Publications by authors named "Hector Urbina"

15 Publications

  • Page 1 of 1

Isolation and Molecular Characterization of the Romaine Lettuce Phylloplane Mycobiome.

J Fungi (Basel) 2021 Apr 7;7(4). Epub 2021 Apr 7.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

Romaine lettuce () is an important staple of American agriculture. Unlike many vegetables, romaine lettuce is typically consumed raw. Phylloplane microbes occur naturally on plant leaves; consumption of uncooked leaves includes consumption of phylloplane microbes. Despite this fact, the microbes that naturally occur on produce such as romaine lettuce are for the most part uncharacterized. In this study, we conducted culture-based studies of the fungal romaine lettuce phylloplane community from organic and conventionally grown samples. In addition to an enumeration of all such microbes, we define and provide a discussion of the genera that form the "core" romaine lettuce mycobiome, which represent 85.5% of all obtained isolates: , , , , , , , , , and . We highlight the need for additional mycological expertise in that 23% of species in these core genera appear to be new to science and resolve some taxonomic issues we encountered during our work with new combinations for and . Finally, our work lays the ground for future studies that seek to understand the effect these communities may have on preventing or facilitating establishment of exogenous microbes, such as food spoilage microbes and plant or human pathogens.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/jof7040277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067711PMC
April 2021

Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.

IMA Fungus 2020 Nov 3;11(1):23. Epub 2020 Nov 3.

Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.

Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths.Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-020-00045-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7607712PMC
November 2020

The Suhomyces clade: from single isolate to multiple species to disintegrating sex loci.

FEMS Yeast Res 2019 03;19(2)

Department of Biological Sciences, Louisiana State University; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.

Candida tanzawaensis clade members are now placed in Suhomyces. The group was virtually unknown until the early 2000s. Here, we review progress made on Suhomyces over the last two decades and provide data from reports of new members of the group from distant localities worldwide, their habitats and a new study of mating loci that helps explain earlier failed compatibility tests. Phylogenetic studies indicate early diverging members are mostly associated with plants, but later diverging species are usually fungus-feeding insect associates. The genome of S. tanzawaensis was known to have a heterothallic mating allele arrangement with a single MAT α idiomorph. For this review, we generate sequence data and compare the MAT gene arrangement of 30 strains from nine Suhomyces species. These varied from MAT α loci containing mating genes α1 and α2, hypothetical MAT a loci without detectable mating genes a1 and a2 to truncated, possibly completely dissociated MAT loci with intraspecific variation. The absence of a second MAT in a genome locus precludes the possibility of mating type switching. Sympatric speciation likely occurred after MAT locus deterioration began in isolated habitats. Although asexual reproduction may be an effective short-term strategy, theory predicts it will not endure over the extreme long term.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/femsyr/foy125DOI Listing
March 2019

A closer look at Sporidiobolales: Ubiquitous microbial community members of plant and food biospheres.

Mycologia 2018 Jan-Feb;110(1):79-92

a Department of Botany and Plant Pathology , Purdue University , West Lafayette , Indiana 47907.

Carotenoid-containing yeasts in Sporidiobolales (Microbotryomycetes, Pucciniomycotina, Basidiomycota) have been reported from contrasting ecosystems, including marine, soil, phylloplane, polar ice, and many others. Here, we present several analyses drawing on 583 new isolates collected from various substrates around the globe and publicly available sequences from numerous published environmental studies. We provide a multilocus phylogenetic reconstruction of the order, estimates for total species richness, a snapshot of global distribution patterns, and analysis of niche preferences in Sporidiobolales, emphasizing their occurrence in commercial crops and food products. We evaluated loci commonly used in fungal phylogenetics, finding that RNA polymerase II subunits 1 and 2 (RPB1, RPB2) are of little utility in this group. We have reconfirmed the monophyly of Sporidiobolales with three well-supported genera, which are, in descending order of number of species, Rhodotorula, Sporobolomyces, and Rhodosporidiobolus. From our data, we estimate ca. 260 species in Sporidiobolales, of which 42 are described, and ca. 52,000 species in Pucciniomycotina. The majority of data regarding Sporidiobolales are from North America and Europe, highlighting severe knowledge gaps for most of South and Central America and Africa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2018.1438020DOI Listing
December 2018

Two new endophytic Atractiellomycetes, Atractidochium hillariae and Proceropycnis hameedii.

Mycologia 2018 Jan-Feb;110(1):136-146

c Department of Ecology, Evolution, and Marine Biology , University of California-Santa Barbara , Santa Barbara , California 93106.

Sterile fungal isolates are often recovered in leaf and root endophytic studies, although these seldom play a significant role in downstream analyses. The authors sought to identify and characterize two such endophytes-one representing the most commonly recovered fungal isolate in recent studies of needle endophytes of Pinus taeda and the other representing a rarely isolated root endophyte of Populus trichocarpa. Both are shown by DNA sequencing to be undescribed species of Atractiellomycetes (Pucciniomycotina, Basidiomycota), a poorly characterized class of mostly plant-associated and presumably saprobic microfungi. The authors describe the new genus and species Atractidochium hillariae (Phleogenaceae) and the new species Proceropycnis hameedii (Hoehnelomycetaceae), both in the Atractiellales, to accommodate these unusual isolates. Following incubations of 1-2 mo, A. hillariae produces minute white sporodochia, similar to those produced by several other members of Atractiellales, whereas Pr. hameedii forms conidia singly or in chains in a manner similar to its sister species Pr. pinicola. Additionally, we provide a taxonomic revision of Atractiellomycetes based on multilocus analyses and propose the new genera Neogloea (Helicogloeaceae) and Bourdotigloea (Phleogenaceae) to accommodate ex-Helicogloea species that are not congeneric with the type H. lagerheimii. Atractiellomycetes consists of a single order, Atractiellales, and three families, Hoehnelomycetaceae, Phleogenaceae, and Helicogloeaceae. Accumulated evidence suggests that Atractiellomycetes species are common but infrequently isolated members of plant foliar and root endobiomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2018.1446650DOI Listing
December 2018

Xylaria karyophthora: a new seed-inhabiting fungus of Greenheart from Guyana.

Mycologia 2018 Mar-Apr;110(2):434-447. Epub 2018 May 24.

a Department of Botany and Plant Pathology , Purdue University , West Lafayette , Indiana 47907.

In 2010-2011, a Xylaria sp. was documented growing from seeds of both Chlorocardium rodiei and Chlorocardium venenosum, a commercially valuable timber in Guyana. We conducted extensive surveys in 2015-2016, where this Xylaria sp. was observed fruiting from ca. 80% of dispersed seeds in both natural and logged forests in the Upper Demerara-Berbice, Potaro-Siparuni, and the Cuyuni-Mazaruni districts of central Guyana. Species of Xylaria are ascomycetous fungi generally characterized by black, carbonaceous, multiperitheciate ascoma commonly found growing on dead wood. Combined teleomorphic and molecular data indicate that the fungus represents a novel species, described here as Xylaria karyophthora.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2018.1457349DOI Listing
January 2019

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere.

Fungal Biol 2018 04 10;122(4):231-240. Epub 2018 Jan 10.

Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden. Electronic address:

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2017.12.013DOI Listing
April 2018

Phosphorus cycling in deciduous forest soil differs between stands dominated by ecto- and arbuscular mycorrhizal trees.

New Phytol 2016 Feb 28;209(3):1184-95. Epub 2015 Oct 28.

Biology Department, Indiana University, Bloomington, IN, 47405, USA.

Although much is known about how trees and their associated microbes influence nitrogen cycling in temperate forest soils, less is known about biotic controls over phosphorus (P) cycling. Given that mycorrhizal fungi are instrumental for P acquisition and that the two dominant associations - arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi - possess different strategies for acquiring P, we hypothesized that P cycling would differ in stands dominated by trees associated with AM vs ECM fungi. We quantified soil solution P, microbial biomass P, and sequentially extracted inorganic and organic P pools from May to November in plots dominated by trees forming either AM or ECM associations in south-central Indiana, USA. Overall, fungal communities in AM and ECM plots were functionally different and soils exhibited fundamental differences in P cycling. Organic forms of P were more available in ECM plots than in AM plots. Yet inorganic P decreased and organic P accumulated over the growing season in both ECM and AM plots, resulting in increasingly P-limited microbial biomass. Collectively, our results suggest that P cycling in hardwood forests is strongly influenced by biotic processes in soil and that these are driven by plant-associated fungal communities.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nph.13720DOI Listing
February 2016

Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species.

Fungal Biol 2014 Dec 4;118(12):943-55. Epub 2014 Sep 4.

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden.

The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600(T) (=CBS138755(ExT)) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2014.08.005DOI Listing
December 2014

Zombie bugs? The fungus Purpureocillium cf. lilacinum may manipulate the behavior of its host bug Edessa rufomarginata.

Mycologia 2014 Nov-Dec;106(6):1065-72. Epub 2014 Aug 20.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803.

Just before dying, Edessa rufomarginata (Hemiptera, Pentotomidae) individuals that are infected with the fungus Purpureocillium cf. lilacinum (Ascomycota: Ophiocordycipitaceae) move from the leaves onto the stems of their Solanum sp. host and firmly grasp the stems in ways seldom employed by uninfected bugs. These alterations in host behavior probably improve the chances that the subsequently produced fungal spores will be dispersed aerially. Purpureocillium cf. lilacinum is a member of the Ophiocordycipitaceae, a group in which other species also modify the behavior of their hosts. As in the case of newly distinguished relatives of Ophiocordyceps unilateralis associated with "zombie ants" the discovery of P. cf. lilacinum infecting bugs reveals that P. lilacinum may be more diverse than previously appreciated.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3852/13-264DOI Listing
May 2015

Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade.

Mycologia 2013 May-Jun;105(3):650-60. Epub 2012 Dec 11.

Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.

The gut of wood-feeding insects is a microhabitat for a specialized community of microbes, including bacteria and several groups of eukaryotes such as nematodes, parabasalids and fungi. The characterization of gut yeast communities from a variety of insects has shown that certain yeasts often are associated with the insects. The gut of wood-feeding insects is rich in ascomycete yeasts and in particular xylose-fermenting (X-F) and assimilating yeasts have been consistently present in the gut of lignicolous insects. The objective of this study was the characterization of the yeast flora from the gut of the wood roach Cryptocercus sp. (Blattodea: Cryptocercidae). Five wood roaches were collected along the Appalachian Trail near the border between Tennessee and North Carolina, USA. We isolated 18 yeast strains from the wood roaches identified as Sugiyamaella paludigena and Sugiyamaella lignohabitans, xylose-assimilating yeasts, and Scheffersomyces cryptocercus (NRRL Y-48824(T) = CBS 12658) a new species of X-F yeast. The presence of X-F and certain non X-F yeasts in the gut of the subsocial wood roach Cryptocercus sp. extends the previous findings of associations between certain ascomycete yeasts and lignicolous insects. New combinations were made for 13 asexual members of the Sugiyamaella clade.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3852/12-094DOI Listing
July 2013

Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene.

PLoS One 2012 14;7(6):e39128. Epub 2012 Jun 14.

Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America.

Many of the known xylose-fermenting (X-F) yeasts are placed in the Scheffersomyces clade, a group of ascomycete yeasts that have been isolated from plant tissues and in association with lignicolous insects. We formally recognize fourteen species in this clade based on a maximum likelihood (ML) phylogenetic analysis using a multilocus dataset. This clade is divided into three subclades, each of which exhibits the biochemical ability to ferment cellobiose or xylose. New combinations are made for seven species of Candida in the clade, and three X-F taxa associated with rotted hardwood are described: Scheffersomyces illinoinensis (type strain NRRL Y-48827(T) = CBS 12624), Scheffersomyces quercinus (type strain NRRL Y-48825(T) = CBS 12625), and Scheffersomyces virginianus (type strain NRRL Y-48822(T) = CBS 12626). The new X-F species are distinctive based on their position in the multilocus phylogenetic analysis and biochemical and morphological characters. The molecular characterization of xylose reductase (XR) indicates that the regions surrounding the conserved domain contain mutations that may enhance the performance of the enzyme in X-F yeasts. The phylogenetic reconstruction using XYL1 or RPB1 was identical to the multilocus analysis, and these loci have potential for rapid identification of cryptic species in this clade.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039128PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375246PMC
December 2012

First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri.

Microb Biotechnol 2011 Sep 30;4(5):663-72. Epub 2011 May 30.

Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Mor. 62250 México.

A fungal strain isolated from a microbial consortium growing in a natural asphalt lake is able to grow in purified asphaltenes as the only source of carbon and energy. The asphaltenes were rigorously purified in order to avoid contamination from other petroleum fractions. In addition, most of petroporphyrins were removed. The 18S rRNA and β-tubulin genomic sequences, as well as some morphologic characteristics, indicate that the isolate is Neosartorya fischeri. After 11 weeks of growth, the fungus is able to metabolize 15.5% of the asphaltenic carbon, including 13.2% transformed to CO(2) . In a medium containing asphaltenes as the sole source of carbon and energy, the fungal isolate produces extracellular laccase activity, which is not detected when the fungus grow in a rich medium. The results obtained in this work clearly demonstrate that there are microorganisms able to metabolize and mineralize asphaltenes, which is considered the most recalcitrant petroleum fraction.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1751-7915.2011.00269.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819015PMC
September 2011

Isolation of autochthonous non-white rot fungi with potential for enzymatic upgrading of Venezuelan extra-heavy crude oil.

Biocatal Biotransformation 2007 Mar;25(2-4):341-349

Unidad de Biotecnología del Petróleo, Centro de Biotecnología, Fundación Instituto de Estudios Avanzados (IDEA), C/Hoyo de la Puerta-Baruta, Sartenejas, Caracas 1080, Venezuela.

The increasing world demand for fuels makes it necessary to exploit the largest reserve of extra-heavy crude oil (EHCO) of the Orinoco Oil Belt from Venezuela. We propose the use of extracellular oxidative enzymes, in particular, lignin-degrading enzyme systems (LDS) of fungi, for enzymatic improvement of EHCO. Autochthonous non-white rot fungal strains able to use EHCO, and several polycyclic aromatic hydrocarbons (PAHs) as sole carbon source and energy, were isolated from EHCO-polluted soils and identified as belonging to the genera Fusarium, Penicillium , Trichoderma , Aspergillus , Neosartorya, Pseudallescheria, Cladosporium, Pestalotiopsis , Phoma and Paecillomyces. Phenotypic and biochemical assays revealed the ability of these filamentous fungi to synthesize extracellular oxidative enzymes, and suggested a relationship between the LDS and EHCO bioconversion. This work reports, for the first time, the use of o-phenylenediamine dihydrochloride (OPD) as substrate to measure extracellular ligninolytic peroxidases (ELP) in culture broths of filamentous fungi (Fusarium solani HP-1), and constitutes the first formal study of the fungal community associated with the EHCO of the Orinoco Oil Belt.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/10242420701379908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556186PMC
March 2007

Dissection of the components for PIP2 activation and thermosensation in TRP channels.

Proc Natl Acad Sci U S A 2007 Jun 4;104(24):10246-51. Epub 2007 Jun 4.

Laboratory of Biophysics and Molecular Physiology, Centro de Estudios Cientificos, Valdivia 509-9100, Chile.

Phosphatidylinositol 4,5-bisphosphate (PIP2) plays a central role in the activation of several transient receptor potential (TRP) channels. The role of PIP2 on temperature gating of thermoTRP channels has not been explored in detail, and the process of temperature activation is largely unexplained. In this work, we have exchanged different segments of the C-terminal region between cold-sensitive (TRPM8) and heat-sensitive (TRPV1) channels, trying to understand the role of the segment in PIP2 and temperature activation. A chimera in which the proximal part of the C-terminal of TRPV1 replaces an equivalent section of TRPM8 C-terminal is activated by PIP2 and confers the phenotype of heat activation. PIP2, but not temperature sensitivity, disappears when positively charged residues contained in the exchanged region are neutralized. Shortening the exchanged segment to a length of 11 aa produces voltage-dependent and temperature-insensitive channels. Our findings suggest the existence of different activation domains for temperature, PIP2, and voltage. We provide an interpretation for channel-PIP2 interaction using a full-atom molecular model of TRPV1 and PIP2 docking analysis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0703420104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891241PMC
June 2007
-->