungal morphotypes can be isolated from the foliar tissue (Singh et al. 2017Singh DK, Sharma VK, Kumar J, et al. 2017. Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn. f.: Spatiotemporal and tissue type effects. Scientific Reports 7: 3745. doi: 10.1038/s41598-017-03933-0
https://doi.org/10.1038/s41598-017-03933...
).

In this study, we observed that seasonal differences have an influence on the community of endophytic fungi. However, practically no influence was observed on the fungal communities for different cultivars of coconut. Thus, our hypothesis was only partially confirmed. As coconut is an important crop, studying the diversity of endophytic fungi in different cultivars and seasons is important for better understanding the dynamics of these fungal communities. Environmental factors (i.e., the season) can alter the communities of endophytic fungi in coconut leaves. Considering that some of these endophytic fungi can be latent pathogens, knowledge about their ecology, pertaining to differences between seasons and cultivars, can contribute towards future work on phytopathology in order to assist farmers with the management of this plant. However, more studies are necessary to better understand these relationships and how they can benefit crop systems.

Acknowledgements

We thank the Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE) and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for providing fellowships to R.J.V. de Oliveira, J.L. Bezerra, and G.A. da Silva.

References

  • Anderson MJ. 2001. A new method for non‐parametric multivariate analysis of variance. Austral Ecology 26: 32-46.
  • Anderson MJ. 2006. Distance‐based tests for homogeneity of multivariate dispersions. Biometrics 62: 245-253.
  • Araújo WL, Lima ADS, Azevedo JLD, Marcon J, Sobral JK, Lacava PT. 2002. Manual: isolamento de microrganismos endofíticos. Piracicaba, Centro Acadêmico "Luiz de Queiroz".
  • Arnold AE, Lutzoni F. 2007. Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88: 541-549.
  • Azevedo JL, Araujo WL. 2007. Diversity and applications of endophytic fungi isolated from tropical palnts. In: Ganguli BN, Deshmukh SK. (eds.) Fungi: multifaceted microbes. Boca Raton p, Chemical Rubber Company Press. p. 189-207.
  • Bates D, Mächler M, Bolker B, Walker S. 2014. Fitting linear mixed-effects models using lme4. Journal of Statistical Software 67. https://arxiv.org/pdf/1406.5823.pdf
    » https://arxiv.org/pdf/1406.5823.pdf
  • Bezerra JDP, Machado AR, Firmino AL, et al 2018. Mycological Diversity Description I. Acta Botanica Brasilica 32: 656-666.
  • Bezerra JDP, Oliveira RJV, Paiva LM, et al 2017b. Bezerromycetales and Wiesneriomycetales ord. nov. (class Dothideomycetes), with two novel genera to accommodate endophytic fungi from Brazilian cactus. Mycological Progress 16: 297-309.
  • Bezerra JDP, Sandoval-Denis M, Paiva LM, et al 2017a. New endophytic Toxicocladosporium species from cacti in Brazil, and description of Neocladosporium gen. nov. International Mycological Association Fungus 8: 77-97.
  • DebMandal M, Mandal S. 2011. Coconut (Cocos nucifera L.: Arecaceae): in health promotion and disease prevention. Asian Pacific Journal of Tropical Medicine 4: 241-247.
  • Dormann C, Gruber B, Fründ J. 2008. Introducing the bipartite package: analysing ecological networks. R News 8: 8-11.
  • Ek-Ramos MJ, Zhou W, Valencia CU, et al 2013. Spatial and temporal variation in fungal endophyte communities isolated from cultivated cotton (Gossypium hirsutum). PLOS ONE 8: e66049. doi: 10.1371/journal.pone.0066049
    » https://doi.org/10.1371/journal.pone.0066049
  • Fernando WMADB, Martins IJ, Goozee KG, Brennan CS, Jayasena V, Martins RN. 2015. The role of dietary coconut for the prevention and treatment of Alzheimer's disease: potential mechanisms of action. British Journal of Nutrition 114: 1-14.
  • Halász K, Borbély C, Pós V, Gáspár L, Haddadderafshi N, Winter Z, Lukács N. 2016. Effect of crop management and cultivar on colonization of Capsicum annuum L. by Endophytic Fungi. Acta Universitatis Sapientiae, Agriculture and Environment 8: 5-15.
  • Hsieh TC, Ma KH, Chao A. 2016. iNEXT: an R package for rarefaction and extrapolation of species diversity (H ill numbers). Methods in Ecology and Evolution 7: 1451-1456.
  • Hubbard M, Germida JJ, Vujanovic V. 2014. Fungal endophytes enhance wheat heat and drought tolerance in terms of grain yield and second‐generation seed viability. Journal of Applied Microbiology 116: 109-122.
  • Jost L. 2006. Entropy and diversity. Oikos 113: 363-375.
  • Lamdande AG, Prakash M, KSMS R. 2018. Storage study and quality evaluation of fresh coconut grating. Journal of Food Processing and Preservation 42: e13350. doi: 10.1111/jfpp.13350
    » https://doi.org/10.1111/jfpp.13350
  • Larran S, Simon MR, Moreno MV, Siurana MS, Perelló A. 2016. Endophytes from wheat as biocontrol agents against tan spot disease. Biological Control 92: 17-23.
  • Lima TEF, Oliveira RJV, Bezerra JL, Cavalcanti MDQ. 2014. Endophytic fungi from leaves and roots of Vitis labrusca cv. Isabel in Pernambuco/Brazil. Sydowia 66: 115-128.
  • Lumyong S, Techa W, Lumyong P, McKenzie EHC, Hyde KD. 2009. Endophytic fungi from Calamus kerrianus and Wallichia caryotoides (Arecaceae) at Doi Suthep-Pui National Park, Thailand. Chiang Mai Journal Science 36: 158-167.
  • Malhadas C, Malheiro R, Pereira JA, Pinho PG, Baptista P. 2017. Antimicrobial activity of endophytic fungi from olive tree leaves. World Journal of Microbiology and Biotechnology 33: 46. doi: 10.1007/s11274-017-2216-7
    » https://doi.org/10.1007/s11274-017-2216-7
  • Mariano RLR, Lira RVI, Silveira EB, Menezes M. 1997. Levantamento de fungos endofíticos e epifíticos em folhas de coqueiro no Nordeste do Brasil. I. Frequência da população fúngica e efeito da hospedeira. Agrotópica 9: 127-134.
  • Martins F, Pereira JA, Bota P, Bento A, Baptista P. 2016. Fungal endophyte communities in above-and belowground olive tree organs and the effect of season and geographic location on their structures. Fungal Ecology 20: 193-201.
  • Materatski P, Varanda C, Carvalho T, et al 2019. Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars. Fungal Biology 123: 66-76.
  • McArdle BH, Anderson MJ. 2001. Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82: 290- 297.
  • Mejía LC, Rojas EI, Maynard Z, et al 2008. Endophytic fungi as biocontrol agents of Theobroma cacao pathogens. Biological Control 46: 4-14.
  • Mendiburu F. 2016. Package agricolae: Statistic procedure for agricultural research. https://CRAN.R-project.org/package=agricolae 21 Oct. 2017.
    » https://CRAN.R-project.org/package=agricolae
  • Mishra A, Gond SK, Kumar A, Sharma VK, Verma SK, Kharwar RN, Sieber TN. 2012. Season and tissue type affect fungal endophyte communities of the Indian medicinal plant Tinospora cordifolia more strongly than geographic location. Microbial Ecology 64: 388-398.
  • Naik BS, Shashikala J, Krishnamurthy YL. 2009. Study on the diversity of endophytic communities from rice (Oryza sativa L.) and their antagonistic activities in vitro. Microbiological Research 164: 290-296.
  • Oksanen J, Blanchet F, Kindt R, et al 2015. vegan: community ecology package. R package v.2.2-1. http://CRAN.R-project.org/package=vegan 21 Oct. 2017.
    » http://CRAN.R-project.org/package=vegan
  • Oliveira R, Souza R, Lima T, Cavalcanti M. 2014a. Endophytic fungal diversity in coffee leaves (Coffea arabica) cultivated using organic and conventional crop management systems. Mycosphere 5: 523-530.
  • Oliveira RJV, Bezerra JL, Lima TEF, Silva GA, Cavalcanti MADQ. 2016. Phaeosphaeria nodulispora, a new endophytic coelomycete isolated from tropical palm (Cocos nucifera) in Brazil. Nova Hedwigia 185-192.
  • Oliveira RJV, Lima TE, Cunha IB, Coimbra VR, Silva GA, Bezerra JL, Cavalcanti MA. 2014b Corniculariella brasiliensis, a new species of coelomycetes in the rhizosphere of Caesalpinia echinata (Fabaceae, Caesalpinioideae) in Brazil. Phytotaxa 178: 197-204.
  • Oliveira RJV, Lima TEF, Silva GA, Cavalcanti MAQ. 2014c. Cladosporium species from hypersaline environments as endophytes in leaves of Cocos nucifera and Vitis labrusca Mycotaxon 129: 25-31.
  • Pancher M, Ceol M, Corneo PE, et al 2012. Fungal endophytic communities in grapevines (Vitis vinifera L.) respond to crop management. Applied and Environmental Microbiology 78: 4308-4317.
  • Pereira JO, Azevedo JL, Petrini O. 1993. Endophytic fungi of Stylosanthes. Mycologia 85: 362-364.
  • Pimentel IC, Glienke-Blanco C, Gabardo J, Stuart RM, Azevedo JL. 2006. Identification and colonization of endophytic fungi from soybean (Glycine max (L.) Merril) under different environmental conditions. Brazilian Archives of Biology and Technology 49: 705-711.
  • Rodrigues KF, Samuels GJ. 1990. Preliminary study of endophytic fungi in a tropical palm. Mycological Research 94: 827-830.
  • Rodrigues KF. 1994. The foliar fungal endophytes of the Amazonian palm Euterpe oleracea Mycologia 86: 376-385.
  • Roopan SM, Elango G. 2015. Exploitation of Cocos nucifera a non-food toward the biological and nanobiotechnology field. Industrial Crops and Products 67: 130-136.
  • Saad MM, Ghareeb RY, Saeed AA. 2019. The potential of endophytic fungi as bio-control agents against the cotton leafworm, Spodoptera littoralis (Boisd.) (Lepidoptera: Noctuidae). Egyptian Journal of Biological Pest Control 29: 7. doi: 10.1186/s41938-019-0108-x
    » https://doi.org/10.1186/s41938-019-0108-x
  • Sadeghi F, Samsampour D, Seyahooei M A, Bagheri A, Soltani J. 2019. Diversity and spatiotemporal distribution of fungal endophytes associated with Citrus reticulata cv. Siyahoo. Current Microbiology 76: 279-289.
  • Sette LD, Passarini MRZ, Delarmelina C, Salati F, Duarte MCT. 2006. Molecular characterization and antimicrobial activity of endophytic fungi from coffee plants. World Journal of Microbiology and Biotechnology 22: 1185-1195.
  • Silva RR, Silva DO, Fontes HR, Alviano CS, Fernandes PD, Alviano DS. 2013. Anti-inflammatory, antioxidant, and antimicrobial activities of Cocos nucifera var. typica BMC complementary and alternative medicine 13: 1-8.
  • Silva NI, Brooks S, Lumyong S, Hyde KD. 2019. Use of endophytes as biocontrol agents. Fungal Biology Reviews 33: 133-148.
  • Silva RMF, Oliveira RJV, Bezerra JDP, Bezerra JL, Souza-Motta CM, Silva GA. 2019b. Bifusisporella sorghi gen. et sp. nov. (Magnaporthaceae) to accommodate an endophytic fungus from Brazil. Mycological Progress 18: 847-854.
  • Silva RMF, Soares AM, Pádua APSL, et al 2019a. Mycological Diversity Description II. Acta Botanica Brasilica 33: 163-173.
  • Singh DK, Sharma VK, Kumar J, et al 2017. Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn. f.: Spatiotemporal and tissue type effects. Scientific Reports 7: 3745. doi: 10.1038/s41598-017-03933-0
    » https://doi.org/10.1038/s41598-017-03933-0
  • Southcott KA, Johnson JA. 1997. Isolation of endophytes from two species of palm from Bermuda. Canadian Journal of Microbiology 43: 789-792.
  • Taylor JE, Hyde KD, Jones EBG. 1999. Endophytic associated with the temperate palm Trachycarpus fortunei within and outside its natural geographical range. New Phytologist 142: 335-346.
  • U'Ren JM, Lutzoni F, Miadlikowska J, Laetsch AD, Arnold AE. 2012. Host and geographic structure of endophytic and endolichenic fungi at a continental scale. American Journal of Botany 99: 898-914.
  • Varanda CMR, Oliveira M, Materatski P, Landum M, Clara MIE, Rosário FM. 2016. Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management. Fungal Biology 120: 1525-1536.
  • Vaz AB, Fontenla S, Rocha FS, et al 2014. Fungal endophyte β-diversity associated with Myrtaceae species in an Andean Patagonian forest (Argentina) and an Atlantic forest (Brazil). Fungal Ecology 8: 28-36.
  • White TJ, Bruns T, Lee SJWT, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: a Guide to Methods and Applications 18: 315-322.
  • Wood S. 2017. R Package mgcv: Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation. https://CRAN.R-project.org/package=mgcv . 21 Oct. 2017.
    » https://CRAN.R-project.org/package=mgcv
  • Yadav M, Yadav A, Kumar S, Yadav JP. 2016. Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains. BMC Microbiology 16: 44. doi: 10.1186/s12866-016-0664-0
    » https://doi.org/10.1186/s12866-016-0664-0

Publication Dates

  • Publication in this collection
    25 Jan 2021
  • Date of issue
    Oct-Dec 2020

History

  • Received
    17 Mar 2020
  • Accepted
    08 Oct 2020
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