Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species

Oono, Ryoko; Lutzoni, François; Arnold, A. Elizabeth; Kaye, Laurel; U’Ren, Jana M.; May, Georgiana; Carbone, Ignazio

doi:10.3732/ajb.1400141

Cited by 38 publications

(44 citation statements)

References 94 publications

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“…This outcome is consistent with the data contained in the studies of Angelini et al (2012) and Oono et al (2014) . It would be interesting to compare the fungal communities not only in stems but also in other plant parts such as roots, seeds, and leaves (Cook et al 2009) to have a fuller picture of the endophyte communities in M. pigra.…”

Section: Pathogenicity Chaptersupporting

confidence: 80%

Mimosa pigra dieback in the Northern Territory, Australia: Investigation into possible causes

Sacdalan¹

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In this study, Mimosa pigra dieback is described as plants or population of plants which appeared to suffer from ill health, death of their growing points and the emergence of green reshoots coming from the base. Dieback is an important phenomenon, not only in many crops and natural forests worldwide, but also in many invasive trees and shrubs in Australia. The dieback phenomenon is thought to be caused by complex and interacting factors and causes are often difficult to disentangle. In some cases it is a result of an interaction between both biotic and abiotic factors. Since 1988, dieback has been widely observed in Mimosa pigra L.(Fabaceae), a woody shrub that is one of the most serious exotic invaders of floodplains and riparian areas in the Top End of the Northern Territory. However, there has been no conclusive evidence of links between M. pigra dieback and specific causal factors. In addition, the dieback phenomenon has not been previously quantified.This thesis aimed to describe M. pigra dieback phenomenon at plant and population levels and its effect on plant growth, survival and demography. Specifically, the aim of this thesis was to evaluate the role of biotic factors (insect borers and fungal pathogens), and abiotic factors (soil pH and salinity), in relation to the development of M. pigra dieback. In addition, the thesis examines the pathogenicity of the fungal endophytes/pathogens associated with diebackaffected and healthy M. pigra. M. pigra has been a focus of biological control programs for more than 30 years, but it still remains a serious threat in the wetlands and conservation areas in the Top End of the Northern Territory. While extensive studies have been conducted to evaluate the impact of biological control programs, little is actually known about dieback and its causal factors.To evaluate the causal factors of M. pigra dieback, repeated ground surveys, plant health assessment and specimen collection of stems and soils, were conducted in the period 2011 to 2013 in established M. pigra sites on Melaleuca Station, Mary River, Northern Territory. Insect borers were quantified and putative fungal pathogen abundance were surveyed. A combined morphological and phylogenetic approach was used for fungal pathogens/endophyte identification. Using a subset of isolates, trials were performed to examine differences in the pathogenicity of the recovered fungal pathogens/endophytes.Results of field research showed that dieback in M. pigra is highly dynamic and fluctuates in its severity. Different sites showed increases and/or decreases in plant health over time.iii Dieback affects plants in all age classes, from seedlings, juveniles to adult plants, resulting in partial mortality of plants in all age categories over the trial period. Contrary to expectations, none of the biotic and abiotic factors examined showed a direct relationship to the changing population dynamics of M. pigra dieback over time. Nevertheless, fungal isolations demonstrated that M. pigra is a host to a diverse range of endop...

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Section: Pathogenicity Chaptersupporting

confidence: 80%

Mimosa pigra dieback in the Northern Territory, Australia: Investigation into possible causes

Sacdalan¹

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“…L. australe isolates are labeled with M (major), C (cryptic), or H (hybrid) based on a population structure analysis by Oono et al. (2014). Putative L. molitoris isolates are labeled with P ( Pinus ) or shaded bars labeled Strobus based on host species.…”

Section: Resultsmentioning

confidence: 99%

“…The well‐resolved terminal branches of the 70/30N tree corresponded to previously identified (e.g., L. australe major vs . cryptic; Oono et al., 2014) or potential cryptic species (within L. nitens and L. sp. nov .).…”

Section: Discussionmentioning

confidence: 99%

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Salas‐Lizana

Oono

2018

Ecology and Evolution

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The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low‐cost double‐digest restriction site‐associated DNA sequencing (ddRADseq) protocol to reveal among‐ and within‐species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality‐filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality‐filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories.

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“…Thus culture-free methods are warranted in future work. At present, our study contributes publically available cultures that can be used to diagnose new lineages or population structure based on multi-locus data sets [20, 29, 64], evaluate roles of endophytes in plant health or metabolite production [13, 22, 30, 32, 35, 65, 75, 80], and generate hypotheses for culture-independent, next-generation studies.…”

Section: Discussionmentioning

confidence: 99%

Fungal Endophytes in Aboveground Tissues of Desert Plants: Infrequent in Culture, but Highly Diverse and Distinctive Symbionts

et al. 2015

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In hot deserts, plants cope with aridity, high temperatures, and nutrient-poor soils with morphological and biochemical adaptations that encompass intimate microbial symbioses. Whereas the root microbiomes of arid-land plants have received increasing attention, factors influencing assemblages of symbionts in above-ground tissues have not been evaluated for many woody plants that flourish in desert environments. We evaluated the diversity, host affiliations, and distributions of endophytic fungi associated with photosynthetic tissues of desert trees and shrubs, focusing on non-succulent woody plants in the species-rich Sonoran Desert. To inform our strength of inference, we evaluated the effects of two different nutrient media, incubation temperatures, and collection seasons on the apparent structure of endophyte assemblages. Analysis of >22,000 tissue segments revealed that endophytes were isolated four times more frequently from photosynthetic stems than leaves. Isolation frequency was lower than expected given the latitude of the study region, and varied among species a function of sampling site and abiotic factors. However, endophytes were very species-rich and phylogenetically diverse, consistent with less-arid sites of a similar latitudinal position. Community composition differed among host species, but not as a function of tissue type, sampling site, sampling month, or exposure. Estimates of abundance, diversity and composition were not influenced by isolation medium or incubation temperature. Phylogenetic analyses of the most commonly isolated genus (Preussia) revealed multiple evolutionary origins of desert-plant endophytism and little phylogenetic structure with regard to seasonality, tissue preference, or optimal temperatures and nutrients for growth in vitro. Together, these results provide insight into endophytic symbioses in desert plant communities, and can be used to optimize strategies for capturing endophyte biodiversity at regional scales.

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Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species

Cited by 38 publications

References 94 publications

Mimosa pigra dieback in the Northern Territory, Australia: Investigation into possible causes

Mimosa pigra dieback in the Northern Territory, Australia: Investigation into possible causes

Double‐digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Fungal Endophytes in Aboveground Tissues of Desert Plants: Infrequent in Culture, but Highly Diverse and Distinctive Symbionts

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