Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves

Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T. cacao and their responsiveness towards agroforestry management systems.

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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽

10.3390/d11120234 ◽

2019 ◽

Vol 11 (12) ◽

pp. 234 ◽

Cited By ~ 2

Author(s):

Eric A. Griffin ◽

Joshua G. Harrison ◽

Melissa K. McCormick ◽

Karin T. Burghardt ◽

John D. Parker

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tree Diversity ◽

Trophic Levels ◽

Community Diversity ◽

And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

10.1101/210641 ◽

2017 ◽

Author(s):

Dan Thomas ◽

Roo Vandegrift ◽

Yu-Ming Ju ◽

Monica Hsieh ◽

Bitty Roy

Keyword(s):

Tree Species ◽

Spatial Scales ◽

Cloud Forest ◽

Fungal Endophytes ◽

Amplicon Sequencing ◽

Fungal Endophyte ◽

Core Microbiome ◽

The Core ◽

Host Tree Species ◽

Ecological Importance

AbstractFungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, “core” mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, “minimal” core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.

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Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes

Journal of Fungi ◽

10.3390/jof7070538 ◽

2021 ◽

Vol 7 (7) ◽

pp. 538

Author(s):

Rebecca Creamer ◽

Deana Baucom Hille ◽

Marwa Neyaz ◽

Tesneem Nusayr ◽

Christopher L. Schardl ◽

...

Keyword(s):

Amino Acid ◽

Polyketide Synthase ◽

Genetic Relationships ◽

Protein Sequences ◽

Fungal Endophyte ◽

Melanin Synthesis ◽

Melanin Biosynthesis ◽

Protein Levels ◽

Oxytropis Sericea ◽

And Function

The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.

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Isolation and Characterization of Root-Associated Bacterial Endophytes and Their Biocontrol Potential against Major Fungal Phytopathogens of Rice (Oryza sativa L.)

Pathogens ◽

10.3390/pathogens9030172 ◽

2020 ◽

Vol 9 (3) ◽

pp. 172

Author(s):

Maqsood Ahmed Khaskheli ◽

Lijuan Wu ◽

Guoqing Chen ◽

Long Chen ◽

Sajid Hussain ◽

...

Keyword(s):

Oryza Sativa ◽

Fungal Pathogens ◽

Oryza Sativa L ◽

Defense Responses ◽

Growth And Yield ◽

Bacterial Endophytes ◽

16S Rrna Sequence ◽

Resistance Response ◽

Isolation And Characterization ◽

Fungal Phytopathogens

Rice (Oryza sativa L.) is a major cereal food crop worldwide, and its growth and yield are affected by several fungal phytopathogens, including Magnaporthe oryzae, Fusarium graminearum, F. moniliforme, and Rhizoctonia solani. In the present study, we have isolated and characterized root-associated bacterial endophytes that have antifungal activities against rice fungal phytopathogens. A total of 122 root-associated bacterial endophytes, belonging to six genera (Bacillus, Fictibacillus, Lysinibacillus, Paenibacillus, Cupriavidus, and Microbacterium) and 22 species were isolated from three rice cultivars. Furthermore, the 16S rRNA sequence-based phylogeny results revealed that Bacillus was the most dominant bacterial genera, and that there were 15 different species among the isolates. Moreover, 71 root-associated endophytes showed antagonistic effects against four major fungal phytopathogens, including M. oryzae, F. graminearum, F. moniliforme, and R. solani. Additionally, the biochemical, physiological, and PCR amplification results of the antibiotic-related genes further supported the endophytes as potential biocontrolling agents against the rice fungal pathogens. Consequently, the findings in this study suggested that the isolated bacterial endophytes might have beneficial roles in rice defense responses, including several bioactive compound syntheses. The outcomes of this study advocate the use of natural endophytes as an alternative strategy towards the rice resistance response.

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A light and electron microscope study of the fungal endophytes in the sporophyte and gametophyte of Lycopodium cernuum with observations on the gametophyte–sporophyte junction

Canadian Journal of Botany ◽

10.1139/b92-008 ◽

1992 ◽

Vol 70 (1) ◽

pp. 58-72 ◽

Cited By ~ 40

Author(s):

Jeffrey G. Duckett ◽

Roberto Ligrone

Keyword(s):

Root Nodules ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Peninsular Malaysia ◽

Epidermal Cells ◽

Host Cells ◽

Wall Material ◽

Intercellular Spaces ◽

Host Cytoplasm ◽

Fungal Associations

The ventral epidermal cells of the photosynthetic, surface-living gametophytes of Lycopodium cernuum, collected from moist shaded banks in Peninsular Malaysia, contain an aseptate fungus. In some cells the hyphae are thick walled and form coils encapsulated by a thin layer of host wall material. In others the fungus is thin walled and shows limited differentiation into larger trunk hyphae and arbuscules. The adjacent host cytoplasm, separated from the fungus by a granular interfacial matrix, contains numerous chloroplasts, mitochondria, and microtubules. The hyphae contact the substratum via the ventral walls of the epidermal cells and the rhizoids are free from infection. In the protocorm and root nodules, aseptate hyphae initially colonize mucilage-filled schizogenous intercellular spaces. Subsequent invasion of the host cells is associated with the development of massive overgrowths of host wall material. The fungal associations in L. cernuum share a mixture of attributes otherwise found in different angiosperm mycorrhizae and in mycotrophic relationships in liverworts. Wall ingrowths are present in both the gametophyte and sporophyte cells in the placenta of L. cernuum. The very limited development of the placenta, compared with L. appressum, certain bryophytes and ferns, the diminutive size, and early senescence of the gametophytes of L. cernuum are all linked to the presence of the protocorm. This massive absorptive organ, homologous to a foot, in terms of its position in sporophyte ontogeny, but external to the parent gametophyte, derives its nutrition partly from photosynthesis and partly from its fungal endophyte. Key words: chloroplasts, Lycopodium, mycorrhiza, pteridophytes, root nodules, symbiosis, transfer cells.

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Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽

10.11646/phytotaxa.514.3.5 ◽

2021 ◽

Vol 514 (3) ◽

pp. 247-260

Author(s):

KASUN THAMBUGALA ◽

DINUSHANI DARANAGAMA ◽

SAGARIKA KANNANGARA ◽

THENUKA KODITUWAKKU

Keyword(s):

Sri Lanka ◽

Camellia Sinensis ◽

Endophytic Fungi ◽

Sequence Data ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tea Leaves ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

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The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.707708 ◽

2021 ◽

Vol 9 ◽

Author(s):

Abdullah ◽

Sahar Faraji ◽

Parviz Heidari ◽

Péter Poczai

Keyword(s):

Gene Family ◽

Theobroma Cacao ◽

Critical Role ◽

Divergence Time ◽

Purifying Selection ◽

Plant Metabolites ◽

Corchorus Capsularis ◽

Cell Stability ◽

Duplication Events ◽

And Function

The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

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Relationships between Foliar Fungal Endophyte Communities and Ecophysiological Traits of CAM and C3 Epiphytic Bromeliads in a Neotropical Rainforest

Diversity ◽

10.3390/d12100378 ◽

2020 ◽

Vol 12 (10) ◽

pp. 378 ◽

Cited By ~ 2

Author(s):

Peter H. Tellez ◽

Carrie L. Woods ◽

Stephen Formel ◽

Sunshine A. Van Bael

Keyword(s):

Fungal Endophytes ◽

Leaf Traits ◽

Fungal Endophyte ◽

Leaf Water Content ◽

Leaf Toughness ◽

Vascular Epiphytes ◽

Ecophysiological Traits ◽

Photosynthetic Pathways ◽

Relative Abundances ◽

Epiphytic Bromeliads

Vascular epiphytes contribute up to 35% of the plant diversity and foliar biomass of flowering plants. The family Bromeliaceae is a monophyletic group of plants native to the Neotropics. Epiphytic bromeliads form associations with distinct groups of organisms but their relationship with foliar fungal endophytes remain underexplored. In this study we examined the relationship of foliar fungal endophytes to host photosynthetic pathways and associated ecophysiological traits. We sampled the fungal endophyte communities of 67 host individuals in six epiphytic bromeliad species differing in C3 and crassulacean acid metabolism (CAM) photosynthetic pathways. We tested whether endophyte assemblages were associated with ecophysiological leaf traits related to host photosynthetic pathways. Our results indicate that (1) C3 and CAM bromeliads host dissimilar endophyte assemblages, (2) endophyte communities in C3 bromeliads are characterized by variable relative abundances of fungal orders; conversely, CAM associated endophyte communities were characterized by consistent relative abundances of fungal orders, and (3) endophyte communities in bromeliads are distributed along a continuum of leaf toughness and leaf water content. Taken together, our study suggests that host physiology and associated ecophysiological traits of epiphytic bromeliads may represent biotic filters for communities of fungal endophytes in the tropics.

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A Survey of Culturable Fungal Endophytes From Festuca rubra subsp. pruinosa, a Grass From Marine Cliffs, Reveals a Core Microbiome

Frontiers in Microbiology ◽

10.3389/fmicb.2018.03321 ◽

2019 ◽

Vol 9 ◽

Cited By ~ 9

Author(s):

Eric Pereira ◽

Beatriz R. Vázquez de Aldana ◽

Leticia San Emeterio ◽

Iñigo Zabalgogeazcoa

Keyword(s):

Fungal Endophytes ◽

Festuca Rubra ◽

Core Microbiome

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21 Profiling sow vaginal and fecal and piglet gastrointestinal microbiome and the passage of sow microbiome to their progeny from birth to weaning

Journal of Animal Science ◽

10.1093/jas/skz258.039 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 21-21

Author(s):

Huyen Tran ◽

Brenda de Rodas ◽

Manohar M Lahoti ◽

Timothy J Johnson

Keyword(s):

Alpha Diversity ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Gastrointestinal Microbiome ◽

Core Microbiome ◽

Linear Discriminant ◽

Fecal Microbiome ◽

The Core ◽

Vaginal Swabs ◽

Sampling Points

Abstract The objectives of this study were 1) to profile the sow vaginal and fecal microbiome and the corresponding piglet gastrointestinal microbiome from birth to weaning, and 2) to identify the core microbiome shared between sows and piglets. A total of 226 samples collected from sows (vaginal swabs pre-farrow; fecal samples at farrow, d 3, 7, 10, 17 post-farrow) and their progenies (stomach, ileum, and colon digesta at birth, d 2, and 14 after birth) were used for the analyses of microbial community structure using 16S rRNA V4 amplicon sequencing with Illumina MiSeq. Our data indicated that the piglet and sow microbiome were quite distinct. Piglets had lower bacterial alpha diversity (chao1, richness, Shannon, Simpson indices; P < 0.01) than sows across all timepoints. Beta diversity of piglets by sample types was significantly different (P < 0.001) than sows by sample types when averaged across all timepoints or separation by timepoints. Feature selection by the Linear discriminant analysis effect size (LEfSe) indicated that the genera associated with piglets included those classified as Lactobacillus, unclassified Micrococcaceae, and Rothia when averaged across sampling points and sample types. Genera associated with sows included those classified as Treponema, YRC22, Unclassified RF39, Unclassified Christensenellaceae, Turicibacter, Unclassified RFP12, Unclassified F16, Collinsella, Coprococcus, Unclassified Coriobacteriaceae, and Unclassified Mogibacteriaceae. The genera shared between sow vaginal samples and piglets included those classified as Bacteroides, Fusobacterium, Haemophilus, Prevotella, Veillonella, and unclassified Clostridiadiaceae. The genera shared between sow fecal and piglet samples included those classified as Bacteroides, Lactobacillus, unclassified Clostridiadiaceae, unclassified Ruminococceae, and Prevotella. Overall, there are evidences that bacterial genera were passed from sows to piglets and influenced the microbial communities of piglets later in life.

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