Morphological and molecular studies on Resinicium s. str.

Treesearch

Karen K. Nakasone

2007-01-01

Resinicium Parmasto is typified by Resinicium bicolor (Alb. & Schwein.: Fr.) Parm., (Hymenochaetales, Basidiomycota), a readily recognized and widely distributed corticioid, lignicolous species in the northern hemisphere. Five new species of Resinicium closely allied to R. bicolor...

Molecular gene organisation and secondary structure of the mitochondrial large subunit ribosomal RNA from the cultivated Basidiomycota Agrocybe aegerita: a 13 kb gene possessing six unusual nucleotide extensions and eight introns.

PubMed

Gonzalez, P; Barroso, G; Labarère, J

1999-04-01

The complete gene sequence and secondary structure of the mitochondrial LSU rRNA from the cultivated Basidiomycota Agrocybe aegerita was derived by chromosome walking. The A.aegerita LSU rRNA gene (13 526 nt) represents, to date, the longest described, due to the highest number of introns (eight) and the occurrence of six long nucleotidic extensions. Seven introns belong to group I, while the intronic sequence i5 constitutes the first typical group II intron reported in a fungal mitochondrial LSU rDNA. As with most fungal LSU rDNA introns reported to date, four introns (i5-i8) are distributed in domain V associated with the peptidyl-transferase activity. One intron (i1) is located in domain I, and three (i2-i4) in domain II. The introns i2-i8 possess homologies with other fungal, algal or protozoan introns located at the same position in LSU rDNAs. One of them (i6) is located at the same insertion site as most Ascomycota or algae LSU introns, suggesting a possible inheritance from a common ancestor. On the contrary, intron i1 is located at a so-far unreported insertion site. Among the six unusual nucleotide extensions, five are located in domain I and one in domain V. This is the first report of a mitochondrial LSU rRNA gene sequence and secondary structure for the whole Basidiomycota division.

Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes.

PubMed

Liu, Yajuan J; Hodson, Matthew C; Hall, Benjamin D

2006-09-29

At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination.

PubMed

Gonzalez, E; Pitre, F E; Pagé, A P; Marleau, J; Guidi Nissim, W; St-Arnaud, M; Labrecque, M; Joly, S; Yergeau, E; Brereton, N J B

2018-03-21

One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.

Molecular analysis of the split cox1 gene from the Basidiomycota Agrocybe aegerita: relationship of its introns with homologous Ascomycota introns and divergence levels from common ancestral copies.

PubMed

Gonzalez, P; Barroso, G; Labarère, J

1998-10-05

The Basidiomycota Agrocybe aegerita (Aa) mitochondrial cox1 gene (6790 nucleotides), encoding a protein of 527aa (58377Da), is split by four large subgroup IB introns possessing site-specific endonucleases assumed to be involved in intron mobility. When compared to other fungal COX1 proteins, the Aa protein is closely related to the COX1 one of the Basidiomycota Schizophyllum commune (Sc). This clade reveals a relationship with the studied Ascomycota ones, with the exception of Schizosaccharomyces pombe (Sp) which ranges in an out-group position compared with both higher fungi divisions. When comparison is extended to other kingdoms, fungal COX1 sequences are found to be more related to algae and plant ones (more than 57.5% aa similarity) than to animal sequences (53.6% aa similarity), contrasting with the previously established close relationship between fungi and animals, based on comparisons of nuclear genes. The four Aa cox1 introns are homologous to Ascomycota or algae cox1 introns sharing the same location within the exonic sequences. The percentages of identity of the intronic nucleotide sequences suggest a possible acquisition by lateral transfers of ancestral copies or of their derived sequences. These identities extend over the whole intronic sequences, arguing in favor of a transfer of the complete intron rather than a transfer limited to the encoded ORF. The intron i4 shares 74% of identity, at the nucleotidic level, with the Podospora anserina (Pa) intron i14, and up to 90.5% of aa similarity between the encoded proteins, i.e. the highest values reported to date between introns of two phylogenetically distant species. This low divergence argues for a recent lateral transfer between the two species. On the contrary, the low sequence identities (below 36%) observed between Aa i1 and the homologous Sp i1 or Prototheca wickeramii (Pw) i1 suggest a long evolution time after the separation of these sequences. The introns i2 and i3 possessed intermediate percentages of identity with their homologous Ascomycota introns. This is the first report of the complete nucleotide sequence and molecular organization of a mitochondrial cox1 gene of any member of the Basidiomycota division.

Fungal endophyte diversity in Sarracenia

USDA-ARS?s Scientific Manuscript database

Fungal endophytes were isolated from four species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, eight within the Ascomycota and four within the Basidiomycota, were identified based on PCR amplification and sequencing ...

Taxonomy of Epithele (Polyporales, Basidiomycota)

Treesearch

Karen K. Nakasone

2013-01-01

Seventeen species are accepted in the genus Epithele, including new species E. belizensis, E. ceracea, E. reunionis, and E. ryvardenii. Descriptions and illustrations are provided for all species. The generic concept is emended to include Corticium bambusae, from Trinidad on bamboo, which lacks...

Sarcodon in the Neotropics I: new species from Guyana, Puerto Rico and Belize

Treesearch

A. C. Grupe; A. D. Baker; J. K. Uehling; M. E. Smith; T. J. Baroni; D. J. Lodge; T. W. Henkel

2015-01-01

Four species of the ectomycorrhizal (ECM) genus Sarcodon (Bankeraceae, Thelephorales, Basidiomycota) are described as new to science. Sarcodon pakaraimensis sp. nov. is described from forests dominated by the ECM trees Pakaraimaea dipterocarpacea (Dipterocarpaceae) and Dicymbe jenmanii (...

Comparative taxonomy of desert truffles of the Australian outback and the African Kalahari

Treesearch

James M. Trappe; Gabor M. Kovacs; Andrew W. Claridge

2010-01-01

Seven truffle species are reported from the Australian Outback-six Ascomycota (Elderia arenivaga, Mattirolomyces mulpu sp. nov., Mycoclelandia arenacea, M. bulundari, Reddelomyces westraliensis, Ulurua nonparaphysata gen. & sp. nov.) and one Basidiomycota (Horakiella watarrkana sp. nov.) Three...

Two new species of Aleurodiscus s.l. (Russulales, Basidiomycota) on bamboo from tropics

Treesearch

Li-Dan Dai; Sheng-Hua Wu; Karen K. Nakasone; Harold H. Burdsall; Shuang-Hui He

2017-01-01

Aleurodiscus tenuissimus and A. tropicus, on dead bamboo, are new species from tropical Asia. Both species have effused basidiocarps and simple-septate generative hyphae. Aleurodiscus tenuissimus, from southern China, lacks acanthophyses and possesses echinulate basidiospores, whereas A. tropicus...

Neocampanella, a new corticioid fungal genus, and a note on Dendrothele bispora

Treesearch

Karen K. Nakasone; David S. Hibbett; Greta Goranova

2009-01-01

The new genus Neocampanella (Agaricales, Agaricomycetes, Basidiomycota) is established for Dentocorticium btastanos Boidin & Gilles, a crustose species, and the new combination, Neocampanella blastanos, is proposed. Morphological and molecular studies support the recognition of the new genus and its close...

The genus Dendrothele (Agaricales, Basidiomycota) in New Zealand

Treesearch

K.K. Nakasone; H.H. Burdsall

2011-01-01

Sixteen species of Dendrothele sensu lato are confirmed from New Zealand. Nine new taxa are described: Dendrothele arachispora, D. aucklandica, D. australis, D. cymbiformis, D. leptostachys, D. magnenavicularis, D. navicularis, D. novae-zelandiae and D. subellipsoidea. Ten species were previously reported, but...

Comparative Genomics of the Ectomycorrhizal Sister Species Rhizopogon vinicolor and Rhizopogon vesiculosus (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type B Locus

PubMed Central

Mujic, Alija Bajro; Kuo, Alan; Tritt, Andrew; Lipzen, Anna; Chen, Cindy; Johnson, Jenifer; Sharma, Aditi; Barry, Kerrie; Grigoriev, Igor V.; Spatafora, Joseph W.

2017-01-01

Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales)—the first genomes available for Basidiomycota truffles—and characterized gene content and organization surrounding their mating type loci. Both species possess a pair of homeodomain transcription factor homologs at the mating type A-locus as well as pheromone receptor and pheromone precursor homologs at the mating type B-locus. Comparison of Rhizopogon genomes with genomes from Boletales, Agaricales, and Polyporales revealed synteny of the A-locus region within Boletales, but several genomic rearrangements across orders. Our findings suggest correlation between gene content at the B-locus region and breeding system in Boletales with tetrapolar species possessing more diverse gene content than bipolar species. Rhizopogon vinicolor possesses a greater number of B-locus pheromone receptor and precursor genes than R. vesiculosus, as well as a pair of isoprenyl cysteine methyltransferase genes flanking the B-locus compared to a single copy in R. vesiculosus. Examination of dikaryotic single nucleotide polymorphisms within genomes revealed greater heterozygosity in R. vinicolor, consistent with increased rates of outcrossing. Both species possess the components of a heterothallic breeding system with R. vinicolor possessing a B-locus region structure consistent with tetrapolar Boletales and R. vesiculosus possessing a B-locus region structure intermediate between bipolar and tetrapolar Boletales. PMID:28450370

Turkish truffles I: 18 new records for Turkey

Treesearch

Aziz TÜRKOĞLU; Michael Castellano; James Martin TRAPPE; Mehrican YARATANAKUL GÜNGÖR

2015-01-01

We report the first records of 18 truffle species in Turkey. Three belong to the Ascomycota: Elaphomyces leucocarpus, E. muricatus, and Genea sphaerica; and 15 to the Basidiomycota: Alpova corsicus, Gautieria otthii, G. retirugosa, G. trabutii, Hymenogaster citrinus, H. hessei, H. luteus, H. lycoperdineus,...

Isolation and evaluation of terrestrial fungi with algicidal ability from Zijin Mountain, Nanjing, China.

PubMed

Han, Guomin; Feng, Xiaoguang; Jia, Yong; Wang, Congyan; He, Xingbing; Zhou, Qiyou; Tian, Xingjun

2011-08-01

Approximately 60 fungal isolates from Zijin Mountain (Nanjing, China) were screened to determine their algicidal ability. The results show that 8 fungi belonging to Ascomycota and 5 belonging to Basidiomycota have algicidal ability. Of these fungi, Irpex lacteus T2b, Trametes hirsuta T24, Trametes versicolor F21a, and Bjerkandera adusta T1 showed strong algicidal ability. The order of fungal chlorophyll-a removal efficiency was as follows: T. versicolor F21a > I. lacteus T2b > B. adusta T1 > T. hirsuta T24. In particular, T. versicolor F21a completely removed algal cells within 30 h, showing the strongest algicidal ability. The results also show that all 4 fungal species degraded algal cells through direct attack. In addition, most of the tested fungi from the order Polyporales of Basidiomycota exhibited strong algicidal activity, suggesting that most fungi that belong to this order have algicidal ability. The findings of this work could direct the search for terrestrial fungi for bloom control.

Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12

Treesearch

Jill Gaskell; Phil Kersten; Luis F. Larrondo; Paulo Canessa; Diego Martinez; David Hibbett; Monika Schmoll; Christian P. Kubicek; Angel T. Martinez; Jagjit Yadav; Emma Master; Jon Karl Magnuson; Debbie Yaver; Randy Berka; Kathleen Lail; Cindy Chen; Kurt LaButti; Matt Nolan; Anna Lipzen; Andrea Aerts; Robert Riley; Kerrie Barry; Bernard Henrissat; Robert Blanchette; Igor V. Grigoriev; Dan Cullen

2017-01-01

We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin.

A Contribution to the Taxonomy of Rhizochaete (Polyporales, Basidiomycota)

Treesearch

Karen K. Nakasone; Kymberly R. Draeger; Beatriz Ortiz-Santana

2017-01-01

Rhizochaete is a small genus of crust fungi that is closely related to Phanerochaete. A new species Rhizochaete belizensis is described, and three new combinations are proposed. Morphological studies and molecular sequence data from two nuclear ribosomal DNA regions (ITS and LSU) support the recognition of...

Wood decay fungus Flavodon ambrosius (Basidiomycota: Polyporales) is widely farmed by two genera of ambrosia beetles

Treesearch

You Li; Craig Christopher Bateman; James Skelton; Michelle Alice Jusino; Zachary John Nolen; David Rabern Simmons; Jiri Hulcr

2017-01-01

The ambrosia fungus Flavodon ambrosius is the primary nutritional mutualist of ambrosia beetles Ambrosiodmus and Ambrosiophilus in North America. F. ambrosius is the only known ambrosial basidiomycete, unique in its efficient lignocellulose degradation. F. ambrosius is associated with...

Biogeography of Hysterangiales (Phallomycetidae, Basidiomycota)

Treesearch

Kentaro Hosaka; Michael A. Castellano; Joseph W. Spatafora

2008-01-01

To understand the biogeography of truffle-like fungi, DNA sequences were analysed from representative taxa of Hysterangiales. Multigene phylogenies and the results of ancestral area reconstructions are consistent with the hypothesis of an Australian, or eastern Gondwanan, origin of Hysterangiales with subsequent range expansions to the Northern Hemisphere. However,...

Morphological and molecular studies on Resinicium s. str.

Treesearch

K. K. Nakasone

2007-01-01

Resinicium Parmasto is typified by Resinicium bicolor (Alb. & Schwein.: Fr.) Parm., (Hymenochaetales, Basidiomycota), a readily recognized and widely distributed corticioid, lignicolous species in the northern hemisphere. Five new species of Resinicium closely allied to R. bicolor from the Caribbean region are described and illustrated: Resinicium conferturn...

A new species of Laetiporus (Basidiomycota, Polyporales) from the Caribbean basin

Treesearch

Mark T. Banik; Daniel L. Lindner; Beatriz Ortiz-Santana; Deborah J. Lodge

2012-01-01

Laetiporus caribensis is described as a new species, causing brown rot on hardwoods in the Caribbean basin. Laetiporus caribensis is distinguished from described species in the genus by smaller basidiospores. In addition, single spore isolates of L. caribensis are incompatible with those of the known species of...

A revised family-level classification of the Polyporales (Basidiomycota)

Treesearch

Alfredo Justo; Otto Miettinen; Dimitrios Floudas; Beatriz Ortiz-Santana; Elisabet Sjökvist; Daniel Lindner; Karen Nakasone; Tuomo Niemelä; Karl-Henrik Larsson; Leif Ryvarden; David S. Hibbett

2017-01-01

Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We...

Mycoaciella : a synonym of phlebia

Treesearch

Karen K. Nakasone

2002-01-01

Mycoaciella (Steccherinaceae, Stereales, Basidiomycota) is a genus of resupinate, hydnaceous, corticioid fungi with a dimitic hyphal system. Presently, three taxa are accepted in the genus: M. bispora, the generic type, M. brunnea, and M. hinnulea. As a result of this microscopic study, Mycoaciella is placed in synonymy with Phlebia (Meruliaceae, Stereales), two new...

Dendrominia burdsallii (Corticiales, Basidiomycota), a new species from Arizona

Treesearch

Karen K. Nakasone

2014-01-01

Dendrominia burdsallii is proposed as a new species that occurs on bark of living Arbutus arizonica in southern Arizona. Its most striking feature is the very large, narrowly cylindrical to allantoid basidiospores, (30-) 37-50 × 10-12 (-13.5) µm, with hyaline, thin, smooth, acyanophilous walls.

RECONSTRUCTING THE EVOLUTIONARY HISTORY OF THE FOREST FUNGAL PATHOGEN, ARMILLARIA MELLEA, IN A TEMPERATE WORLDWIDE POPULATIONS

USDA-ARS?s Scientific Manuscript database

The forest pathogen Armillaria mellea s.s. (Basidiomycota, Physalacriaceae) is among the most significant forest pathogens causing root rot in northern temperate forest trees worldwide. Phylogenetic reconstructions for A. mellea show distinct European, Asian and North American lineages. The North Am...

A new species of Phlebopus (Botales, Basidiomycota) from Mexico

Treesearch

Timothy J. Baroni; Joaquin Cifuentes; Beatriz Ortiz Santana; Silvia Cappello

2015-01-01

A new species, Phlebopus mexicanus, is described from southern tropical rainforests of Mexico based on morphological and molecular characters. Several features distinguish this species from others of Phlebopus including the medium to small basidiomata with olivaceous brown tomentose pileus that becomes finely areolate cracked with age, the dark...

Mating and Progeny Isolation in The Corn Smut Fungus Ustilago maydis

USDA-ARS?s Scientific Manuscript database

The corn smut pathogen, Ustilago maydis (U. maydis) (DC.) Corda, is a semi-obligate plant pathogenic fungus in the phylum Basidiomycota (Alexopoulos, Mims and Blackwell, 1996). The fungus can be easily cultured in its haploid yeast phase on common laboratory media. However, to complete its sexual cy...

Leptocorticium (Corticiaceae s.l., Basidiomycota): new species and combinations

Treesearch

Karen K. Nakasone

2005-01-01

The genus Leptocorticium is redescribed, and a key to the species is provided. A new taxon, Leptocorticium tenellum, is described, and two new combinations, L. sasae and L. utribasidiatum, are proposed. Dentocorticium nephrolepidis is determined to be conspecific with L. cyatheae. All four species are described and illustrated.

Veluticeps fasciculata sp. nov. (Gloeophyllaceae, Basidiomycota), a close relative to V. berkeleyi

Treesearch

Jiao Yang; Karen K. Nakasone; Shuang-Hui He

2016-01-01

A new brown-rot fungal species, Veluticeps fasciculata, is described from southern China. It is characterized by perennial effused basidiocarps with smooth or tuberculose hymenophore, nodose-septate generative hyphae, fasciculate cystidia (as hyphal pegs in hymenophore) and relatively small basidiospores. It occurs on wood of Cunninghamia...

Investigation of Peniophora nuda for biological control of Cercospora beticola and Pyrenophora teres

USDA-ARS?s Scientific Manuscript database

Peniophora nuda (Fr.) Bres. belongs to the class Agaricomycetes under the phylum Basidiomycota and has been isolated in Europe, Great Britain, North America, Hawaii (US in Oceania) and New Zealand. Net blotch caused by Pyrenophora teres and Cercospora leaf spot (CLS) caused by Cercospora beticola ar...

Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Treesearch

Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina Capelari

2014-01-01

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

Arrasia rostrata (Basidiomycota), a new corticioid genus and species from Italy

Treesearch

Annarosa Bernicchia; Sergio P. Gorj& #243; n; Karen K. Nakasone

2011-01-01

An unusual corticioid species with distinctive large basidiospores that develop a distal refractive rostrum when fully mature is described as new. It grows on living bark of Juniperus phoenicea on the Italian island of Sardinia. Because it is morphologically distinct from any known genus of corticioid fungi, the new genus Arrasia...

Patterns of vegetative growth and gene flow in Rhizopogon vinicolor and R. vesiculosus (Boletales, Basidiomycota).

Treesearch

Annette M. Kretzer; Susie Dunham; Randy Molina; Joseph W. Spatafora

2005-01-01

We have collected sporocarps and tuberculate ectomycorrhizae of both Rhizopogon vinicolor and Rhizopogon vesiculosus from three 50 x 100 m plots located at Mary's Peak in the Oregon Coast Range (USA); linear map distances between plots ranged from c. 1 km to c. 5.5 km. Six and...

Microsatellite markers reveal the below ground distribution of genets in two species of Rhizopogon forming tuberculate ectomycorrhizas on Douglas-fir.

Treesearch

Annette M. Kretzer; Susie Dunham; Randy Molina; Joseph W. Spatafora

2003-01-01

We have developed microsatellite markers for two sister species of Rhizopogon, R. vesiculosus and R. vinicolor (Boletales, Basidiomycota), and used selected markers to investigate genet size and distribution from ectomycorrhizal samples. Both species form ectomycorrhizas with tuberculate morphology on Douglas-fir (...

Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951

DOE PAGES

Toome, Merje; Kuo, Alan; Henrissat, Bernard; ...

2014-06-12

We present the draft genome sequence of the smut fungus Tilletiaria anomala UBC 951 (Basidiomycota, Ustilaginomycotina). The sequenced genome size is 18.7 Mb, consisting of 289 scaffolds and a total of 6,810 predicted genes. This is the first genome sequence published for a fungus in the order Georgefisheriales (Exobasidiomycetes).

Traversing the fungal terpenome

PubMed Central

Quin, Maureen B.; Flynn, Christopher M.; Schmidt-Dannert, Claudia

2014-01-01

Fungi (Ascomycota and Basidiomycota) are prolific producers of structurally diverse terpenoid compounds. Classes of terpenoids identified in fungi include the sesqui-, di- and triterpenoids. Biosynthetic pathways and enzymes to terpenoids from each of these classes have been described. These typically involve the scaffold generating terpene synthases and cyclases, and scaffold tailoring enzymes such as e.g. cytochrome P450 monoxygenases, NAD(P)+ and flavin dependent oxidoreductases, and various group transferases that generate the final bioactive structures. The biosynthesis of several sesquiterpenoid mycotoxins and bioactive diterpenoids has been well-studied in Ascomycota (e.g. filamentous fungi). Little is known about the terpenoid biosynthetic pathways in Basidiomycota (e.g. mushroom forming fungi), although they produce a huge diversity of terpenoid natural products. Specifically, many trans-humulyl cation derived sesquiterpenoid natural products with potent bioactivities have been isolated. Biosynthetic gene clusters responsible for the production of trans-humulyl cation derived protoilludanes, and other sesquiterpenoids, can be rapidly identified by genome sequencing and bioinformatic methods. Genome mining combined with heterologous biosynthetic pathway refactoring has the potential to facilitate discovery and production of pharmaceutically relevant fungal terpenoids. PMID:25171145

Genome size analyses of Pucciniales reveal the largest fungal genomes.

PubMed

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Genome size analyses of Pucciniales reveal the largest fungal genomes

PubMed Central

Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G.; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T.; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research. PMID:25206357

Draft genome sequence of the white-rot fungus Obba rivulosa 3A-2

Treesearch

Otto Miettinen; Robert Riley; Kerrie Barry; Daniel Cullen; Ronald P. de Vries; Matthieu Hainaut; Annele Hatakka; Bernard Henrissat; Kristiina Hilden; Rita Kuo; Kurt LaButti; Anna Lipzen; Miia R. Makela; Laura Sandor; Joseph W. Spatafora; Igor V. Grigoriev; David S. Hibbett

2016-01-01

We report here the first genome sequence of the white-rot fungus Obba rivulsa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

Spore dispersal of a resupinate ectomycorrhizal fungus, Tomentella sublilacina, via soil food webs

Treesearch

Erik A. Lilleskov; Thomas D. Bruns

2005-01-01

Patterns of fungal spore dispersal affect gene flow, population structure and fungal community structure. Many Basidiomycota produce resupinate (crust-like) basidiocarps buried in the soil. Although spores are actively discharged, they often do not appear to be well positioned for aerial dispersal. We investigated the potential spore dispersal mechanisms of one...

Competing sexual and asexual generic names in Pucciniomycotina and Ustilaginomycotina (Basidiomycota) and recommendations for use

USDA-ARS?s Scientific Manuscript database

With the change to one scientific name for fungi, generic names representing sexual and asexual morphs have been evaluated to determine which name to use when two names represent the same genus and thus compete for use. In this paper generic names of the Pucciniomycotina and Ustilaginomycotina are e...

A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)

Treesearch

Beatriz Ortiz-Santana; Daniel L. Lindner; Otto Miettinen; Alfredo Justo; David S. Hibbett

2013-01-01

Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were...

A new species of Daedalea (Basidiomycota) and a synopsis of core species in Daedalea sensu stricto

Treesearch

Daniel L. Lindner; Leif Ryvarden; Timothy J. Baroni

2011-01-01

Daedalea neotropica, a species with striking violet stains on the pileus and pore surface, is described from material collected in the Maya Mountains of Belize. A synopsis of Daedalea sensu stricto is provided based on morphological and DNA sequence data. Analyses indicate that at least four species should be included in ...

Taxonomy of the Rhizopogon vinicolor species complex based on analysis of ITS sequences and microsatellite loci.

Treesearch

Annette M. Kretzer; Daniel L. Luoma; Randy Molina; Joseph W. Spatafora

2003-01-01

We are re-addressing species concepts in the Rhizopogon vinicolor species complex (Boletales, Basidiomycota) using sequence data from the interna transcribed spacer (ITS) region of the nuclear ribosomal repeat, as well as genoLypic data from five microsatellite loci. The R. vinicolor species complex by our definition includes,...

Taxonomy and phylogeny of Lopharia s.s., Dendrodontia, Dentocorticium and Fuscocerrena (Basidiomycota, Polyporales)

Treesearch

Shi-Liang Liu; Karen K. Nakasone; Sheng-Hua Wu; Shuang-Hui He; Yu-Cheng Dai

2018-01-01

Eleven taxa of Lopharia s.s., Dendrodontia, Dentocorticium and Fuscocerrena in Polyporales are included in the phylogenetic analyses of nuc rDNA ITS1-5.8S-ITS2 (ITS), D1-D2 domains of nuc 28S rDNA (28S) and RNA polymerase II second-largest subunit (rpb2) sequences. New species Lopharia resupinata...

Arthromyces and Blastosporella, two new genera of conidia-producing lyophylloid agarics (Agaricales, Basidiomycota) from the neotropics

Treesearch

Timothy J. Baroni; Ana Esperanza Franco-Molano; D. Jean Lodge; Daniel L. Lindner; Egon Horak; Valerie Hofstetter

2007-01-01

Two new genera encompassing three new species of lyophylloid agarics that produce conidia on the basidiomata are described. Arthromyces is a genus comprised of two very different arthrospore-producing mushroom species found in the Greater Antilles and Central America. Blastosporella is a monotypic genus with spherical balls of blastospores covering the pileus surface...

Sarcoporia polyspora (Basidiomycota, Polyporales): a rare wood-decay fungus newly recorded from South America

Treesearch

Daiana Bortoluzzi Baldoni; Beatriz Ortiz-Santana; Gilberto Coelho; Zaida I. Antoniolli; Rodrigo J.S. Jacques

2014-01-01

Brown-rot fungi degrade almost exclusively wood cellulosic materials participating in the, carbon cycle and soil formation of many forest regions, these are especially important on boreal and cultivated coniferous forests. These fungi and forests may have a common co-evolutionary history. Studying wood-inhabiting fungi in cultivated pine forests in Southern Brazil, we...

Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms.

PubMed

Bagella, Simonetta; Filigheddu, Rossella; Caria, Maria Carmela; Girlanda, Mariangela; Roggero, Pier Paolo

2014-12-01

The aims of this paper were (i) to define how contrasting land uses affected plant biodiversity in Mediterranean agro-silvo-pastoral-systems across a gradient of disturbance regimes: cork oak forests, secondary grasslands, hay crops, grass covered vineyards, tilled vineyards; (ii) to determine whether these patterns mirrored those of below-ground microorganisms and whether the components of γ-diversity followed a similar model. The disturbance regimes affected plant assemblage composition. Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops. Plant assemblage composition patterns mirrored those of Basidiomycota and Ascomycota. Richness in Basidiomycota, denitrifying bacteria and microbial biomass showed the same trend as that observed for vascular plant richness. The Shannon index pattern of below-ground microorganisms was different from that of plants. The plant γ-diversity component model weakly mirrored those of Ascomycota. Patchy diversity patterns suggest that the maintenance of contrasting land uses associated with different productions typical of agro-silvo-pastoral-systems can guarantee the conservation of biodiversity. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Agricultural and Food Processing Applications of Pulsed Power and Plasma Technologies

NASA Astrophysics Data System (ADS)

Takaki, Koichi

Agricultural and food processing applications of pulsed power and plasma technologies are described in this paper. Repetitively operated compact pulsed power generators with a moderate peak power are developed for the agricultural and the food processing applications. These applications are mainly based on biological effects and can be categorized as germination control of plants such as Basidiomycota and arabidopsis inactivation of bacteria in soil and liquid medium of hydroponics; extraction of juice from fruits and vegetables; decontamination of air and liquid, etc. Types of pulsed power that have biological effects are caused with gas discharges, water discharges, and electromagnetic fields. The discharges yield free radicals, UV radiation, intense electric field, and shock waves. Biologically based applications of pulsed power and plasma are performed by selecting the type that gives the target objects the adequate result from among these agents or byproducts. For instance, intense electric fields form pores on the cell membrane, which is called electroporation, or influence the nuclei. This paper mainly describes the application of the pulsed power for the germination control of Basidiomycota i.e. mushroom, inactivation of fungi in the soil and the liquid medium in hydroponics, and extraction of polyphenol from skins of grape.

[Intestinal fungal diversity of sub-adult giant panda].

PubMed

Ai, Shengquan; Zhong, Zhijun; Peng, Guangneng; Wang, Chengdong; Luo, Yongjiu; He, Tingmei; Gu, Wuyang; Li, Caiwu; Li, Gangshi; Wu, Honglin; Liu, Xuehan; Xia, Yu; Liu, Yanhong; Zhou, Xiaoxiao

2014-11-04

The fungi diversity in the guts of five sub-adult giant pandas was analyzed. We analyzed the fungal internal transcribed spacer sequences (ITS) using restriction fragment length polymorphism (RFLP). ITS regions were amplified with fungal universal primers to construct ITS clone libraries. The fingerprints were analyzed by restriction fragment length polymorphism using the Hha I and Hae III enzymes. The cloned PCR products were analyzed by sequencing and diversities were demonstrated by phylogenetic tree. The gut fungi of 5 sub-adult giant pandas were mainly composed of Ascomycota (average of 46.24%), Basidiomycota ( average of 15.79%), unclassified (average of 29.14%), uncultured fungus (average of 8.83% ). Ascomycota was mainly composed of Saccharomycetes (average of 63.74%) and Dothideomycetes ( average of 35.91%); Basidiomycota was mainly composed of Tremellomycetes (average of 65.80%) and Microbotryomycetes (average of 33.15%). Four classes were mainly composed of Candida and Debaryomyces; Pleosporales and Myriangium; Cystofilobasidium and Trichosporon; Leucosporidium, and Leucosporidiella, whereas the proportions were different for each sample. Fungal flora existing in the intestines of sub-adult giant pandas expand our knowledge on the structure of the giant panda gut microbes and also help us to further study whether fungal flora can help giant pandas digest high-fiber foods.

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor.

PubMed

Liu, Chang-Hong; Huang, Xin; Xie, Tian-Ning; Duan, Ning; Xue, Ya-Rong; Zhao, Tan-Xi; Lever, Mark A; Hinrichs, Kai-Uwe; Inagaki, Fumio

2017-02-01

Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal-associated sediment samples collected at depths ranging from 1289 to 2457 m below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species). Penicillium and Aspergillus relatives were the most dominant genera within the Ascomycetes, followed by the members of genera Cladosporium, Hamigera, Chaetomium, Eutypella, Acremonium, Aureobasidium, Candida, Eurotium, Exophiala, Nigrospora, Bionectria and Pseudocercosporella. Four Basidiomycota species were identified as genera Schizophyllum, Irpex, Bjerkandera and Termitomyces. Among these isolates, Cladosporium sphaerospermum and Aspergillus sydowii relatives were isolated from a thin lignite coal-sandstone formation at 2457 mbsf. Our results indicate that these cultivable fungal populations are indigenous, originating from past terrigenous environments, which have persisted, possibly as spores, through ∼20 million years of depositional history. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Treesearch

Robert Riley; Asaf A. Salamov; Daren W. Brown; Laszlo G. Nagy; Dimitrios Floudas; Benjamin W. Held; Anthony Levasseur; Vincent Lombard; Emmanuelle Morin; Robert Otillar; Erika A. Lindquist; Hui Sun; Kurt M. LaButti; Jeremy Schmutz; Dina Jabbour; Hong Luo; Scott E. Baker; Antonio G. Pisabarro; Jonathan D. Walton; Robert A. Blanchette; Bernard Henrissat; Francis Martin; Daniel Cullen; David S. Hibbett; Igor V. Grigoriev

2014-01-01

Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic...

Tracking the distribution of Puccinia psidii genotypes that cause rust disease on diverse myrtaceous trees and shrubs

Treesearch

Amy L. Ross-Davis; Rodrigo N. Graca; Acelino C. Alfenas; Tobin L. Peever; Jack W. Hanna; Janice Y. Uchida; Rob D. Hauff; Chris Y. Kadooka; Mee-Sook Kim; Phil G. Cannon; Shigetou Namba; Nami Minato; Sofia Simeto; Carlos A. Perez; Min B. Rayamajhi; Mauricio Moran; D. Jean Lodge; Marcela Arguedas; Rosario Medel-Ortiz; M. Armando Lopez-Ramirez; Paula Tennant; Morag Glen; Ned B. Klopfenstein

2014-01-01

Puccinia psidii Winter (Basidiomycota, Uredinales) is a biotrophic rust fungus that was first reported in Brazil from guava in 1884 (Psidium guajava; Winter 1884) and later from eucalypt in 1912 (Joffily 1944). Considered to be of neotropical origin, the rust has also been reported to infect diverse myrtaceous hosts elsewhere in South America, Central America, the...

Hypholoma lateritium isolated from coarse woody debris, the forest floor, and mineral soil in a deciduous forest in New Hampshire

Treesearch

Therese A. Thompson; R. Greg Thorn; Kevin T. Smith

2012-01-01

Fungi in the Agaricomycetes (Basidiomycota) are the primary decomposers in temperate forests of dead wood on and in the forest soil. Through the use of isolation techniques selective for saprotrophic Agaricomycetes, a variety of wood decay fungi were isolated from a northern hardwood stand in the Bartlett Experimental Forest, New Hampshire, USA. In particular,

Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA

Treesearch

Jozsef Geml; Gary A. Laursen; Ina Timling; Jack M. McFarland; Michael G. Booth; Niall Lennon; Chad Nusbaum; D. Lee Taylor

2009-01-01

Despite the critical roles fungi play in the functioning of ecosystems, especially as symbionts of plants and recyclers of organic matter, their biodiversity is poorly known in high-latitude regions. In this paper, we discuss the molecular diversity of one of the most diverse and abundant groups of ectomycorrhizal fungi: the genus Lactarius Pers....

Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota)

Treesearch

József Geml; Gary A. Laursen; Ian C. Herriott; Jack M. McFarland; Michael G. Booth; Niall Lennon; H. Chad Nusbaum; D. Lee Taylor

2010-01-01

Although critical for the functioning of ecosystems, fungi are poorly known in high-latitude regions. Here, we provide the first genetic diversity assessment of one of the most diverse and abundant ectomycorrhizal genera in Alaska: Russula. We analyzed internal transcribed spacer rDNA sequences from sporocarps and soil samples using phylogenetic...

Study on the ice nucleation activity of fungal spores (Ascomycota and Basidiomycota)

NASA Astrophysics Data System (ADS)

Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

2012-04-01

Biogenic ice nucleation (IN) in the atmosphere is a topic of growing interest, as, according to IPCC, the impact of IN on global climate is crucial to perform reliable climate model calculations. About 20 years ago IN activity of a few lichen and Fusarium species [1,2] was reported, while all other investigated fungi were IN-negative. However, as the fungal kingdom is vast, many abundant species, especially the Basidiomycota (most mushrooms), were not tested before. Furthermore, the focus of the past studies was on the IN activity of the mycelium as a cryoprotective mechanism, and not on the airborne spores. We carried out oil immersion measurements [3] with spores from 17 different fungal species of ecological, economical or sanitary importance. Most of these species have not been investigated before, like exponents of Aspergillus, Trichoderma and Agaricales (most mushrooms). Apart from F. avenaceum, spores of all measured species showed moderate or no IN activity, supporting the hypothesis that significant IN activity is a rather exclusive property of only a few species within the fungal kingdom. [1] Kieft TL and Ruscetti T: J. Bacteriol. 172, 3519-3523, 1990. [2] Pouleur S et al.: Appl. Environ. Microbiol., 58, 2960-2964, 1992. [3] Marcolli C et al.: Atmos. Chem. Phys. 7, 5081-5091, 2007.

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans

PubMed Central

Dumesic, Phillip A.; Rosenblad, Magnus A.; Samuelsson, Tore; Nguyen, Tiffany; Moresco, James J.; Yates, John R.; Madhani, Hiten D.

2015-01-01

Despite conservation of the signal recognition particle (SRP) from bacteria to man, computational approaches have failed to identify SRP components from genomes of many lower eukaryotes, raising the possibility that they have been lost or altered in those lineages. We report purification and analysis of SRP in the human pathogen Cryptococcus neoformans, providing the first description of SRP in basidiomycetous yeast. The C. neoformans SRP RNA displays a predicted structure in which the universally conserved helix 8 contains an unprecedented stem-loop insertion. Guided by this sequence, we computationally identified 152 SRP RNAs throughout the phylum Basidiomycota. This analysis revealed additional helix 8 alterations including single and double stem-loop insertions as well as loop diminutions affecting RNA structural elements that are otherwise conserved from bacteria to man. Strikingly, these SRP RNA features in Basidiomycota are accompanied by phylum-specific alterations in the RNA-binding domain of Srp54, the SRP protein subunit that directly interacts with helix 8. Our findings reveal unexpected fungal SRP diversity and suggest coevolution of the two most conserved SRP features—SRP RNA helix 8 and Srp54—in basidiomycetes. Because members of this phylum include important human and plant pathogens, these noncanonical features provide new targets for antifungal compound development. PMID:26275773

Shooting Mechanisms in Nature: A Systematic Review.

PubMed

Sakes, Aimée; van der Wiel, Marleen; Henselmans, Paul W J; van Leeuwen, Johan L; Dodou, Dimitra; Breedveld, Paul

2016-01-01

In nature, shooting mechanisms are used for a variety of purposes, including prey capture, defense, and reproduction. This review offers insight into the working principles of shooting mechanisms in fungi, plants, and animals in the light of the specific functional demands that these mechanisms fulfill. We systematically searched the literature using Scopus and Web of Knowledge to retrieve articles about solid projectiles that either are produced in the body of the organism or belong to the body and undergo a ballistic phase. The shooting mechanisms were categorized based on the energy management prior to and during shooting. Shooting mechanisms were identified with projectile masses ranging from 1·10-9 mg in spores of the fungal phyla Ascomycota and Zygomycota to approximately 10,300 mg for the ballistic tongue of the toad Bufo alvarius. The energy for shooting is generated through osmosis in fungi, plants, and animals or muscle contraction in animals. Osmosis can be induced by water condensation on the system (in fungi), or water absorption in the system (reaching critical pressures up to 15.4 atmospheres; observed in fungi, plants, and animals), or water evaporation from the system (reaching up to -197 atmospheres; observed in plants and fungi). The generated energy is stored as elastic (potential) energy in cell walls in fungi and plants and in elastic structures in animals, with two exceptions: (1) in the momentum catapult of Basidiomycota the energy is stored in a stalk (hilum) by compression of the spore and droplets and (2) in Sphagnum energy is mainly stored in compressed air. Finally, the stored energy is transformed into kinetic energy of the projectile using a catapult mechanism delivering up to 4,137 J/kg in the osmotic shooting mechanism in cnidarians and 1,269 J/kg in the muscle-powered appendage strike of the mantis shrimp Odontodactylus scyllarus. The launch accelerations range from 6.6g in the frog Rana pipiens to 5,413,000g in cnidarians, the launch velocities from 0.1 m/s in the fungal phylum Basidiomycota to 237 m/s in the mulberry Morus alba, and the launch distances from a few thousands of a millimeter in Basidiomycota to 60 m in the rainforest tree Tetraberlinia moreliana. The mass-specific power outputs range from 0.28 W/kg in the water evaporation mechanism in Basidiomycota to 1.97·109 W/kg in cnidarians using water absorption as energy source. The magnitude of accelerations involved in shooting is generally scale-dependent with the smaller the systems, discharging the microscale projectiles, generating the highest accelerations. The mass-specific power output is also scale dependent, with smaller mechanisms being able to release the energy for shooting faster than larger mechanisms, whereas the mass-specific work delivered by the shooting mechanism is mostly independent of the scale of the shooting mechanism. Higher mass-specific work-values are observed in osmosis-powered shooting mechanisms (≤ 4,137 J/kg) when compared to muscle-powered mechanisms (≤ 1,269 J/kg). The achieved launch parameters acceleration, velocity, and distance, as well as the associated delivered power output and work, thus depend on the working principle and scale of the shooting mechanism.

A gilled mushroom, Gerontomyces lepidotus gen. et sp. nov. (Basidiomycota: Agaricales), in Baltic amber.

PubMed

Poinar, George

2016-09-01

A densely scaled small mushroom in Baltic amber is described as Gerontomyces lepidotus gen. et sp. nov. and is characterized by a convex pileus 1.0 mm in diameter, distant to subdistant lamellae with smooth margins and a centrally inserted cylindrical, solid stipe. Its taxonomic placement is uncertain. This is the first mushroom described from Baltic amber. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Fungal communities from the calcareous deep-sea sediments in the Southwest India Ridge revealed by Illumina sequencing technology.

PubMed

Zhang, Likui; Kang, Manyu; Huang, Yangchao; Yang, Lixiang

2016-05-01

The diversity and ecological significance of bacteria and archaea in deep-sea environments have been thoroughly investigated, but eukaryotic microorganisms in these areas, such as fungi, are poorly understood. To elucidate fungal diversity in calcareous deep-sea sediments in the Southwest India Ridge (SWIR), the internal transcribed spacer (ITS) regions of rRNA genes from two sediment metagenomic DNA samples were amplified and sequenced using the Illumina sequencing platform. The results revealed that 58-63 % and 36-42 % of the ITS sequences (97 % similarity) belonged to Basidiomycota and Ascomycota, respectively. These findings suggest that Basidiomycota and Ascomycota are the predominant fungal phyla in the two samples. We also found that Agaricomycetes, Leotiomycetes, and Pezizomycetes were the major fungal classes in the two samples. At the species level, Thelephoraceae sp. and Phialocephala fortinii were major fungal species in the two samples. Despite the low relative abundance, unidentified fungal sequences were also observed in the two samples. Furthermore, we found that there were slight differences in fungal diversity between the two sediment samples, although both were collected from the SWIR. Thus, our results demonstrate that calcareous deep-sea sediments in the SWIR harbor diverse fungi, which augment the fungal groups in deep-sea sediments. This is the first report of fungal communities in calcareous deep-sea sediments in the SWIR revealed by Illumina sequencing.

Fungal communities in soils along a vegetative ecotone.

PubMed

Karst, Justine; Piculell, Bridget; Brigham, Christy; Booth, Michael; Hoeksema, Jason D

2013-01-01

We investigated the community composition and diversity of soil fungi along a sharp vegetative ecotone between coastal sage scrub (CSS) and nonnative annual grassland habitat at two sites in coastal California. USA- We pooled soil samples across 29 m transects on either side of the ecotone at each of the two sites, and. using clone libraries of fungal ribosomal DNA, we identified 280 operational taxonomic units (OTUs) from a total 40 g soil. We combined information from partial LSU and ITS sequences and found that the majority of OTUs belonged to the phylum Ascomycota, followed by Basidiomycota. Within the Ascomycota. a quarter of OTUs were Sordariomycetes. 17% were Leotiomycet.es, 16% were Dothideomycetes and the remaining OTUs were distributed among the classes Eurotiomycetes, Pezizomycetes, Lecanoromycetes, Orbiliomycetes and Arthoniomycetes. Within the Basidiomycota. all OTUs but one belonged to the subphylum Agaricomycotina. We also sampled plant communities at the same sites to offer a point of comparison for patterns in richness of fungal communities. Fungal communities had higher alpha and beta diversity than plant communities; fungal communities were approximately 20 times as rich as plant communities and the majority of OTUs were found in single soil samples. Soils harbored a unique mycoflora that did not reveal vegetative boundaries or site differences. High alpha and beta diversity and possible sampling artifacts necessitate extensive sampling to reveal differentiation in these fungal communities.

Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic): Aquatic Fungi in the Arctic.

PubMed

Zhang, Tao; Wang, Neng-Fei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-04-01

We assessed the diversity and distribution of fungi in 13 water samples collected from four aquatic environments (stream, pond, melting ice water, and estuary) in the Ny-Ålesund Region, Svalbard (High Arctic) using 454 pyrosequencing with fungi-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Aquatic fungal communities in this region showed high diversity, with a total of 43,061 reads belonging to 641 operational taxonomic units (OTUs) being found. Of these OTUs, 200 belonged to Ascomycota, 196 to Chytridiomycota, 120 to Basidiomycota, 13 to Glomeromycota, and 10 to early diverging fungal lineages (traditional Zygomycota), whereas 102 belonged to unknown fungi. The major orders were Helotiales, Eurotiales, and Pleosporales in Ascomycota; Chytridiales and Rhizophydiales in Chytridiomycota; and Leucosporidiales and Sporidiobolales in Basidiomycota. The common fungal genera Penicillium, Rhodotorula, Epicoccum, Glaciozyma, Holtermanniella, Betamyces, and Phoma were identified. Interestingly, the four aquatic environments in this region harbored different aquatic fungal communities. Salinity, conductivity, and temperature were important factors in determining the aquatic fungal diversity and community composition. The results suggest the presence of diverse fungal communities and a considerable number of potentially novel fungal species in Arctic aquatic environments, which can provide reliable data for studying the ecological and evolutionary responses of fungi to climate change in the Arctic ecosystem.

Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest

NASA Astrophysics Data System (ADS)

Womack, A. M.; Artaxo, P. E.; Ishida, F. Y.; Mueller, R. C.; Saleska, S. R.; Wiedemann, K. T.; Bohannan, B. J. M.; Green, J. L.

2015-11-01

Fungi are ubiquitous in the atmosphere and may play an important role in atmospheric processes. We investigated the composition and diversity of fungal communities over the Amazon rainforest canopy and compared these communities to fungal communities found in terrestrial environments. We characterized the total fungal community and the metabolically active portion of the community using high-throughput DNA and RNA sequencing and compared these data to predictions generated by a mass-balance model. We found that the total community was primarily comprised of fungi from the phylum Basidiomycota. In contrast, the active community was primarily composed of members of the phylum Ascomycota and included a high relative abundance of lichen fungi, which were not detected in the total community. The relative abundance of Basidiomycota and Ascomycota in the total and active communities was consistent with our model predictions, suggesting that this result was driven by the relative size and number of spores produced by these groups. When compared to other environments, fungal communities in the atmosphere were most similar to communities found in tropical soils and leaf surfaces. Our results demonstrate that there are significant differences in the composition of the total and active fungal communities in the atmosphere, and that lichen fungi, which have been shown to be efficient ice nucleators, may be abundant members of active atmospheric fungal communities over the forest canopy.

High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.

PubMed

Xu, Wei; Pang, Ka-Lai; Luo, Zhu-Hua

2014-11-01

Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.

Shooting Mechanisms in Nature: A Systematic Review

PubMed Central

Sakes, Aimée; van der Wiel, Marleen; Henselmans, Paul W. J.; van Leeuwen, Johan L.; Dodou, Dimitra; Breedveld, Paul

2016-01-01

Background In nature, shooting mechanisms are used for a variety of purposes, including prey capture, defense, and reproduction. This review offers insight into the working principles of shooting mechanisms in fungi, plants, and animals in the light of the specific functional demands that these mechanisms fulfill. Methods We systematically searched the literature using Scopus and Web of Knowledge to retrieve articles about solid projectiles that either are produced in the body of the organism or belong to the body and undergo a ballistic phase. The shooting mechanisms were categorized based on the energy management prior to and during shooting. Results Shooting mechanisms were identified with projectile masses ranging from 1·10−9 mg in spores of the fungal phyla Ascomycota and Zygomycota to approximately 10,300 mg for the ballistic tongue of the toad Bufo alvarius. The energy for shooting is generated through osmosis in fungi, plants, and animals or muscle contraction in animals. Osmosis can be induced by water condensation on the system (in fungi), or water absorption in the system (reaching critical pressures up to 15.4 atmospheres; observed in fungi, plants, and animals), or water evaporation from the system (reaching up to −197 atmospheres; observed in plants and fungi). The generated energy is stored as elastic (potential) energy in cell walls in fungi and plants and in elastic structures in animals, with two exceptions: (1) in the momentum catapult of Basidiomycota the energy is stored in a stalk (hilum) by compression of the spore and droplets and (2) in Sphagnum energy is mainly stored in compressed air. Finally, the stored energy is transformed into kinetic energy of the projectile using a catapult mechanism delivering up to 4,137 J/kg in the osmotic shooting mechanism in cnidarians and 1,269 J/kg in the muscle-powered appendage strike of the mantis shrimp Odontodactylus scyllarus. The launch accelerations range from 6.6g in the frog Rana pipiens to 5,413,000g in cnidarians, the launch velocities from 0.1 m/s in the fungal phylum Basidiomycota to 237 m/s in the mulberry Morus alba, and the launch distances from a few thousands of a millimeter in Basidiomycota to 60 m in the rainforest tree Tetraberlinia moreliana. The mass-specific power outputs range from 0.28 W/kg in the water evaporation mechanism in Basidiomycota to 1.97·109 W/kg in cnidarians using water absorption as energy source. Discussion and conclusions The magnitude of accelerations involved in shooting is generally scale-dependent with the smaller the systems, discharging the microscale projectiles, generating the highest accelerations. The mass-specific power output is also scale dependent, with smaller mechanisms being able to release the energy for shooting faster than larger mechanisms, whereas the mass-specific work delivered by the shooting mechanism is mostly independent of the scale of the shooting mechanism. Higher mass-specific work-values are observed in osmosis-powered shooting mechanisms (≤ 4,137 J/kg) when compared to muscle-powered mechanisms (≤ 1,269 J/kg). The achieved launch parameters acceleration, velocity, and distance, as well as the associated delivered power output and work, thus depend on the working principle and scale of the shooting mechanism. PMID:27454125

New luminescent mycenoid fungi (Basidiomycota, Agaricales) from São Paulo State, Brazil.

PubMed

Desjardin, Dennis E; Perry, Brian A; Stevani, Cassius V

Four species of mycenoid fungi are reported as luminescent (or putatively luminescent) on the basis of specimens collected from São Paulo State, Brazil. Two of them represent new species (Mycena oculisnymphae, Resinomycena petarensis), and two represent new reports of luminescence in previously described species (M. deformis, M. globulispora). Comprehensive descriptions, illustrations, photographs, and comparisons with phenetically similar species are provided. Sequences of nuc rDNA internal transcribed spacer regions were generated for barcoding purposes and for comparisons with similar species.

Links between Soil Fungal Diversity and Plant and Soil Properties on the Loess Plateau

PubMed Central

Yang, Yang; Dou, Yanxing; Huang, Yimei; An, Shaoshan

2017-01-01

Previous studies have revealed inconsistent correlations between fungal diversity and plant/soil properties from local to global scales. Here, we investigated the internal relationships between soil fungal diversity and plant/soil properties on the Loess Plateau following vegetation restoration, using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region for fungal identification. We found significant effects of land use types (Af, Artificial forest; Ns, Natural shrub; Ag, Artificial grassland; Ng, Natural grassland; Sc, slope cropland) on soil fungal communities composition, and the dominant phyla were Ascomycota, Basidiomycota, and Zygomycota, which transitioned from Basidiomycota-dominant to Ascomycota-dominant community due to vegetation restoration. The Chao1 richness, Shannon’s diversity and ACE indices were significantly influenced by land use types with the order of Ns > Af > Ng > Ag > Sc, and the total number of OTUs varied widely. In contrast, Good’s coverage and Simpson’s diversity indicated no significant difference among land use types (p > 0.05). Correlation analysis showed that plant and soil properties were closely related to fungal diversity regardless of land use types. In addition, soil organic carbon (SOC) and Hplant (plant richness, Shannon-Wiener index) were strong driving factors that explained fungal diversity. As revealed by the structural equation model (SEM) and generalized additive models (GAMs), fungal diversity was directly and indirectly affected by soil and plant properties, respectively, providing evidence for strong links between soil fungal diversity and plant and soil properties on the Loess Plateau. PMID:29163460

Links between Soil Fungal Diversity and Plant and Soil Properties on the Loess Plateau.

PubMed

Yang, Yang; Dou, Yanxing; Huang, Yimei; An, Shaoshan

2017-01-01

Previous studies have revealed inconsistent correlations between fungal diversity and plant/soil properties from local to global scales. Here, we investigated the internal relationships between soil fungal diversity and plant/soil properties on the Loess Plateau following vegetation restoration, using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region for fungal identification. We found significant effects of land use types (Af, Artificial forest; Ns, Natural shrub; Ag, Artificial grassland; Ng, Natural grassland; Sc, slope cropland) on soil fungal communities composition, and the dominant phyla were Ascomycota, Basidiomycota , and Zygomycota , which transitioned from Basidiomycota -dominant to Ascomycota -dominant community due to vegetation restoration. The Chao1 richness, Shannon's diversity and ACE indices were significantly influenced by land use types with the order of Ns > Af > Ng > Ag > Sc, and the total number of OTUs varied widely. In contrast, Good's coverage and Simpson's diversity indicated no significant difference among land use types ( p > 0.05). Correlation analysis showed that plant and soil properties were closely related to fungal diversity regardless of land use types. In addition, soil organic carbon (SOC) and H plant (plant richness, Shannon-Wiener index) were strong driving factors that explained fungal diversity. As revealed by the structural equation model (SEM) and generalized additive models (GAMs), fungal diversity was directly and indirectly affected by soil and plant properties, respectively, providing evidence for strong links between soil fungal diversity and plant and soil properties on the Loess Plateau.

Fungal Sex: The Basidiomycota.

PubMed

Coelho, Marco A; Bakkeren, Guus; Sun, Sheng; Hood, Michael E; Giraud, Tatiana

2017-06-01

Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation. Independent segregation of the two compatibility factors can create four haploid mating genotypes from meiosis, referred to as tetrapolarity. This condition is thought to be ancestral to the basidiomycetes. Alternatively, cosegregation by linkage of the two mating factors, or in some cases the absence of the pheromone-based discrimination, yields only two mating types from meiosis, referred to as bipolarity. Several species are now known to have large and highly rearranged chromosomal regions linked to mating-type genes. At the population level, polymorphism of the mating-type genes is an exceptional aspect of some basidiomycete fungi, where selection under outcrossing for rare, intercompatible allelic variants is thought to be responsible for numbers of mating types that may reach several thousand. Advances in genome sequencing and assembly are yielding new insights by comparative approaches among and within basidiomycete species, with the promise to resolve the evolutionary origins and dynamics of mating compatibility genetics in this major eukaryotic lineage.

Human Fungal Pathogens of Mucorales and Entomophthorales.

PubMed

Mendoza, Leonel; Vilela, Raquel; Voelz, Kerstin; Ibrahim, Ashraf S; Voigt, Kerstin; Lee, Soo Chan

2014-11-06

In recent years, we have seen an increase in the number of immunocompromised cohorts as a result of infections and/or medical conditions, which has resulted in an increased incidence of fungal infections. Although rare, the incidence of infections caused by fungi belonging to basal fungal lineages is also continuously increasing. Basal fungal lineages diverged at an early point during the evolution of the fungal lineage, in which, in a simplified four-phylum fungal kingdom, Zygomycota and Chytridiomycota belong to the basal fungi, distinguishing them from Ascomycota and Basidiomycota. Currently there are no known human infections caused by fungi in Chytridiomycota; only Zygomycotan fungi are known to infect humans. Hence, infections caused by zygomycetes have been called zygomycosis, and the term "zygomycosis" is often used as a synonym for "mucormycosis." In the four-phylum fungal kingdom system, Zygomycota is classified mainly based on morphology, including the ability to form coenocytic (aseptated) hyphae and zygospores (sexual spores). In the Zygomycota, there are 10 known orders, two of which, the Mucorales and Entomophthorales, contain species that can infect humans, and the infection has historically been known as zygomycosis. However, recent multilocus sequence typing analyses (the fungal tree of life [AFTOL] project) revealed that the Zygomycota forms not a monophyletic clade but instead a polyphyletic clade, whereas Ascomycota and Basidiomycota are monophyletic. Thus, the term "zygomycosis" needed to be further specified, resulting in the terms "mucormycosis" and "entomophthoramycosis." This review covers these two different types of fungal infections. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

Response of Soil Fungi Community Structure to Salt Vegetation Succession in the Yellow River Delta.

PubMed

Wang, Yan-Yun; Guo, Du-Fa

2016-10-01

High-throughput sequencing technology was used to reveal the composition and distribution of fungal community structure in the Yellow River Delta under bare land and four kinds of halophyte vegetation (saline seepweed, Angiospermae, Imperata and Apocynum venetum [A. venetum]). The results showed that the soil quality continuously improved with the succession of salt vegetation types. The soil fungi richness of mild-salt communities (Imperata and A. venetum) was relatively higher, with Shannon index values of 5.21 and 5.84, respectively. The soil fungi richness of severe-salt-tolerant communities (saline seepweed, Angiospermae) was relatively lower, with Shannon index values of 4.64 and 4.66, respectively. The UniFrac metric values ranged from 0.48 to 0.67 when the vegetation was in different succession stages. A total of 60,174 valid sequences were obtained for the five vegetation types, and they were classified into Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota and Mucoromycotina. Ascomycota had the greatest advantage among plant communities of Imperata and A. venetum, as indicated by relative abundances of 2.69 and 69.97 %, respectively. Basidiomycota had the greatest advantage among mild-salt communities of saline seepweed and Angiospermae, with relative abundances of 9.43 and 6.64 %, respectively. Soil physical and chemical properties were correlated with the distribution of the fungi, and Mucor was significantly correlated with soil moisture (r = 0.985; P < 0.01). Soil quality, salt vegetation and soil fungi were influenced by each other.

How far and how fast can mushroom spores fly? Physical limits on ballistospore size and discharge distance in the Basidiomycota

PubMed Central

Fischer, Mark W. F.; Stolze-Rybczynski, Jessica L.; Cui, Yunluan; Money, Nicholas P.

2010-01-01

Active discharge of basidiospores in most species of Basidiomycota is powered by the rapid movement of a droplet of fluid, called Buller’s drop, over the spore surface. This paper is concerned with the operation of the launch mechanism in species with the largest and smallest ballistospores. Aleurodiscus gigasporus (Russulales) produces the largest basidiospores on record. The maximum dimensions of the spores, 34 × 28 µm, correspond to a volume of 14 pL and to an estimated mass of 17 ng. The smallest recorded basidiospores are produced by Hyphodontia latitans (Hymenochaetales). Minimum spore dimensions in this species, 3.5 × 0.5 µm, correspond to a volume of 0.5 fL and mass of 0.6 pg. Neither species has been studied using high-speed video microscopy, but this technique was used to examine ballistospore discharge in species with spores of similar sizes (slightly smaller than A. gigasporus and slightly larger than those of H. latitans). Extrapolation of velocity measurements from these fungi provided estimates of discharge distances ranging from a maximum of almost 2 mm in A. gigasporus to a minimum of 4 µm in H. latitans. These are, respectively, the longest and shortest predicted discharge distances for ballistospores. Limitations to the distances traveled by basidiospores are discussed in relation to the mechanics of the discharge process and the types of fruit-bodies from which the spores are released. PMID:20835365

Human Fungal Pathogens of Mucorales and Entomophthorales

PubMed Central

Mendoza, Leonel; Vilela, Raquel; Voelz, Kerstin; Ibrahim, Ashraf S.; Voigt, Kerstin; Lee, Soo Chan

2015-01-01

In recent years, we have seen an increase in the number of immunocompromised cohorts as a result of infections and/or medical conditions, which has resulted in an increased incidence of fungal infections. Although rare, the incidence of infections caused by fungi belonging to basal fungal lineages is also continuously increasing. Basal fungal lineages diverged at an early point during the evolution of the fungal lineage, in which, in a simplified four-phylum fungal kingdom, Zygomycota and Chytridiomycota belong to the basal fungi, distinguishing them from Ascomycota and Basidiomycota. Currently there are no known human infections caused by fungi in Chytridiomycota; only Zygomycotan fungi are known to infect humans. Hence, infections caused by zygomycetes have been called zygomycosis, and the term “zygomycosis” is often used as a synonym for “mucormycosis.” In the four-phylum fungal kingdom system, Zygomycota is classified mainly based on morphology, including the ability to form coenocytic (aseptated) hyphae and zygospores (sexual spores). In the Zygomycota, there are 10 known orders, two of which, the Mucorales and Entomophthorales, contain species that can infect humans, and the infection has historically been known as zygomycosis. However, recent multilocus sequence typing analyses (the fungal tree of life [AFTOL] project) revealed that the Zygomycota forms not a monophyletic clade but instead a polyphyletic clade, whereas Ascomycota and Basidiomycota are monophyletic. Thus, the term “zygomycosis” needed to be further specified, resulting in the terms “mucormycosis” and “entomophthoramycosis.” This review covers these two different types of fungal infections. PMID:25377138

Identifying airborne fungi in Seoul, Korea using metagenomics.

PubMed

Oh, Seung-Yoon; Fong, Jonathan J; Park, Myung Soo; Chang, Limseok; Lim, Young Woon

2014-06-01

Fungal spores are widespread and common in the atmosphere. In this study, we use a metagenomic approach to study the fungal diversity in six total air samples collected from April to May 2012 in Seoul, Korea. This springtime period is important in Korea because of the peak in fungal spore concentration and Asian dust storms, although the year of this study (2012) was unique in that were no major Asian dust events. Clustering sequences for operational taxonomic unit (OTU) identification recovered 1,266 unique OTUs in the combined dataset, with between 223᾿96 OTUs present in individual samples. OTUs from three fungal phyla were identified. For Ascomycota, Davidiella (anamorph: Cladosporium) was the most common genus in all samples, often accounting for more than 50% of all sequences in a sample. Other common Ascomycota genera identified were Alternaria, Didymella, Khuskia, Geosmitha, Penicillium, and Aspergillus. While several Basidiomycota genera were observed, Chytridiomycota OTUs were only present in one sample. Consistency was observed within sampling days, but there was a large shift in species composition from Ascomycota dominant to Basidiomycota dominant in the middle of the sampling period. This marked change may have been caused by meteorological events. A potential set of 40 allergy-inducing genera were identified, accounting for a large proportion of the diversity present (22.5᾿7.2%). Our study identifies high fungal diversity and potentially high levels of fungal allergens in springtime air of Korea, and provides a good baseline for future comparisons with Asian dust storms.

Biodegradation of phenolic compounds by Basidiomycota and its phenol oxidases: A review.

PubMed

Martínková, L; Kotik, M; Marková, E; Homolka, L

2016-04-01

The phylum Basidiomycota include organisms with enormous bioremediation potential. A variety of processes were proposed at the lab scale for using these fungi and their phenol oxidases in the degradation of phenolics. Here we present a survey of this topic using literature published mostly over the last 10 years. First, the sources of the enzymes are summarized. The laccase and tyrosinase were mainly from Trametes versicolor and Agaricus bisporus, respectively. Recently, however, new promising wild-type producers of the enzymes have emerged and a number of recombinant strains were also constructed, based mainly on yeasts or Aspergillus strains as hosts. The next part of the study summarizes the enzyme and whole-cell applications for the degradation of phenols, polyphenols, cresols, alkylphenols, naphthols, bisphenols and halogenated (bis)phenols in model mixtures or real wastewaters from the food, paper and coal industries, or municipal and hospital sewage. The enzymes were applied as free (crude or purified) enzymes or as enzymes immobilized in various supports or CLEAs, and optionally recycled or used in continuous mode. Alternatively, growing cultures or harvested mycelia were used instead. The products, which were characterized as quinones and their polymers in some cases, could be eliminated by filtration, flocculation or adsorption onto chitosan. The purity of a treated wastewater was monitored using a sensitive aquatic organism. It is concluded that low-cost sources of these enzymes should be searched for and the benefits of enzymatic, biological and physico-chemical methods could be combined to make the processes fit for industrial use. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Robert; Salamov, Asaf; Otillar, Robert

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes revealsmore » that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.« less

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

PubMed Central

Wu, Guangxi; Zhao, He; Li, Chenhao; Rajapakse, Menaka Priyadarsani; Wong, Wing Cheong; Xu, Jun; Saunders, Charles W.; Reeder, Nancy L.; Reilman, Raymond A.; Scheynius, Annika; Sun, Sheng; Billmyre, Blake Robert; Li, Wenjun; Averette, Anna Floyd; Mieczkowski, Piotr; Heitman, Joseph; Theelen, Bart; Schröder, Markus S.; De Sessions, Paola Florez; Butler, Geraldine; Maurer-Stroh, Sebastian; Boekhout, Teun; Nagarajan, Niranjan; Dawson, Thomas L.

2015-01-01

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin. PMID:26539826

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Endophytic fungi associated with Macrosolen tricolor and its host Camellia oleifera.

PubMed

Sheng-Liang, Zhou; Shu-Zhen, Yan; Zhen-Ying, Wu; Shuang-Lin, Chen

2014-06-01

Endophytic fungi play an important role in terrestrial ecosystem, while little is known about those in hemi-parasitic plants, a group of special plants which absorb nutrients from its hosts by haustoria. The relationship of the endophytes in the two parts of the bipartite systems (hemiparasites together with their hosts) is also poorly understood. Endophytic fungi of a hemi-parasitic plant Macrosolen tricolor, and its host plant Camellia oleifera were investigated and compared in this study. M. tricolor contained rich and diversified endophytic fungi (H' = 2.829), which consisted mainly of ascomycetes, distributed in more than ten orders of four classes (Sordariomycetes, Dothideomycetes, Leotiomycetes and Eurotiomycetes) besides Incertae sedis strains (23.2 % of total). In addition, 2.2 % of isolates were identified to be Basidiomycota, all of which belonged to Agaricomycetes. Obvious differences were observed between the endophytic fungal assembles in the leaves and those in the branches of M. tricolor. The endophytic fungi isolated from C. oleifera distributed in nearly same orders of the four classes of Ascomycota and one class (Agaricomycetes) of Basidiomycota as those from M. tricolor with similar proportion. For both M. tricolor and C. oleifera, Valsa sp. was the dominant endophyte species in the leaves, Torula sp. 1 and Fusarium sp. 1 were the dominant endophytic fungi in the branches. The similarity coefficient of the endophyte assembles in the two host was 64.4 %. Canonical correspondence analysis showed that the endophyte assembles of M. tricolor and C. oleifera were significantly different (p < 0.01).

Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland.

PubMed

Sohlberg, Elina; Bomberg, Malin; Miettinen, Hanna; Nyyssönen, Mari; Salavirta, Heikki; Vikman, Minna; Itävaara, Merja

2015-01-01

The diversity and functional role of fungi, one of the ecologically most important groups of eukaryotic microorganisms, remains largely unknown in deep biosphere environments. In this study we investigated fungal communities in packer-isolated bedrock fractures in Olkiluoto, Finland at depths ranging from 296 to 798 m below surface level. DNA- and cDNA-based high-throughput amplicon sequencing analysis of the fungal internal transcribed spacer (ITS) gene markers was used to examine the total fungal diversity and to identify the active members in deep fracture zones at different depths. Results showed that fungi were present in fracture zones at all depths and fungal diversity was higher than expected. Most of the observed fungal sequences belonged to the phylum Ascomycota. Phyla Basidiomycota and Chytridiomycota were only represented as a minor part of the fungal community. Dominating fungal classes in the deep bedrock aquifers were Sordariomycetes, Eurotiomycetes, and Dothideomycetes from the Ascomycota phylum and classes Microbotryomycetes and Tremellomycetes from the Basidiomycota phylum, which are the most frequently detected fungal taxa reported also from deep sea environments. In addition some fungal sequences represented potentially novel fungal species. Active fungi were detected in most of the fracture zones, which proves that fungi are able to maintain cellular activity in these oligotrophic conditions. Possible roles of fungi and their origin in deep bedrock groundwater can only be speculated in the light of current knowledge but some species may be specifically adapted to deep subsurface environment and may play important roles in the utilization and recycling of nutrients and thus sustaining the deep subsurface microbial community.

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

PubMed

Wu, Guangxi; Zhao, He; Li, Chenhao; Rajapakse, Menaka Priyadarsani; Wong, Wing Cheong; Xu, Jun; Saunders, Charles W; Reeder, Nancy L; Reilman, Raymond A; Scheynius, Annika; Sun, Sheng; Billmyre, Blake Robert; Li, Wenjun; Averette, Anna Floyd; Mieczkowski, Piotr; Heitman, Joseph; Theelen, Bart; Schröder, Markus S; De Sessions, Paola Florez; Butler, Geraldine; Maurer-Stroh, Sebastian; Boekhout, Teun; Nagarajan, Niranjan; Dawson, Thomas L

2015-11-01

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge

NASA Astrophysics Data System (ADS)

Xu, Wei; Gong, Lin-feng; Pang, Ka-Lai; Luo, Zhu-Hua

2018-01-01

Deep-sea hydrothermal sediment is known to support remarkably diverse microbial consortia. In deep sea environments, fungal communities remain less studied despite their known taxonomic and functional diversity. High-throughput sequencing methods have augmented our capacity to assess eukaryotic diversity and their functions in microbial ecology. Here we provide the first description of the fungal community diversity found in deep sea sediments collected at the Southwest Indian Ridge (SWIR) using culture-dependent and high-throughput sequencing approaches. A total of 138 fungal isolates were cultured from seven different sediment samples using various nutrient media, and these isolates were identified to 14 fungal taxa, including 11 Ascomycota taxa (7 genera) and 3 Basidiomycota taxa (2 genera) based on internal transcribed spacers (ITS1, ITS2 and 5.8S) of rDNA. Using illumina HiSeq sequencing, a total of 757,467 fungal ITS2 tags were recovered from the samples and clustered into 723 operational taxonomic units (OTUs) belonging to 79 taxa (Ascomycota and Basidiomycota contributed to 99% of all samples) based on 97% sequence similarity. Results from both approaches suggest that there is a high fungal diversity in the deep-sea sediments collected in the SWIR and fungal communities were shown to be slightly different by location, although all were collected from adjacent sites at the SWIR. This study provides baseline data of the fungal diversity and biogeography, and a glimpse to the microbial ecology associated with the deep-sea sediments of the hydrothermal vent system of the Southwest Indian Ridge.

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

PubMed Central

Zuccaro, Alga; Lahrmann, Urs; Güldener, Ulrich; Langen, Gregor; Pfiffi, Stefanie; Biedenkopf, Dagmar; Wong, Philip; Samans, Birgit; Grimm, Carolin; Basiewicz, Magdalena; Murat, Claude; Martin, Francis; Kogel, Karl-Heinz

2011-01-01

Recent sequencing projects have provided deep insight into fungal lifestyle-associated genomic adaptations. Here we report on the 25 Mb genome of the mutualistic root symbiont Piriformospora indica (Sebacinales, Basidiomycota) and provide a global characterization of fungal transcriptional responses associated with the colonization of living and dead barley roots. Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism and saprotrophism. The tightly controlled expression of the lifestyle-associated gene sets during the onset of the symbiosis, revealed by microarray analysis, argues for a biphasic root colonization strategy of P. indica. This is supported by a cytological study that shows an early biotrophic growth followed by a cell death-associated phase. About 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP), including several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. Similar to effectors found in other filamentous organisms, the occurrence of the DELDs correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome. This is the first in depth genomic study describing a mutualistic symbiont with a biphasic lifestyle. Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in the evolution of mycorrhizal association from decomposer fungi. PMID:22022265

Fungal diversity in major oil-shale mines in China.

PubMed

Jiang, Shaoyan; Wang, Wenxing; Xue, Xiangxin; Cao, Chengyou; Zhang, Ying

2016-03-01

As an insufficiently utilized energy resource, oil shale is conducive to the formation of characteristic microbial communities due to its special geological origins. However, little is known about fungal diversity in oil shale. Polymerase chain reaction cloning was used to construct the fungal ribosomal deoxyribonucleic acid internal transcribed spacer (rDNA ITS) clone libraries of Huadian Mine in Jilin Province, Maoming Mine in Guangdong Province, and Fushun Mine in Liaoning Province. Pure culture and molecular identification were applied for the isolation of cultivable fungi in fresh oil shale of each mine. Results of clone libraries indicated that each mine had over 50% Ascomycota (58.4%-98.9%) and 1.1%-13.5% unidentified fungi. Fushun Mine and Huadian Mine had 5.9% and 28.1% Basidiomycota, respectively. Huadian Mine showed the highest fungal diversity, followed by Fushun Mine and Maoming Mine. Jaccard indexes showed that the similarities between any two of three fungal communities at the genus level were very low, indicating that fungi in each mine developed independently during the long geological adaptation and formed a community composition fitting the environment. In the fresh oil-shale samples of the three mines, cultivable fungal phyla were consistent with the results of clone libraries. Fifteen genera and several unidentified fungi were identified as Ascomycota and Basidiomycota using pure culture. Penicillium was the only genus found in all three mines. These findings contributed to gaining a clear understanding of current fungal resources in major oil-shale mines in China and provided useful information for relevant studies on isolation of indigenous fungi carrying functional genes from oil shale. Copyright © 2015. Published by Elsevier B.V.

High concentration of basidiolichens in a single family of agaricoid mushrooms (Basidiomycota: Agaricales: Hygrophoraceae).

PubMed

Lawrey, James D; Lücking, Robert; Sipman, Harrie J M; Chaves, José L; Redhead, Scott A; Bungartz, Frank; Sikaroodi, Masoumeh; Gillevet, Patrick M

2009-10-01

The Agaricales is the largest and most diverse order of mushroom-forming Basidiomycota, with over 100 natural groups recognized in recent Fungal Tree of Life studies. Most agarics are either saprotrophic or ectomycorrhizal fungi, but the family Hygrophoraceae is in part characterized by a unique and remarkable diversity of lichenized forms. The most familiar of these is the chlorolichen genus Lichenomphalia, whose phylogenetic position in the Agaricales has been established. Recent limited evidence suggested that Hygrophoraceae also contains cyanolichens in the genus Dictyonema, which indicates a remarkable concentration and diversity of lichen-formers in a single family of agarics. To demonstrate the relationships of lichen-formers to other fungi in the family, we assembled ribosomal sequences from 52 species representing recognized groups within the Hygrophoraceae, among them new sequences representing Acantholichen and most species and forms of Dictyonema. The molecular data were evaluated using parsimony, likelihood, Bayesian, and distance analyses, including coding of ambiguous regions by means of INAASE and ARC, all of which indicate that Dictyonema and Acantholichen form a monophyletic clade derived from the primarily bryophilous genus Arrhenia and sister to the enigmatic Athelia pyriformis, a species unrelated to the Atheliales for which we are proposing a new genus name Eonema. The chlorolichen genus Lichenomphalia may be polyphyletic. Fungi in the Dictyonema-Acantholichen clade are typically tropical, entirely lichenized, and associate with cyanobacterial photobionts. Our data indicate a transition from agaricoid-omphalinoid basidiomes observed in Arrhenia to stereoid-corticioid forms in Dictyonema, and also support a previous suggestion of a connection between loss of clamp connections and lichenization. The diverse basidiome and thallus morphologies and nutritional ecologies of these fungi indicate a remarkable evolutionary flexibility that appears to have developed in part as a consequence of symbiosis.

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach.

PubMed

Borges, Francis M; de Paula, Thaís O; Sarmiento, Marjorie R A; de Oliveira, Maycon G; Pereira, Maria L M; Toledo, Isabela V; Nascimento, Thiago C; Ferreira-Machado, Alessandra B; Silva, Vânia L; Diniz, Cláudio G

2018-06-01

Fungi have a complex role in the intestinal tract, influencing health and disease, with dysbiosis contributing to obesity. Our objectives were to investigate fungal diversity in human gut microbiota among eutrophic, overweight, and obese. Epidemiological and nutritional information were collected from adult individuals, as well as stool samples processed for selective fungi isolation and identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (yeasts) or microculture (filamentous fungi). Further 18S rDNA sequencing was performed to confirm identification. The mean count of fungi was 241 CFU/g of feces. Differences in the population level of the filamentous fungi were observed within eutrophic and obese groups. Overall, 34 genera were identified. The predominant phylum was Ascomycota with 20 different genera, followed by Basidiomycota and Zygomycota. As for Ascomycota, the most prevalent species were Paecilomyces sp., Penicillium sp., Candida sp., Aspergillus sp., Fonsecaea sp., and Geotrichum sp. (76.39, 65.28, 59.72, 58.33, 12.50, and 9.72%, respectively). As for Basidiomycota, Trichosporon sp. and Rhodotorula sp. were the most prevalent (30.56 and 15.28%, respectively), and for Zygomycota, Rhizopus sp. and Mucor sp. were the most numerous (15.28 and 9.72%, respectively). As expected there is a mycobiota shift towards obesity, with slightly higher diversity associated to eutrophic individuals. This mycobiota shift seems also to be related to the nutritional behavior of the individuals, as observed that the macronutrients intake may be positively related to the different fungi occurrences. Other studies are needed to better understand relationships between mycobiota and obesity, which could be used in future obesity treatments.

Advances in the phylogenesis of Agaricales and its higher ranks and strategies for establishing phylogenetic hypotheses§

PubMed Central

Zhao, Rui-lin; Desjardin, Dennis E.; Soytong, Kasem; Hyde, Kevin D.

2008-01-01

We present an overview of previous research results on the molecular phylogenetic analyses in Agaricales and its higher ranks (Agaricomycetes/Agaricomycotina/Basidiomycota) along with the most recent treatments of taxonomic systems in these taxa. Establishing phylogenetic hypotheses using DNA sequences, from which an understanding of the natural evolutionary relationships amongst clades may be derived, requires a robust dataset. It has been recognized that single-gene phylogenies may not truly represent organismal phylogenies, but the concordant phylogenetic genealogies from multiple-gene datasets can resolve this problem. The genes commonly used in mushroom phylogenetic research are summarized. PMID:18837104

Fungal endophyte diversity in Sarracenia.

PubMed

Glenn, Anthony; Bodri, Michael S

2012-01-01

Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers.

Identification of fungal ene-reductase activity by means of a functional screening.

PubMed

Romagnolo, Alice; Spina, Federica; Brenna, Elisabetta; Crotti, Michele; Parmeggiani, Fabio; Varese, Giovanna Cristina

2015-06-01

Bioeconomy stresses the need of green processes promoting the development of new methods for biocatalyzed alkene reductions. A functional screening of 28 fungi belonging to Ascomycota, Basidiomycota, and Zygomycota isolated from different habitats was performed to analyze their capability to reduce C=C double bonds towards three substrates (cyclohexenone, α-methylnitrostyrene, and α-methylcinnamaldehyde) with different electron-withdrawing groups, i.e., ketone, nitro, and aldehyde, respectively. Almost all the fungi showed this reducing activity. Noteworthy Gliomastix masseei, Mucor circinelloides, and Mucor plumbeus resulted versatile and effective, being able to reduce all the model substrates quickly and with high yields. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Four New Species of Amanita in Inje County, Korea

PubMed Central

Cho, Hae Jin; Park, Myung Soo; Lee, Hyun; Oh, Seung-Yoon; Jang, Yeongseon; Fong, Jonathan J.

2015-01-01

Amanita (Agaricales, Basidiomycota) is one of the most well-known genera composed of poisonous mushrooms. This genus of almost 500 species is distributed worldwide. Approximately 240 macrofungi were collected through an ongoing survey of indigenous fungi of Mt. Jeombong in Inje County, Korea in 2014. Among these specimens, 25 were identified as members of Amanita using macroscopic features. Specimens were identified to the species level by microscopic features and molecular sequence analyses of the internal transcribed spacer and large subunit of nuclear ribosomal RNA. We molecularly identified 13 Amanita species, with seven species matching previously recorded species, four species (A. caesareoides, A. griseoturcosa, A. imazekii, and A. sepiacea) new to Korea, and two unknown species. PMID:26839500

Tinea capitis-like infection caused by Rhodotorula mucilaginosa in a shelter for African Refugee Children in Northern Israel.

PubMed

Peretz, Avi; Nitzan, Orna; Freidus, Victoria; Kassem, Riad

2018-03-01

Rhodotorula is a genus of unicellular pigmented yeasts, part of the division Basidiomycota. In this article, we report three cases of refugee children in a day care shelter in northern Israel who were clinically diagnosed and treated empirically as with ringworm infection but with clean and exclusive growth of Rhodotorula mucilaginosa in repeated cultures of several skin samples. Skin infections caused by this yeast are rare and there are few reports in the literature, mainly in patients who are immunocompromised. Here we report an infectious process of the scalp in immunocompetent children, caused by Rhodotorula mucilaginosa mimicking tinea capitis. Copyright © 2017 Elsevier B.V. All rights reserved.

Marine fungi from Mira river salt marsh in Portugal.

PubMed

Barata, Margarida

2006-09-01

The occurrence of fungi in the Mira salt marsh, Portugal was investigated for 12 months. Baits of Spartina maritima stems were exposed to permanent or temporary submersion at the upper and lower limits of the intertidal zone. The baits were observed for fruit bodies and spores directly and after incubation in moist chambers. Twenty six marine species were identified (17 Ascomycota, two Basidiomycota and seven mitosporic fungi). Twenty four are new records for Portugal. Nia globospora Barata and Basílio was published as a new species. Species were characterized with respect to frequency of occurrence, colonization capability and substrate succession. The diversity and similarity indexes of the fungi under different conditions were determined.

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods

PubMed Central

Pudasaini, Sarita; Wilson, John; Ji, Mukan; van Dorst, Josie; Snape, Ian; Palmer, Anne S.; Burns, Brendan P.; Ferrari, Belinda C.

2017-01-01

Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation. PMID:28439263

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau

PubMed Central

Dang, Peng; Yu, Xuan; Le, Hien; Liu, Jinliang; Shen, Zhen

2017-01-01

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau. PMID:29049349

PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing

PubMed Central

Barbi, Florian; Bragalini, Claudia; Vallon, Laurent; Prudent, Elsa; Dubost, Audrey; Fraissinet-Tachet, Laurence; Marmeisse, Roland; Luis, Patricia

2014-01-01

Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities. PMID:25545363

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau.

PubMed

Dang, Peng; Yu, Xuan; Le, Hien; Liu, Jinliang; Shen, Zhen; Zhao, Zhong

2017-01-01

The effects of Chinese pine (Pinus tabuliformis) on soil variables after afforestation have been established, but microbial community changes still need to be explored. Using high-throughput sequencing technology, we analyzed bacterial and fungal community composition and diversity in soils from three stands of different-aged, designated 12-year-old (PF1), 29-year-old (PF2), and 53-year-old (PF3), on a Chinese pine plantation and from a natural secondary forest (NSF) stand that was almost 80 years old. Abandoned farmland (BL) was also analyzed. Shannon index values of both bacterial and fungal community in PF1 were greater than those in PF2, PF3 and NSF. Proteobacteria had the lowest abundance in BL, and the abundance increased with stand age. The abundance of Actinobacteria was greater in BL and PF1 soils than those in other sites. Among fungal communities, the dominant taxa were Ascomycota in BL and PF1 and Basidiomycota in PF2, PF3 and NSF, which reflected the successional patterns of fungal communities during the development of Chinese pine plantations. Therefore, the diversity and dominant taxa of soil microbial community in stands 12 and 29 years of age appear to have undergone significant changes; afterward, the soil microbial community achieved a relatively stable state. Furthermore, the abundances of the most dominant bacterial and fungal communities correlated significantly with organic C, total N, C:N, available N, and available P, indicating the dependence of these microbes on soil nutrients. Overall, our findings suggest that the large changes in the soil microbial community structure of Chinese pine plantation forests may be attributed to the phyla present (e.g., Proteobacteria, Actinobacteria, Ascomycota and Basidiomycota) which were affected by soil carbon and nutrients in the Loess Plateau.

Fungal Endophyte Diversity in Sarracenia

PubMed Central

Glenn, Anthony; Bodri, Michael S.

2012-01-01

Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers. PMID:22427921

Phylogenetic and metabolic diversity of Tunisian forest wood-degrading fungi: a wealth of novelties and opportunities for biotechnology.

PubMed

Daâssi, Dalel; Zouari-Mechichi, Héla; Belbahri, Lassaad; Barriuso, Jorge; Martínez, María Jesús; Nasri, Moncef; Mechichi, Tahar

2016-06-01

In this study, 51 fungal strains were isolated from decaying wood samples collected from forests located in the Northwest of Tunisia in the vicinity of Bousalem, Ain Draham and Kef. Phylogenetic analysis based on the sequences of the internal transcribed spacers of the ribosomal DNA showed a high diversity among the 51 fungal isolates collection. Representatives of 25 genera and 29 species were identified, most of which were members of one of the following phyla (Ascomycota, Basidiomycota and Zygomycota). In addition to the phylogenetic diversity, a high diversity of secreted enzyme profiles was also detected among the fungal isolates. All fungal strains produced at least one of the following enzymes: laccase, cellulase, protease and/or lipase.

Restingomyces, a new sequestrate genus from the Brazilian Atlantic rainforest that is phylogenetically related to early-diverging taxa in Trappeaceae (Phallales).

PubMed

Sulzbacher, Marcelo A; Grebenc, Tine; Cabral, Tiara S; Giachini, Admir J; Goto, Bruno T; Smith, Matthew E; Baseia, Iuri G

2016-09-01

Restingomyces reticulatus gen. et sp. nov. is a recently discovered false truffle species from Atlantic "restinga" rainforest in northeastern Brazil. Molecular and morphological characters separate this new sequestrate species from other described taxa in the order Phallales (Phallomycetidae, Basidiomycota). In our phylogenetic analysis based on nuc 28S rDNA and atp6, R. reticulatus forms a sister clade to Trappea darkeri and Phallobata alba, with the three taxa forming the earliest diverging lineage within Phallales. Morphological and molecular data warrant the recognition of the new genus and species, described here, and we also amend the taxonomic description for the family Trappeaceae. © 2016 by The Mycological Society of America.

High diversity of fungi in air particulate matter.

PubMed

Fröhlich-Nowoisky, Janine; Pickersgill, Daniel A; Després, Viviane R; Pöschl, Ulrich

2009-08-04

Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 microm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.

Fungi on the Skin: Dermatophytes and Malassezia

PubMed Central

White, Theodore C.; Findley, Keisha; Dawson, Thomas L.; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A.; Xu, Jun; Saunders, Charles W.

2014-01-01

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. PMID:25085959

Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

PubMed

Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

2011-04-01

Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.

Biogeography in the air: fungal diversity over land and oceans

NASA Astrophysics Data System (ADS)

Fröhlich-Nowoisky, J.; Burrows, S. M.; Xie, Z.; Engling, G.; Solomon, P. A.; Fraser, M. P.; Mayol-Bracero, O. L.; Artaxo, P.; Begerow, D.; Conrad, R.; Andreae, M. O.; Després, V. R.; Pöschl, U.

2012-03-01

Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we find that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the "blue ocean" and "green ocean" regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the understanding of global changes in biodiversity.

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

PubMed Central

2008-01-01

Background The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera. Results Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusion Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework. PMID:18282272

Fungi on the skin: dermatophytes and Malassezia.

PubMed

White, Theodore C; Findley, Keisha; Dawson, Thomas L; Scheynius, Annika; Boekhout, Teun; Cuomo, Christina A; Xu, Jun; Saunders, Charles W

2014-08-01

Several human skin diseases and disorders are associated with two groups of fungi, the dermatophytes and Malassezia. Although these skin-related problems are not generally life threatening, they are among the most common diseases and disorders of mankind. These fungi are phylogenetically divergent, with the dermatophytes within the Ascomycota and Malassezia within Basidiomycota. Genome analysis indicates that the adaptations to the skin environment are different in these two groups of fungi. Malassezia are dependent on host lipids and secrete lipases and phospholipases that likely release host fatty acids. The dermatophytes encode multiple enzymes with potential roles in modulating host interactions: polyketide synthases, nonribosomal peptide synthetases, LysM, proteases, kinases, and pseudokinases. These two fungal groups have maximized their interactions with the host using two very different mechanisms. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

PubMed Central

Ge, Zai-Wei; Jacobs, Adriaana; Vellinga, Else C.; Sysouphanthong, Phongeun; van der Walt, Retha; Lavorato, Carmine; An, Yi-Feng; Yang, Zhu L.

2018-01-01

Abstract Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-α (tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum. PMID:29681738

Biogeography in the air: fungal diversity over land and oceans

NASA Astrophysics Data System (ADS)

Fröhlich-Nowoisky, J.; Burrows, S. M.; Xie, Z.; Engling, G.; Solomon, P. A.; Fraser, M. P.; Mayol-Bracero, O. L.; Artaxo, P.; Begerow, D.; Conrad, R.; Andreae, M. O.; Després, V. R.; Pöschl, U.

2011-07-01

Biogenic aerosols are relevant for the Earth system, climate, and public health on local, regional, and global scales. Up to now, however, little is known about the diversity and biogeography of airborne microorganisms. We present the first DNA-based analysis of airborne fungi on global scales, showing pronounced geographic patterns and boundaries. In particular we found that the ratio of species richness between Basidiomycota and Ascomycota is much higher in continental air than in marine air. This may be an important difference between the "blue ocean" and "green ocean" regimes in the formation of clouds and precipitation, for which fungal spores can act as nuclei. Our findings also suggest that air flow patterns and the global atmospheric circulation are important for the evolution of microbial ecology and for the understanding of global changes in biodiversity.

Phylogeny and comparative genome analysis of a Basidiomycete fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor

2011-03-14

Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein familiesmore » that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.« less

Eighteen new oleaginous yeast species.

PubMed

Garay, Luis A; Sitepu, Irnayuli R; Cajka, Tomas; Chandra, Idelia; Shi, Sandy; Lin, Ting; German, J Bruce; Fiehn, Oliver; Boundy-Mills, Kyria L

2016-07-01

Of 1600 known species of yeasts, about 70 are known to be oleaginous, defined as being able to accumulate over 20 % intracellular lipids. These yeasts have value for fundamental and applied research. A survey of yeasts from the Phaff Yeast Culture Collection, University of California Davis was performed to identify additional oleaginous species within the Basidiomycota phylum. Fifty-nine strains belonging to 34 species were grown in lipid inducing media, and total cell mass, lipid yield and triacylglycerol profiles were determined. Thirty-two species accumulated at least 20 % lipid and 25 species accumulated over 40 % lipid by dry weight. Eighteen of these species were not previously reported to be oleaginous. Triacylglycerol profiles were suitable for biodiesel production. These results greatly expand the number of known oleaginous yeast species, and reveal the wealth of natural diversity of triacylglycerol profiles within wild-type oleaginous Basidiomycetes.

Biofouling of reverse osmosis membranes: effects of cleaning on biofilm microbial communities, membrane performance, and adherence of extracellular polymeric substances.

PubMed

Al Ashhab, Ashraf; Sweity, Amer; Bayramoglu, Bihter; Herzberg, Moshe; Gillor, Osnat

2017-05-01

Laboratory-scale reverse osmosis (RO) flat-sheet systems were used with two parallel flow cells, one treated with cleaning agents and a control (ie undisturbed). The cleaning efforts increased the affinity of extracellular polymeric substances (EPS) to the RO membrane and altered the biofilm surface structure. Analysis of the membrane biofilm community composition revealed the dominance of Proteobacteria. However, within the phylum Proteobacteria, γ-Proteobacteria dominated the cleaned membrane biofilm, while β-Proteobacteria dominated the control biofilm. The composition of the fungal phyla was also altered by cleaning, with enhancement of Ascomycota and suppression of Basidiomycota. The results suggest that repeated cleaning cycles select for microbial groups that strongly attach to the RO membrane surface by producing rigid and adhesive EPS that hampers membrane performance.

Spores of most common airborne fungi reveal no ice nucleation activity

NASA Astrophysics Data System (ADS)

Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

2013-06-01

Fungal spores are ubiquitous biological aerosols, which are considered to show ice nucleation (IN) activity. In this study the respective IN activity was tested in oil emulsion in the immersion freezing mode. The focus was laid on species of economical, ecological or sanitary significance. For the first time, not only common moulds, but also edible mushrooms (Basidiomycota, Agaricomycetes) were investigated, as they contribute massively to the total amount of fungal spores in the atmosphere. Only Fusarium avenaceum showed freezing events at low subzero-temperatures, while the other investigated fungal spores showed no significant IN activity. Furthermore, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during cultivation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

The complete mitochondrial genome of the medicinal fungus Ganoderma applanatum (Polyporales, Basidiomycota).

PubMed

Wang, Xin-Cun; Shao, Junjie; Liu, Chang

2016-07-01

We have determined the complete nucleotide sequence of the mitochondrial genome of the medicinal fungus Ganoderma applanatum (Pers.) Pat. using the next-generation sequencing technology. The circular molecule is 119,803 bp long with a GC content of 26.66%. Gene prediction revealed genes encoding 15 conserved proteins, 25 tRNAs, the large and small ribosomal RNAs, all genes are located on the same strand except trnW-CCA. Compared with previously sequenced genomes of G. lucidum, G. meredithiae and G. sinense, the order of the protein and rRNA genes is highly conserved; however, the types of tRNA genes are slightly different. The mitochondrial genome of G. applanatum will contribute to the understanding of the phylogeny and evolution of Ganoderma and Ganodermataceae, the group containing many species with high medicinal values.

A new species and a new record of Laccaria (Fungi, Basidiomycota) found in a relict forest of the endangered Fagus grandifolia var. mexicana

PubMed Central

Ramos, Antero; Bandala, Victor M.; Montoya, Leticia

2017-01-01

Abstract Two species of Laccaria discovered in relicts of Fagus grandifolia var. mexicana forests in eastern Mexico are described based on the macro- and micromorphological features, and their identity supported by molecular analysis of the internal transcribed spacer (ITS) and large subunit (LSU) of the ribosomal RNA gene. The phylogeny obtained here showed that one of the Mexican species is nested in an exclusive clade which in combination with its striking morphological features, infers that it represents a new species, while the other species is placed as a member in the Laccaria trichodermophora clade. This is the first report in Mexico of Laccaria with Fagus grandifolia var. mexicana trees, with which the reported species may form ectomycorrhizal association. Descriptions are accompanied with illustrations of macro- and micromorphological characters and a discussion of related taxa are presented. PMID:29559819

Comparative Genome Analysis of Basidiomycete Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Robert; Salamov, Asaf; Morin, Emmanuelle

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypesmore » found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.« less

The Genus Wallemia-From Contamination of Food to Health Threat.

PubMed

Zajc, Janja; Gunde-Cimerman, Nina

2018-05-21

The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar salterns, salt crystals, indoor and outdoor air, and agriculture aerosols. Recently, eight species were recognized for the genus Wallemia , among which four are commonly associated with foods: W. sebi , W. mellicola , W. muriae and W. ichthyophaga . To date, only strains of W. sebi , W. mellicola and W. muriae have been reported to be related to human health problems, as either allergological conditions (e.g., farmer’s lung disease) or rare subcutaneous/cutaneous infections. Therefore, this allergological and infective potential, together with the toxins that the majority of Wallemia spp. produce even under saline conditions, defines these fungi as filamentous food-borne pathogenic fungi.

Detection of Fungi from an Indoor Environment using Loop-mediated Isothermal Amplification (LAMP) Method.

PubMed

Nakayama, Takako; Yamazaki, Takashi; Yo, Ayaka; Tone, Kazuya; Mahdi Alshahni, Mohamed; Fujisaki, Ryuichi; Makimura, Koichi

2017-01-01

　Loop-mediated isothermal amplification (LAMP) is a useful DNA detection method with high specificity and sensitivity. The LAMP reaction is carried out within a short time at a constant temperature without the need for thermal cycling. We developed a LAMP primer set for detecting a wide range of fungi by aligning the sequences of the large subunit ribosomal RNA gene of Candida albicans (Ascomycota), Cryptococcus neoformans (Basidiomycota), and Mucor racemosus (Mucorales). The threshold of C. albicans rDNA as template with our LAMP primer set was in the range of 10-100 copies per a reaction. In this study, we evaluated the correlation between colony forming units (CFU) and LAMP detection rate using the LAMP method for environmental fungi. The LAMP method should be a useful means of detecting fungi in indoor environments, disaster areas, or even in confined manned spacecraft to prevent allergies or infections caused by fungi.

Anticancer effect of triterpenes from Ganoderma lucidum in human prostate cancer cells.

PubMed

Qu, Lijun; Li, Sumei; Zhuo, Yumin; Chen, Jianfan; Qin, Xiaoping; Guo, Guoqing

2017-12-01

Ganoderma lucidum , within the Polyporaceae family of Basidiomycota, is a popular traditional remedy medicine used in Asia to promote health and longevity. Compounds extracted from G. lucidum have revealed anticancer, antioxidant and liver protective effects. G. lucidum has been associated with prostate cancer cells. G. lucidum extracts contain numerous bioactive components; however, the exact functional monomer is unknown and the role of triterpenes from G. lucidum (GLT) in prostate cancer remain obscure. The present study investigated the effects of GLT on cell viability, migration, invasion and apoptosis in DU-145 human prostate cancer cells. The results demonstrated that a high dose (2 mg/ml) of GLT inhibits cell viability in a dose- and time-dependent manner by the regulation of matrix metalloproteases. Furthermore, GLT induced apoptosis of DU-145 cells. In general, GLT exerts its effect on cancer cells via numerous mechanisms and may have potential therapeutic use for the prevention and treatment of cancer.

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes

PubMed Central

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-01

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes. PMID:25583346

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes.

PubMed

Ma, Yantian; Zhang, He; Du, Ye; Tian, Tian; Xiang, Ting; Liu, Xiande; Wu, Fasi; An, Lizhe; Wang, Wanfu; Gu, Ji-Dong; Feng, Huyuan

2015-01-13

In this study, we compared the microbial communities colonising ancient cave wall paintings of the Mogao Grottoes exhibiting signs of biodeterioration. Ten samples were collected from five different caves built during different time periods and analysed using culture-independent and culture-dependent methods. The clone library results revealed high microbial diversity, including the bacterial groups Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Chloroflexi and the fungal groups Euascomycetes, Dothideomycetes, Eurotiomycetes, Sordariomycetes, Saccharomycetes, Plectomycetes, Pezizomycetes, Zygomycota, and Basidiomycota. The bacterial community structures differed among the samples, with no consistent temporal or spatial trends. However, the fungal community diversity index correlated with the building time of the caves independent of environmental factors (e.g., temperature or relative humidity). The enrichment cultures revealed that many culturable strains were highly resistant to various stresses and thus may be responsible for the damage to cave paintings in the Mogao Grottoes.

Anti-inflammatory properties of edible mushrooms: A review.

PubMed

Muszyńska, Bożena; Grzywacz-Kisielewska, Agata; Kała, Katarzyna; Gdula-Argasińska, Joanna

2018-03-15

Mushrooms have been used extensively, owing to their nutritional and medicinal value, for thousands of years. Modern research confirms the therapeutic effect of traditionally used species. Inflammation is a natural response of the immune system to damaging factors, e.g. physical, chemical and pathogenic. Deficiencies of antioxidants, vitamins, and microelements, as well as physiological processes, such as aging, can affect the body's ability to resolve inflammation. Mushrooms are rich in anti-inflammatory components, such as polysaccharides, phenolic and indolic compounds, mycosteroids, fatty acids, carotenoids, vitamins, and biometals. Metabolites from mushrooms of the Basidiomycota taxon possess antioxidant, anticancer, and most significantly, anti-inflammatory properties. Recent reports indicate that edible mushroom extracts exhibit favourable therapeutic and health-promoting benefits, particularly in relation to diseases associated with inflammation. In all certainty, edible mushrooms can be referred to as a "superfood" and are recommended as a valuable constituent of the daily diet. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cryptococcus species (Tremellales) from glacial biomes in the southern (Patagonia) and northern (Svalbard) hemispheres.

PubMed

de Garcia, Virginia; Zalar, Polona; Brizzio, Silvia; Gunde-Cimerman, Nina; van Broock, María

2012-11-01

Cryptococcus species (Basidiomycota) were isolated as the predominant yeast from glacial biomes of both Patagonia (Argentina) and the Svalbard archipelago (Norway). For a selected group of Cryptococcus belonging to Tremellales, assimilative profile, production of extracellular hydrolytic enzymes and ribosomal DNA internal transcribed spacer and large subunit (D1/D2) sequences were analysed. Cryptococcus victoriae, which was originally described from Antarctica, was the most frequently found species at both locations. High variability within the species was observed and described at the genotypic and phenotypic levels, two newly described species were found in both Patagonia and Svalbard: Cryptococcus fonsecae and Cryptococcus psychrotolerans. Two other new species were found only in Patagonia: Cryptococcus frias and Cryptococcus tronadorensis. Three additional new taxa were found, but they are not named as they were only represented by single isolates. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Cryptococcus neoformans and Cryptococcus gattii, the Etiologic Agents of Cryptococcosis

PubMed Central

Kwon-Chung, Kyung J.; Fraser, James A.; Doering, Tamara L.; Wang, Zhou; Janbon, Guilhem; Idnurm, Alexander; Bahn, Yong-Sun

2014-01-01

Cryptococcus neoformans and Cryptococcus gattii are the two etiologic agents of cryptococcosis. They belong to the phylum Basidiomycota and can be readily distinguished from other pathogenic yeasts such as Candida by the presence of a polysaccharide capsule, formation of melanin, and urease activity, which all function as virulence determinants. Infection proceeds via inhalation and subsequent dissemination to the central nervous system to cause meningoencephalitis. The most common risk for cryptococcosis caused by C. neoformans is AIDS, whereas infections caused by C. gattii are more often reported in immunocompetent patients with undefined risk than in the immunocompromised. There have been many chapters, reviews, and books written on C. neoformans. The topics we focus on in this article include species description, pathogenesis, life cycle, capsule, and stress response, which serve to highlight the specializations in virulence that have occurred in this unique encapsulated melanin-forming yeast that causes global deaths estimated at more than 600,000 annually. PMID:24985132

Diversity and biochemical features of culturable fungi from the coastal waters of Southern China

PubMed Central

2014-01-01

Fungi play a major role in various biogeochemical cycles of terrestrial and marine ecosystems. However, fungi in marine environments remain to be one of the most under-studied microbial groups. This study investigates the diversity of planktonic fungi from the coastal habitat off Pearl River Delta (China) using culture-dependent approach. A total of 22 fungi and 9 yeast isolates were recovered from 30 seawater and 2 sediment samples. Microscopic and ITS rRNA gene sequence analyses revealed that most of the fungi belonged to the phylum Ascomycota and Basidiomycota with a very small percentage (3%) of the subphylum Mucoromycotina of the Phylum Zygomycota. Most of these fungal isolates exhibited considerable production of extracellular enzymes, cellulase, lipase and laccase. Fungal isolates of two genera Mucor and Aspergillus sp. demonstrated pelletization capability over a wide range of pH, suggesting them as potential agents towards algae harvesting and wastewater treatment. PMID:25401065

Application of micro-computed tomography to microstructure studies of the medicinal fungus Hericium coralloides.

PubMed

Pallua, Johannes D; Kuhn, Volker; Pallua, Anton F; Pfaller, Kristian; Pallua, Anton K; Recheis, Wolfgang; Pöder, Reinhold

2015-01-01

The potential of 3-D nondestructive imaging techniques such as micro-computed tomography (micro-CT) was evaluated to study morphological patterns of the potential medicinal fungus Hericium coralloides (Basidiomycota). Micro-CT results were correlated with histological information gained from scanning electron microscopy (SEM) and light microscopy (LM). It is demonstrated that the combination of these imaging methods results in a more distinct picture of the morphology of the edible and potentially medicinal Hericium coralloides basidiomata. In addition we have created 3-D reconstructions and visualizations based on micro-CT imagery from a randomly selected part of the upper region of a fresh H. coralloides basidioma: Analyses for the first time allowed an approximation of the evolutionary effectiveness of this bizarrely formed basidioma type in terms of the investment of tissue biomass and its reproductive output (production of basidiospores). © 2015 by The Mycological Society of America.

Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand.

PubMed

Somboonna, Naraporn; Assawamakin, Anunchai; Wilantho, Alisa; Tangphatsornruang, Sithichoke; Tongsima, Sissades

2012-01-01

Tha Wang and Tham Phang coasts, though situated at similar oceanographic positions on Sichang island, Chonburi province, Thailand, are different in bay geography and amount of municipal disturbances. These affect the marine ecosystems. The study used metagenomics combined with 16S and 18S rDNA pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm. Following the open bay geography and minimal municipal sewages, Tham Phang coast showed the cleaner water properties, described by color, salinity, pH, conductivity and percent dissolved oxygen. The 16S and 18S rDNA metagenomic profiles for Tha Wang and Tham Phang coasts revealed many differences, highlighting by low Lennon and Yue & Clayton theta similarity indices (66.03-73.03% for 16S rDNA profiles, 2.85-25.38% for 18S rDNA profiles). For 16S rDNA, the percent compositions of species belonging to Proteobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, Gammatimonadetes, Tenericutes, Acidobacteria, Spirochaetes, Chlamydiae, Euryarchaeota, Nitrospirae, Planctomycetes, Thermotogae and Aquificae were higher or distinctly present in Tha Wang. In Tham Phang, except Actinobacteria, the fewer number of prokaryotic species existed. For 18S rDNA, fungi represented 74.745% of the species in Tha Wang, whereas only 6.728% in Tham Phang. Basidiomycota (71.157%) and Ascomycota (3.060%) were the major phyla in Tha Wang. Indeed, Tha Wang-to-Tham Phang percent composition ratios for fungi Basidiomycota and Chytridiomycota were 1264.701 and 25.422, respectively. In Tham Phang, Brachiopoda (lamp shells) and Mollusca (snails) accounted for 80.380% of the 18S rDNA species detected, and their proportions were approximately tenfold greater than those in Tha Wang. Overall, coastal Tham Phang comprised abundant animal species. Tha Wang contained numerous archaea, bacteria and fungi, many of which could synthesize useful biotechnology gas and enzymes that could also function in high-saline and high-temperature conditions. Tham Phang contained less abundant archaea, bacteria and fungi, and the majority of the extracted metagenomes belonged to animal kingdom. Many microorganisms in Tham Phang were essential for nutrient-recycling and pharmaceuticals, for instances, Streptomyces, Pennicilium and Saccharomyces. Together, the study provided metagenomic profiles of free-living prokaryotes and eukaryotes in coastal areas of Sichang island.

Ice Nucleation of Fungal Spores from the Classes Agaricomycetes, Ustilaginomycetes, and Eurotiomycetes, and the effect on the Atmospheric Transport of these Spores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haga, D. I.; Burrows, Susannah M.; Iannone, R.

2014-08-26

Ice nucleation on fungal spores may affect the frequency and properties of ice and mixed-phase clouds. We studied the ice nucleation properties of 12 different species of fungal spores chosen from three classes: Agaricomycetes, Ustilagomycetes, and Eurotiomycetes. Agaricomycetes include many types of mushroom species and are cosmopolitan all over the globe. Ustilagomycetes are agricultural pathogens and have caused widespread damage to crops. Eurotiomycetes are found on all types of decaying material and include important human allergens. We focused on these classes since they are thought to be abundant in the atmosphere and because there is very little information on themore » ice nucleation ability of these classes of spores in the literature. All of the fungal spores investigated were found to cause freezing of water droplets at temperatures warmer than homogeneous freezing. The cumulative number of ice nuclei per spore was 0.001 at temperatures between -19 °C and -29 °C, 0.01 between -25.5 °C and -31 °C, and 0.1 between -26 °C and -36 °C. On average, the order of ice nucleating ability for these spores is Ustilagomycetes > Agaricomycetes ≅ Eurotiomycetes. We show that at temperatures below -20 °C, all of the fungal spores studied here are less efficient ice nuclei compared to Asian mineral dust on a per surface area basis. We used our new freezing results together with data in the literature to compare the freezing temperatures of spores from the phyla Basidiomycota and Ascomycota, which together make up 98 % of known fungal species found on Earth. The data show that within both phyla (Ascomycota and Basidiomycota) there is a wide range of freezing properties, and also that the variation within a phylum is greater than the variation between the average freezing properties of the phyla. Using a global chemistry-climate transport model, we investigated whether ice nucleation on the studied spores, followed by precipitation, can influence the atmospheric transport and global distributions of these spores in the atmosphere. Simulations show that inclusion of ice nucleation scavenging of fungal spores in mixed-phase clouds can decrease the surface annual mean mixing ratios of fungal spores over the oceans and polar regions and decrease annual mean mixing ratios in the upper troposphere.« less

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

PubMed Central

Hedges, S Blair; Blair, Jaime E; Venturi, Maria L; Shoe, Jason L

2004-01-01

Background The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. Results Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20–188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to ~10 types at 1500 Ma and 50 cell types at ~1000 Ma. Conclusions The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2–3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity. PMID:15005799

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

NASA Technical Reports Server (NTRS)

Hedges, S. Blair; Blair, Jaime E.; Venturi, Maria L.; Shoe, Jason L.

2004-01-01

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.

Sesquiterpene Synthase-3-Hydroxy-3-Methylglutaryl Coenzyme A Synthase Fusion Protein Responsible for Hirsutene Biosynthesis in Stereum hirsutum.

PubMed

Flynn, Christopher M; Schmidt-Dannert, Claudia

2018-06-01

The wood-rotting mushroom Stereum hirsutum is a known producer of a large number of namesake hirsutenoids, many with important bioactivities. Hirsutenoids form a structurally diverse and distinct class of sesquiterpenoids. No genes involved in hirsutenoid biosynthesis have yet been identified or their enzymes characterized. Here, we describe the cloning and functional characterization of a hirsutene synthase as an unexpected fusion protein of a sesquiterpene synthase (STS) with a C-terminal 3-hydroxy-3-methylglutaryl-coenzyme A (3-hydroxy-3-methylglutaryl-CoA) synthase (HMGS) domain. Both the full-length fusion protein and truncated STS domain are highly product-specific 1,11-cyclizing STS enzymes with kinetic properties typical of STSs. Complementation studies in Saccharomyces cerevisiae confirmed that the HMGS domain is also functional in vivo Phylogenetic analysis shows that the hirsutene synthase domain does not form a clade with other previously characterized sesquiterpene synthases from Basidiomycota. Comparative gene structure analysis of this hirsutene synthase with characterized fungal enzymes reveals a significantly higher intron density, suggesting that this enzyme may be acquired by horizontal gene transfer. In contrast, the HMGS domain is clearly related to other fungal homologs. This STS-HMGS fusion protein is part of a biosynthetic gene cluster that includes P450s and oxidases that are expressed and could be cloned from cDNA. Finally, this unusual fusion of a terpene synthase to an HMGS domain, which is not generally recognized as a key regulatory enzyme of the mevalonate isoprenoid precursor pathway, led to the identification of additional HMGS duplications in many fungal genomes, including the localization of HMGSs in other predicted sesquiterpenoid biosynthetic gene clusters. IMPORTANCE Hirsutenoids represent a structurally diverse class of bioactive sesquiterpenoids isolated from fungi. Identification of their biosynthetic pathways will provide access to this chemodiversity for the discovery and synthesis of molecules with new bioactivities. The identification and successful cloning of the previously elusive hirsutene synthase from the S. hirsutum provide important insights and strategies for biosynthetic gene discovery in Basidiomycota. The finding of a terpene synthase-HMGS fusion, the discovery of other sesquiterpenoid biosynthetic gene clusters with dedicated HMGS genes, and HMGS gene duplications in fungal genomes give new importance to the role of HMGS as a key regulatory enzyme in isoprenoid and sterol biosynthesis that should be exploited for metabolic engineering. Copyright © 2018 American Society for Microbiology.

Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand

PubMed Central

2012-01-01

Background Tha Wang and Tham Phang coasts, though situated at similar oceanographic positions on Sichang island, Chonburi province, Thailand, are different in bay geography and amount of municipal disturbances. These affect the marine ecosystems. The study used metagenomics combined with 16S and 18S rDNA pyrosequencing to identify types and distributions of archaea, bacteria, fungi and small eukaryotes of sizes ranges 0.45 and ~30 μm. Results Following the open bay geography and minimal municipal sewages, Tham Phang coast showed the cleaner water properties, described by color, salinity, pH, conductivity and percent dissolved oxygen. The 16S and 18S rDNA metagenomic profiles for Tha Wang and Tham Phang coasts revealed many differences, highlighting by low Lennon and Yue & Clayton theta similarity indices (66.03-73.03% for 16S rDNA profiles, 2.85-25.38% for 18S rDNA profiles). For 16S rDNA, the percent compositions of species belonging to Proteobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Verrucomicrobia, Gammatimonadetes, Tenericutes, Acidobacteria, Spirochaetes, Chlamydiae, Euryarchaeota, Nitrospirae, Planctomycetes, Thermotogae and Aquificae were higher or distinctly present in Tha Wang. In Tham Phang, except Actinobacteria, the fewer number of prokaryotic species existed. For 18S rDNA, fungi represented 74.745% of the species in Tha Wang, whereas only 6.728% in Tham Phang. Basidiomycota (71.157%) and Ascomycota (3.060%) were the major phyla in Tha Wang. Indeed, Tha Wang-to-Tham Phang percent composition ratios for fungi Basidiomycota and Chytridiomycota were 1264.701 and 25.422, respectively. In Tham Phang, Brachiopoda (lamp shells) and Mollusca (snails) accounted for 80.380% of the 18S rDNA species detected, and their proportions were approximately tenfold greater than those in Tha Wang. Overall, coastal Tham Phang comprised abundant animal species. Conclusions Tha Wang contained numerous archaea, bacteria and fungi, many of which could synthesize useful biotechnology gas and enzymes that could also function in high-saline and high-temperature conditions. Tham Phang contained less abundant archaea, bacteria and fungi, and the majority of the extracted metagenomes belonged to animal kingdom. Many microorganisms in Tham Phang were essential for nutrient-recycling and pharmaceuticals, for instances, Streptomyces, Pennicilium and Saccharomyces. Together, the study provided metagenomic profiles of free-living prokaryotes and eukaryotes in coastal areas of Sichang island. PMID:23282134

[Phylogenetic diversity of airborne microbes in Qingdao downtown in autumn].

PubMed

Wang, Lin; Song, Zhi-wen; Xu, Ai-ling; Wu, Deng-deng; Xia, Yan

2015-04-01

To determine the community structure of airborne microbes in Qingdao downtown in autumn, the airborne bacteria and fungi were collected by the KC-6120 air sampler and analyzed using the 16S/18S rDNA gene clone library method. Phylogenetic analysis of airborne bacteria showed that they belonged to six major phylogenetic groups: Proteobacteria (78. 8%), Firmicutes (14.6%), Actinobacteria (4.0%), Planctomycetes (1.3%), Cyanobacteria (0.7%), and Deinococcus-Thermus (0.7%). The dominant genera of airborne bacteria included Acinetobacter (39.7%), Staphylococcus (11.3%), Sphingomonas (8.6%), Paracoccus (6.0%) and Massilia (5.3%). The main types of airborne fungi were Ascomycota (97.5%) and Basidiomycota (2.5%). Dominant genera of airborne fungi included Pyrenophora (76.5%), Xylaria (13.6%) and Exophiala (2.5%). The pathogens or conditioned pathogens, such as Acinetobacter, Staphylococcus, or Sphingomonas were detected in the airborne bacteria, whereas certain kinds of fungi, such as P. graminea, X. hypoxylon and Zasmidium angulare that could cause a variety of crop diseases were also detected.

Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi.

PubMed

Lee, Jaikoo; Lee, Sangsun; Young, J Peter W

2008-08-01

A set of PCR primers that should amplify all subgroups of arbuscular mycorrhizal fungi (AMF, Glomeromycota), but exclude sequences from other organisms, was designed to facilitate rapid detection and identification directly from field-grown plant roots. The small subunit rRNA gene was targeted for the new primers (AML1 and AML2) because phylogenetic relationships among the Glomeromycota are well understood for this gene. Sequence comparisons indicate that the new primers should amplify all published AMF sequences except those from Archaeospora trappei. The specificity of the new primers was tested using 23 different AMF spore morphotypes from trap cultures and Miscanthus sinensis, Glycine max and Panax ginseng roots sampled from the field. Non-AMF DNA of 14 plants, 14 Basidiomycota and 18 Ascomycota was also tested as negative controls. Sequences amplified from roots using the new primers were compared with those obtained using the established NS31 and AM1 primer combination. The new primers have much better specificity and coverage of all known AMF groups.

Anti-MRSA Activity of Fruiting Body Extracts of Spectacular Rustgill Mushroom, Gymnopilus junonius (Agaricomycetes).

PubMed

Barneche, Stephanie; Alborés, Silvana; Borthagaray, Graciela; Cerdeiras, María Pía; Vázquez, Alvaro

2017-01-01

Despite the great advances in chemotherapeutics, infectious diseases are still one of the leading causes of death worldwide. Among some of the clinically relevant pathogens, methicillin-resistant Staphylococcus aureus (MRSA) ranks as one of the most difficult bacteria to treat. It is a common cause of skin, soft-tissue, and endovascular infections, as well as pneumonia, septic arthritis, endocarditis, osteomyelitis, and sepsis. The research on Basidiomycota is extensive; many species show a broad spectrum of pharmacological activities, including antimicrobial activity. The vast majority of the literature to date generally focuses on screening the antibacterial properties of mushroom extracts. A gap still exists in the identification of the individual compounds responsible for these properties, and few low molecular weight compounds have been described. Gymnopilus junonius, the big laughter mushroom, grows wild in Uruguay, especially on Eucalyptus spp. plantations; it is known as the "eucalyptus fungus." In this work, we report the bioguided isolation, structural elucidation, and antistaphylococcal activity of the main antimicrobial components of fresh basidiocarps of G. junonius.

Comparative Cold Shock Expression and Characterization of Fungal Dye-Decolorizing Peroxidases.

PubMed

Behrens, Christoph J; Zelena, Kateryna; Berger, Ralf G

2016-08-01

Dye-decolorizing peroxidases (DyPs) from Auricularia auricula-judae, Bjerkandera adusta, Pleurotus ostreatus and Marasmius scorodonius (Basidiomycota) were expressed in Escherichia coli using the cold shock-inducible expression system pCOLD I DNA. Functional expression was achieved without the addition of hemin or the co-expression of any chaperones. The presence or absence of the native signal sequence had a strong impact on the success of the expression, but the effect was not consistent for the different DyPs. While BaDyP and AajDyP were stable at 50 °C, the more thermolabile MsP2 and PoDyp, upon catalytic intervention, lend themselves to more rapid thermal inactivation. The bleaching of norbixin (E 160b) using MsP2 was most efficient at pH 4.0, while BaDyP and AajDypP worked best in the weakly acidic to neutral range, indicating a choice of DyPs for a broad field of applications in different food matrices.

Characterisation of seven Inocybe ectomycorrhizal morphotypes from a semiarid woody steppe.

PubMed

Seress, Diána; Dima, Bálint; Kovács, Gábor M

2016-04-01

Ectomycorrhizas (ECM) of Inocybe species (Inocybaceae, Basidiomycota) formed by three host plant species (Populus alba, Salix rosmarinifolia and Pinus nigra) in a semiarid woody steppe of Hungary were studied. To identify the fungal partners, we performed phylogenetic analyses of nucleotide sequences for the internal transcribed spacer region of nuclear DNA (nrDNA ITS) together with sequences gained from public databases. Seven Inocybe ectomycorrhiza morphotypes were morpho-anatomically characterised. Five morphotypes were identified (I. phaeoleuca, I. psammophila, I. semifulva, I. splendens and I. subporospora), whereas two morphotypes represented unidentified Inocybe species. Differences were discernible among the morphotypes, and they showed general anatomical characteristics of Inocybe ECM, such as the slightly organised plectenchymatic mantle (types A, B and E and the gelatinous C). The ECM of I. subporospora and I. phaeoleuca were detected from the introduced Pinus nigra. These two fungi are probably native to the area but capable of forming a novel ectomycorrhizal association with the invasive host.

Diversity and saline resistance of endophytic fungi associated with Pinus thunbergii in coastal shelterbelts of Korea.

PubMed

Min, Young Ju; Park, Myung Soo; Fong, Jonathan J; Quan, Ying; Jung, Sungcheol; Lim, Young Woon

2014-03-28

The Black Pine, Pinus thunbergii, is widely distributed along the eastern coast of Korea and its importance as a shelterbelt was highlighted after tsunamis in Indonesia and Japan. The root endophytic diversity of P. thunbergii was investigated in three coastal regions; Goseong, Uljin, and Busan. Fungi were isolated from the root tips, and growth rates of pure cultures were measured and compared between PDA with and without 3% NaCl to determine their saline resistance. A total of 259 isolates were divided into 136 morphotypes, of which internal transcribed spacer region sequences identified 58 species. Representatives of each major fungi phylum were present: 44 Ascomycota, 8 Zygomycota, and 6 Basidiomycota. Eighteen species exhibited saline resistance, many of which were Penicillium and Trichoderma species. Shoreline habitats harbored higher saline-tolerant endophytic diversity compared with inland sites. This investigation indicates that endophytes of P. thunbergii living closer to the coast may have higher resistance to salinity and potentially have specific relationships with P. thunbergii.

Biodiversity of fungi in hot desert sands.

PubMed

Murgia, Manuela; Fiamma, Maura; Barac, Aleksandra; Deligios, Massimo; Mazzarello, Vittorio; Paglietti, Bianca; Cappuccinelli, Pietro; Al-Qahtani, Ahmed; Squartini, Andrea; Rubino, Salvatore; Al-Ahdal, Mohammed N

2018-03-05

The fungal community of six sand samples from Saudi Arabia and Jordan deserts was characterized by culture-independent analysis via next generation sequencing of the 18S rRNA genes and by culture-dependent methods followed by sequencing of internal transcribed spacer (ITS) region. By 18S sequencing were identified from 163 to 507 OTUs per sample, with a percentage of fungi ranging from 3.5% to 82.7%. The identified fungal Phyla were Ascomycota, Basal fungi, and Basidiomycota and the most abundant detected classes were Dothideomycetes, Pezizomycetes, and Sordariomycetes. A total of 11 colonies of filamentous fungi were isolated and cultured from six samples, and the ITS sequencing pointed toward five different species of the class Sordariomycetes, belonging to genera Fusarium (F. redolens, F. solani, F. equiseti), Chaetomium (C. madrasense), and Albifimbria (A. terrestris). The results of this study show an unexpectedly large fungal biodiversity in the Middle East desert sand and their possible role and implications on human health. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Lichensphere: a protected natural microhabitat of the non-lichenised fungal communities living in extreme environments of Antarctica.

PubMed

Santiago, Iara F; Soares, Marco Aurélio; Rosa, Carlos A; Rosa, Luiz H

2015-11-01

We surveyed the diversity, distribution and ecology of non-lichenised fungal communities associated with the Antarctic lichens Usnea antarctica and Usnea aurantiaco-atra across Antarctica. The phylogenetic study of the 438 fungi isolates identified 74 taxa from 21 genera of Ascomycota, Basidiomycota and Zygomycota. The most abundant taxa were Pseudogymnoascus sp., Thelebolus sp., Antarctomyces psychrotrophicus and Cryptococcus victoriae, which are considered endemic and/or highly adapted to Antarctica. Thirty-five fungi may represent new and/or endemic species. The fungal communities displayed high diversity, richness and dominance indices; however, the similarity among the communities was variable. After discovering rich and diverse fungal communities composed of symbionts, decomposers, parasites and endemic and cold-adapted cosmopolitan taxa, we introduced the term "lichensphere". We hypothesised that the lichensphere may represent a protected natural microhabitat with favourable conditions able to help non-lichenised fungi and other Antarctic life forms survive and disperse in the extreme environments of Antarctica.

Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeast species.

PubMed

Sitepu, Irnayuli R; Sestric, Ryan; Ignatia, Laura; Levin, David; German, J Bruce; Gillies, Laura A; Almada, Luis A G; Boundy-Mills, Kyria L

2013-09-01

Oleaginous yeasts have been studied for oleochemical production for over 80 years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. Copyright © 2013 Elsevier Ltd. All rights reserved.

Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeasts species

PubMed Central

Sitepu, Irnayuli R.; Sestric, Ryan; Ignatia, Laura; Levin, David; German, J. Bruce; Gillies, Laura A.; Almada, Luis A.G.; Boundy-Mills, Kyria L.

2013-01-01

Oleaginous yeasts have been studied for oleochemical production for over 80 years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. PMID:23891835

Diversity and distribution of fungal communities in the marine sediments of Kongsfjorden, Svalbard (High Arctic)

NASA Astrophysics Data System (ADS)

Zhang, Tao; Fei Wang, Neng; Qin Zhang, Yu; Yu Liu, Hong; Yan Yu, Li

2015-10-01

This study assessed the diversity and distribution of fungal communities in eight marine sediments of Kongsfjorden (Svalbard, High Arctic) using 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Sedimentary fungal communities showed high diversity with 42,219 reads belonging to 113 operational taxonomic units (OTUs). Of these OTUs, 62 belonged to the Ascomycota, 26 to Basidiomycota, 2 to Chytridiomycota, 1 to Zygomycota, 1 to Glomeromycota, and 21 to unknown fungi. The major known orders included Hypocreales and Saccharomycetales. The common fungal genera were Pichia, Fusarium, Alternaria, and Malassezia. Interestingly, most fungi occurring in these Arctic sediments may originate from the terrestrial habitats and different basins in Kongsfjorden (i.e., inner basin, central basin, and outer basin) harbor different sedimentary fungal communities. These results suggest the existence of diverse fungal communities in the Arctic marine sediments, which may serve as a useful community model for further ecological and evolutionary study of fungi in the Arctic.

Anamorphs of the Bolbitiaceae (Basidiomycota, Agaricales).

PubMed

Walther, Grit; Weiss, Michael

2006-01-01

We describe and illustrate thallic conidiogenesis in 14 species of the Bolbitiaceae sensu Singer studied in culture. Conidiogenesis of 12 species is shown for the first time. Bolbitius vitellinus and the investigated species of Conocybe (C. albipes, C. appendiculata, C. magnicapitata, C. semiglobata, C. subovalis, C. subpubescens, C. sulcatipes and C. teneroides) possessed a similar mode of conidiogenesis. Species of both genera formed mostly coiled conidiogenous hyphae arising sympodially from differentiated conidiophores. The anamorphs of the Agrocybe species were not uniform and predominantly differed from those of Conocybe and Bolbitius. The conidia of Agrocybe dura, A. firma and A. praecox developed by the simple fragmentation of normally branched hyphae. Sympodially proliferating conidiophores occurred in Agrocybe arvalis and A. aegerita. Secretory cells of different size and shape were found in Agrocybe and in Conocybe. Our results corroborate a close phylogenetic relationship between Bolbitius and Conocybe as well as the polyphyly of the Bolbitiaceae as currently treated, which is consistent with recent molecular phylogenetic studies. Consequently we emend the family concept based on anamorphic characters.

From one to six: unrecognized species diversity in the genus Acantholichen (lichenized Basidiomycota: Hygrophoraceae).

PubMed

Dal-Forno, Manuela; Lücking, Robert; Bungartz, Frank; Yánez-Ayabaca, Alba; Marcelli, Marcelo P; Spielmann, Adriano A; Coca, Luis Fernando; Chaves, José Luis; Aptroot, Andre; Sipman, Harrie J M; Sikaroodi, Masoumeh; Gillevet, Patrick; Lawrey, James D

2016-01-01

We present a taxonomic revision of the lichenized basidiomycete genus Acantholichen, species of which produce a characteristic blue-gray, microsquamulose thallus with spiny apical hyphal cells known as acanthohyphidia. Since its discovery, the genus was thought to be monospecific, only including the generic type, A. pannarioides. However, a detailed morphological and anatomical study of recently collected specimens from the Galápagos, Costa Rica, Brazil and Colombia, combined with a molecular phylogenetic analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and 28S of the nuc rDNA and RPB2 sequences, revealed a much more diverse and widespread species assemblage. Based on the results of these analyses, we describe five new species in the genus: A. albomarginatus, A. campestris, A. galapagoensis, A. sorediatus and A. variabilis. We also provide an identification key to all species, anatomical and morphological descriptions, photographs and a table comparing main characters of each species. © 2016 by The Mycological Society of America.

Phylogenetic and microscopic studies in the genus Lactifluus (Basidiomycota, Russulales) in West Africa, including the description of four new species.

PubMed

Maba, Dao Lamèga; Guelly, Atsu K; Yorou, Nourou S; Verbeken, Annemieke; Agerer, Reinhard

2015-06-01

Despite the crucial ecological role of lactarioid taxa (Lactifluus, Lactarius) as common ectomycorrhiza formers in tropical African seasonal forests, their current diversity is not yet adequately assessed. During the last few years, numerous lactarioid specimens have been sampled in various ecosystems from Togo (West Africa). We generated 48 ITS sequences and aligned them against lactarioid taxa from other tropical African ecozones (Guineo-Congolean evergreen forests, Zambezian miombo). A Maximum Likelihood phylogenetic tree was inferred from a dataset of 109 sequences. The phylogenetic placement of the specimens, combined with morpho-anatomical data, supported the description of four new species from Togo within the monophyletic genus Lactifluus: within subgen. Lactifluus (L. flavellus), subgen. Russulopsis (L. longibasidius and L. pectinatus), and subgen. Edules (L. melleus). This demonstrates that the current species richness of the genus is considerably higher than hitherto estimated for African species and, in addition, a need to redefine the subgenera and sections within it.

Phylogenetic constrains on mycorrhizal specificity in eight Dendrobium (Orchidaceae) species.

PubMed

Xing, Xiaoke; Ma, Xueting; Men, Jinxin; Chen, Yanhong; Guo, Shunxing

2017-05-01

Plant phylogeny constrains orchid mycorrhizal (OrM) fungal community composition in some orchids. Here, we investigated the structures of the OrM fungal communities of eight Dendrobium species in one niche to determine whether similarities in the OrM fungal communities correlated with the phylogeny of the host plants and whether the Dendrobium-OrM fungal interactions are phylogenetically conserved. A phylogeny based on DNA data was constructed for the eight coexisting Dendrobium species, and the OrM fungal communities were characterized by their roots. There were 31 different fungal lineages associated with the eight Dendrobium species. In total, 82.98% of the identified associations belonging to Tulasnellaceae, and a smaller proportion involved members of the unknown Basidiomycota (9.67%). Community analyses revealed that phylogenetically related Dendrobium tended to interact with a similar set of Tulasnellaceae fungi. The interactions between Dendrobium and Tulasnellaceae fungi were significantly influenced by the phylogenetic relationships among the Dendrobium species. Our results provide evidence that the mycorrhizal specificity in the eight coexisting Dendrobium species was phylogenetically conserved.

Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome

PubMed Central

Mandarano, Alexandra H.; Giloteaux, Ludovic; Keller, Betsy A.; Levine, Susan M.

2018-01-01

Patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) often suffer from gastrointestinal symptoms and many are diagnosed with irritable bowel syndrome (IBS). Previous studies, including from our laboratory, have demonstrated that the ME/CFS gut bacterial composition is altered and less diverse when compared to healthy individuals. Patients have increased biomarkers of inflammation and leaky gut syndrome. To further investigate dysbiosis in the ME/CFS gut microbiome, we sought to characterize the eukaryotes present in the gut of 49 individuals with ME/CFS and 39 healthy controls. Using 18S rRNA sequencing, we have identified eukaryotes in stool samples of 17 healthy individuals and 17 ME/CFS patients. Our analysis demonstrates a small, nonsignificant decrease in eukaryotic diversity in ME/CFS patients compared to healthy individuals. In addition, ME/CFS patients show a nonsignificant increase in the ratio of fungal phyla Basidiomycota to Ascomycota, which is consistent with ongoing inflammation in ME/CFS. We did not identify specific eukaryotic taxa that are associated with ME/CFS disease status. PMID:29375937

Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales).

PubMed

Song, Jie; Cui, Bao-Kai

2017-04-20

The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU). Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area. Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

Effects of biochar amendment on bacterial and fungal diversity for co-composting of gelatin industry sludge mixed with organic fraction of municipal solid waste.

PubMed

Awasthi, Mukesh Kumar; Li, Jiao; Kumar, Sunil; Awasthi, Sanjeev Kumar; Wang, Quan; Chen, Hongyu; Wang, Meijing; Ren, Xiuna; Zhang, Zengqiang

2017-12-01

The aim of the study was to evaluate the bacterial and fungal diversities of 18contrastivecomposts applied with 17 different sources mad biochars applied treatments using 16S rRNA and 18S rDNA technology, while T-1 used as a control. The results showed that bacterial species of the phyla Actinobacteria, Proteobacteria and Chloroflexi, and fungi of the phylum Ascomycota and Basidiomycota were pre-dominant among the all treatments. The bacterial genus Subgroup_6_norank, Nocardioides, Pseudonocardia, Sphingomonas, Solirubrobacter and RB41_norank are first time identified in composting ecosystem. In addition, the fungal genus Ascomycota_unclassified, Aspergillus, Penicillium, Pleosporales_unclassified and Herpotrichlellacease_unclassified ubiquitous among the all compost. The Shannon and refraction-curve biodiversity indices showed a clear heterogeneity among all the treatments, which could be due to isolation of new genera in this system. Finally, the principal component analysis of the relative number of sequences also confirmed that bacterial and fungal population indiscriminate in different sources mad biochar applied treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Splash and grab: biomechanics of peridiole ejection and function of the funicular cord in bird's nest fungi.

PubMed

Hassett, Maribeth O; Fischer, Mark W F; Sugawara, Zachary T; Stolze-Rybczynski, Jessica; Money, Nicholas P

2013-10-01

The bird's nest fungi (Basidiomycota, Agaricales) package millions of spores into peridioles that are splashed from their basidiomata by the impact of raindrops. In this study we report new information on the discharge mechanism in Crucibulum and Cyathus species revealed with high-speed video. Peridioles were ejected at speeds of 1-5 m per second utilizing less than 2 % of the kinetic energy in falling raindrops. Raindrops that hit the rim of the basidiome were most effective at ejecting peridioles. The mean angle of ejection varied from 67 to 73° and the peridioles travelled over an estimated maximum horizontal distance of 1 m. Each peridiole carried a cord or funiculus that remained in a condensed form during flight. The cord unravelled when its adhesive surface stuck to a surrounding obstacle and acted as a brake that quickly reduced the velocity of the projectile. In nature, this elaborate mechanism tethers peridioles to vegetation in a perfect location for browsing by herbivores. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level

PubMed Central

2011-01-01

Background Rhizopus oryzae is a zygomycete filamentous fungus, well-known as a saprobe ubiquitous in soil and as a pathogenic/spoilage fungus, causing Rhizopus rot and mucomycoses. Results Carbohydrate Active enzyme (CAZy) annotation of the R. oryzae identified, in contrast to other filamentous fungi, a low number of glycoside hydrolases (GHs) and a high number of glycosyl transferases (GTs) and carbohydrate esterases (CEs). A detailed analysis of CAZy families, supported by growth data, demonstrates highly specialized plant and fungal cell wall degrading abilities distinct from ascomycetes and basidiomycetes. The specific genomic and growth features for degradation of easily digestible plant cell wall mono- and polysaccharides (starch, galactomannan, unbranched pectin, hexose sugars), chitin, chitosan, β-1,3-glucan and fungal cell wall fractions suggest specific adaptations of R. oryzae to its environment. Conclusions CAZy analyses of the genome of the zygomycete fungus R. oryzae and comparison to ascomycetes and basidiomycete species revealed how evolution has shaped its genetic content with respect to carbohydrate degradation, after divergence from the Ascomycota and Basidiomycota. PMID:21241472

Proteomics shows new faces for the old penicillin producer Penicillium chrysogenum.

PubMed

Barreiro, Carlos; Martín, Juan F; García-Estrada, Carlos

2012-01-01

Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new "omics" era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.

Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields.

PubMed

Bai, Li; Cui, Jiaqi; Jie, Weiguang; Cai, Baiyan

2015-11-01

We used rhizosphere soil sampled from one field during zero year and two years of continuous cropping of high-protein soybean to analyze the taxonomic community compositions of fungi during periods of high-incidence of root rot. Our objectives were to identify the dominant pathogens in order to provide a theoretical basis for the study of pathogenesis as well as control tactics for soybean root rot induced by continuous cropping. A total of 17,801 modified internal transcribed spacer (ITS) sequences were obtained from three different soybean rhizosphere soil samples after zero year and 1 or 2 years of continuous cropping using 454 high-throughput sequencing. The dominant eumycote fungal were identified to be Ascomycota and Basidiomycota in the three soil samples. Continuous cropping of soybean affected the diversity of fungi in rhizosphere soils and increased the abundance of Thelebolus and Mortierellales significantly. Thanatephorus, Fusarium, and Alternaria were identified to be the dominant pathogenic fungal genera in rhizosphere soil from continuously cropped soybean fields. Copyright © 2015 Elsevier GmbH. All rights reserved.

Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.

PubMed

Andrade, B S; Góes-Neto, A

2015-10-30

The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.

Olive mill wastewater biodegradation potential of white-rot fungi--Mode of action of fungal culture extracts and effects of ligninolytic enzymes.

PubMed

Ntougias, Spyridon; Baldrian, Petr; Ehaliotis, Constantinos; Nerud, Frantisek; Merhautová, Věra; Zervakis, Georgios I

2015-01-01

Forty-nine white-rot strains belonging to 38 species of Basidiomycota were evaluated for olive-mill wastewater (OMW) degradation. Almost all fungi caused high total phenolics (>60%) and color (⩽ 70%) reduction, while COD and phytotoxicity decreased to a lesser extent. Culture extracts from selected Agrocybe cylindracea, Inonotus andersonii, Pleurotus ostreatus and Trametes versicolor strains showed non-altered physicochemical and enzymatic activity profiles when applied to raw OMW in the presence or absence of commercial catalase, indicating no interaction of the latter with fungal enzymes and no competition for H2O2. Hydrogen peroxide's addition resulted in drastic OMW's decolorization, with no effect on phenolic content, suggesting that oxidation affects colored components, but not necessarily phenolics. When fungal extracts were heat-treated, no phenolics decrease was observed demonstrating thus their enzymatic rather than physicochemical oxidation. Laccases added to OMW were reversibly inhibited by the effluent's high phenolic load, while peroxidases were stable and active during the entire process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Atractiellomycetes belonging to the ‘rust’ lineage (Pucciniomycotina) form mycorrhizae with terrestrial and epiphytic neotropical orchids

PubMed Central

Kottke, Ingrid; Suárez, Juan Pablo; Herrera, Paulo; Cruz, Dario; Bauer, Robert; Haug, Ingeborg; Garnica, Sigisfredo

2010-01-01

Distinctive groups of fungi are involved in the diverse mycorrhizal associations of land plants. All previously known mycorrhiza-forming Basidiomycota associated with trees, ericads, liverworts or orchids are hosted in Agaricomycetes, Agaricomycotina. Here we demonstrate for the first time that Atractiellomycetes, members of the ‘rust’ lineage (Pucciniomycotina), are mycobionts of orchids. The mycobionts of 103 terrestrial and epiphytic orchid individuals, sampled in the tropical mountain rainforest of Southern Ecuador, were identified by sequencing the whole ITS1-5.8S-ITS2 region and part of 28S rDNA. Mycorrhizae of 13 orchid individuals were investigated by transmission electron microscopy. Simple septal pores and symplechosomes in the hyphal coils of mycorrhizae from four orchid individuals indicated members of Atractiellomycetes. Molecular phylogeny of sequences from mycobionts of 32 orchid individuals out of 103 samples confirmed Atractiellomycetes and the placement in Pucciniomycotina, previously known to comprise only parasitic and saprophytic fungi. Thus, our finding reveals these fungi, frequently associated to neotropical orchids, as the most basal living basidiomycetes involved in mycorrhizal associations of land plants. PMID:20007181

Rhodotorula glutinis meningitis: a case report and review of literature.

PubMed

Menon, Sarala; Gupta, H R; Sequeira, R; Chavan, Shazia; Gholape, D; Amandeep, S; Bhilave, N; Chowdhary, A S

2014-07-01

Rhodotorula is ubiquitous saprophytic yeast belonging to phylum Basidiomycota. These encapsulated basidiomycetes are being increasingly recognised as important emerging human pathogens. There are scanty reports of meningitis caused by Rhodurorula spp in HIV infected patients. We present one such case of meningitis by Rhodutorula glutinis in HIV-infected patient. The patient also had a past history of abdominal tuberculosis. The diagnosis of Rhodotorula was confirmed by Gram staining and culture of the cerebrospinal fluid (CSF). Contamination was ruled out by repeated culturing of CSF from the same patient. Therapy with Amphotericin B showed good results. Patient was discharged from the hospital. However, in the seventh month of follow-up patient was readmitted with complaints of fever, breathlessness, altered sensorium, vomiting and succumbed to his illness. This time the CSF cultures remained negative for Rhodotorula, acid fast bacilli and other pyogenic organisms. Our last 11-year retrospective analysis of 8197 specimens received for mycological work-up showed that this is the first report of R. glutinis isolation from our institute. © 2014 Blackwell Verlag GmbH.

Hybrid histidine kinases in pathogenic fungi.

PubMed

Defosse, Tatiana A; Sharma, Anupam; Mondal, Alok K; Dugé de Bernonville, Thomas; Latgé, Jean-Paul; Calderone, Richard; Giglioli-Guivarc'h, Nathalie; Courdavault, Vincent; Clastre, Marc; Papon, Nicolas

2015-03-01

Histidine kinases (HK) sense and transduce via phosphorylation events many intra- and extracellular signals in bacteria, archaea, slime moulds and plants. HK are also widespread in the fungal kingdom, but their precise roles in the regulation of physiological processes remain largely obscure. Expanding genomic resources have recently given the opportunity to identify uncharacterised HK family members in yeasts and moulds and now allow proposing a complex classification of Basidiomycota, Ascomycota and lower fungi HK. A growing number of genetic approaches have progressively provided new insight into the role of several groups of HK in prominent fungal pathogens. In particular, a series of studies have revealed that members of group III HK, which occur in the highest number of fungal species and contain a unique N-terminus region consisting of multiple HAMP domain repeats, regulate morphogenesis and virulence in various human, plant and insect pathogenic fungi. This research field is further supported by recent shape-function studies providing clear correlation between structural properties and signalling states in group III HK. Since HK are absent in mammals, these represent interesting fungal target for the discovery of new antifungal drugs. © 2015 John Wiley & Sons Ltd.

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats

NASA Astrophysics Data System (ADS)

Comeau, André M.; Vincent, Warwick F.; Bernier, Louis; Lovejoy, Connie

2016-07-01

In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling.

Proteomics Shows New Faces for the Old Penicillin Producer Penicillium chrysogenum

PubMed Central

Barreiro, Carlos; Martín, Juan F.; García-Estrada, Carlos

2012-01-01

Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new “omics” era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus. PMID:22318718

Soil Microbial Community Responses to Short-term Multiple Experimental Climate Change Drivers

NASA Astrophysics Data System (ADS)

Li, Guanlin; Lee, Jongyeol; Lee, Sohye; Roh, Yujin; Son, Yowhan

2016-04-01

It is agreed that soil microbial communities are responsible for the cycling of carbon and nutrients in ecosystems; however, the response of these microbial communities to climate change has not been clearly understood. In this study, we measured the direct and interactive effects of climate change drivers on soil bacterial and fungal communities (abundance and composition) in an open-field multifactor climate change experiment. The experimental treatment system was established with two-year-old Pinus densiflora seedlings at Korea University in April 2013, and consisted of six different treatments with three replicates: two levels of air temperature warming (control and +3° C) were crossed with three levels of precipitation manipulation (control, -30% and +30%). After 2.5 years of treatments, in August, 2015, soil samples were collected from the topsoil (0-15cm) of all plots (n=18). High-throughput sequencing technology was used to assess the abundance and composition of soil bacterial and fungal community. Analysis of variance for a blocked split-plot design was used to detect the effects of climate change drivers and their interaction on the abundance and composition of soil bacterial and fungal community. Our results showed that 1) only the significant effect of warming on fungal community abundance was observed (P <0.05); 2) on average, warming decreased both bacterial and fungal community abundance by 20.90% and 32.30%, 6.69% and 45.89%, 14.71% and 19.56% in control, decreased, and increased precipitation plots, respectively; 3) however, warming increased the relative bacterium/fungus ratio on average by 14.03%, 37.03% and 14.31% in control, decreased, and increased precipitation plots, respectively; 4) the phylogenetic distribution of bacterial and fungal groups and their relative abundance varied among treatments; 5) treatments altered the relative abundance of Ascomycota and Basidiomycota, where Ascomycota decreased with a concomitant increase in the Basidiomycota across all treatments; and 6) the shift induced by treatments in the dominant fungal group was larger than bacterial group. Since soil microorganisms differ in their susceptibility to stressors, the changes in the soil microbial communities may result from treatment-induced shifts in soil temperature and moisture. Our results indicate that climate change drivers and their interactions may cause changes in abundance and composition of soil microbial communities, especially for the fungal community. These results illustrate climate change drivers and their interactions may select for distinct soil microbial communities, and these community changes may shape the way ecosystems function in the future. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

Genetic variation and factors affecting the genetic structure of the lichenicolous fungus Heterocephalacria bachmannii (Filobasidiales, Basidiomycota)

PubMed Central

Laakso, Into; Stenroos, Soili

2017-01-01

Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii. PMID:29253026

Affinities and architecture of Devonian trunks of Prototaxites loganii.

PubMed

Retallack, G J; Landing, Ed

2014-01-01

Devonian fossil logs of Prototaxites loganii have been considered kelp-like aquatic algae, rolled up carpets of liverworts, enormous saprophytic fungal fruiting bodies or giant lichens. Algae and rolled liverwort models cannot explain the proportions and branching described here of a complete fossil of Prototaxites loganii from the Middle Devonian (386 Ma) Bellvale Sandstone on Schunnemunk Mountain, eastern New York. The "Schunnemunk tree" was 8.83 m long and had six branches, each about 1 m long and 9 cm diam, on the upper 1.2 m of the main axis. The coalified outermost layer of the Schunnemunk trunk and branches have isotopic compositions (δ(13)CPDB) of -25.03 ± 0.13‰ and -26.17 ± 0.69‰, respectively. The outermost part of the trunk has poorly preserved invaginations above cortical nests of coccoid cells embraced by much-branched tubular cells. This histology is unlike algae, liverworts or vascular plants and most like lichen with coccoid chlorophyte phycobionts. Prototaxites has been placed within Basidiomycota but lacks clear dikaryan features. Prototaxites and its extinct order Nematophytales may belong within Mucoromycotina or Glomeromycota. © 2014 by The Mycological Society of America.

Transcriptomic analysis of the dimorphic transition of Ustilago maydis induced in vitro by a change in pH.

PubMed

Martínez-Soto, Domingo; Ruiz-Herrera, José

2013-01-01

Dimorphism is the property of fungi to grow as budding yeasts or mycelium, depending on the environmental conditions. This phenomenon is important as a model of differentiation in eukaryotic organisms, and since a large number of fungal diseases are caused by dimorphic fungi, its study is important for practical reasons. In this work, we examined the transcriptome during the dimorphic transition of the basidiomycota phytopathogenic fungus Ustilago maydis using microarrays, utilizing yeast and mycelium monomorphic mutants as controls. This way, we thereby identified 154 genes of the fungus that are specifically involved in the dimorphic transition induced by a pH change. Of these, 82 genes were up-regulated, and 72 were down-regulated. Differential categorization of these genes revealed that they mostly belonged to the classes of metabolism, cell cycle and DNA processing, transcription and protein fate, transport and cellular communication, stress, cell differentiation and biogenesis of cellular components, while a significant number of them corresponded to unclassified proteins. The data reported in this work are important for our understanding of the molecular bases of dimorphism in U. maydis, and possibly of other fungi. Copyright © 2013. Published by Elsevier Inc.

Phylum- and Class-Specific PCR Primers for General Microbial Community Analysis

PubMed Central

Blackwood, Christopher B.; Oaks, Adam; Buyer, Jeffrey S.

2005-01-01

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, and Planctomycetes and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of Basidiomycota were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy. PMID:16204538

Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia.

PubMed

Houles, Anne; Vincent, Bryan; David, Magali; Ducousso, Marc; Galiana, Antoine; Juillot, Farid; Hannibal, Laure; Carriconde, Fabian; Fritsch, Emmanuel; Jourand, Philippe

2018-05-01

This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites.

PubMed

Gomes, Eldon C Q; Godinho, Valéria M; Silva, Débora A S; de Paula, Maria T R; Vitoreli, Gislaine A; Zani, Carlos L; Alves, Tânia M A; Junior, Policarpo A S; Murta, Silvane M F; Barbosa, Emerson C; Oliveira, Jaquelline G; Oliveira, Fabio S; Carvalho, Camila R; Ferreira, Mariana C; Rosa, Carlos A; Rosa, Luiz H

2018-05-01

Molecular biology techniques were used to identify 218 fungi from soil samples collected from four islands of Antarctica. These consisted of 22 taxa of 15 different genera belonging to the Zygomycota, Ascomycota, and Basidiomycota. Mortierella, Antarctomyces, Pseudogymnoascus, and Penicillium were the most frequently isolated genera and Penicillium tardochrysogenum, Penicillium verrucosus, Goffeauzyma gilvescens, and Mortierella sp. 2 the most abundant taxa. All fungal isolates were cultivated using solid-state fermentation to obtain their crude extracts. Pseudogymnoascus destructans, Mortierella parvispora, and Penicillium chrysogenum displayed antiparasitic activities, whilst extracts of P. destructans, Mortierella amoeboidea, Mortierella sp. 3, and P. tardochrysogenum showed herbicidal activities. Reported as pathogenic for bats, different isolates of P. destructans exhibited trypanocidal activities and herbicidal activity, and may be a source of bioactive molecules to be considered for chemotherapy against neglected tropical diseases. The abundant presence of P. destructans in soils of the four islands gives evidence supporting that soils in the Antarctic Peninsula constitute a natural source of strains of this genus, including some P. destructans strains that are phylogenetically close to those that infect bats in North America and Europe/Palearctic Asia.

Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L.

PubMed

Zhou, Xue; Tian, Lei; Zhang, Jianfeng; Ma, Lina; Li, Xiujun; Tian, Chunjie

2017-12-01

Sea buckthorn (Hippophae rhamnoides L.) is a pioneer plant used for land reclamation and an appropriate material for studying the interactions of symbiotic microorganisms because of its nitrogen-fixing root nodules and mycorrhiza. We used high-throughput sequencing to reveal the diversities and community structures of rhizospheric fungi and their link with nitrogen-fixing Frankia harbored in sea buckthorn collected along an altitude gradient from the Qinghai Tibet Plateau to interior areas. We found that the fungal diversities and compositions varied between different sites. Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla. The distribution of sea buckthorn rhizospheric fungi was driven by both environmental factors and the geographic distance. Among all examined soil characteristics, altitude, AP, and pH were found to have significant (p < 0.05) effect on the rhizospheric fungal community. The rhizospheric fungal communities became more distinct as the distance increased. Moreover, co-inertia analysis identified significant co-structures between Frankia and AMF communities in the rhizosphere of sea buckthorn. We conclude that at the large scale, there are certain linkages between nitrogen-fixing bacteria and the AMF expressed in the distributional pattern. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina

PubMed Central

Wang, Q.-M.; Yurkov, A.M.; Göker, M.; Lumbsch, H.T.; Leavitt, S.D.; Groenewald, M.; Theelen, B.; Liu, X.-Z.; Boekhout, T.; Bai, F.-Y.

2016-01-01

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study. PMID:26951631

Indole-3-Acetic Acid-Producing Yeasts in the Phyllosphere of the Carnivorous Plant Drosera indica L

PubMed Central

Shin, Li-Ying; Wei, Jyuan-Yu; Fu, Shih-Feng; Chou, Jui-Yu

2014-01-01

Yeasts are widely distributed in nature and exist in association with other microorganisms as normal inhabitants of soil, vegetation, and aqueous environments. In this study, 12 yeast strains were enriched and isolated from leaf samples of the carnivorous plant Drosera indica L., which is currently threatened because of restricted habitats and use in herbal industries. According to similarities in large subunit and small subunit ribosomal RNA gene sequences, we identified 2 yeast species in 2 genera of the phylum Ascomycota, and 5 yeast species in 5 genera of the phylum Basidiomycota. All of the isolated yeasts produced indole-3-acetic acid (IAA) when cultivated in YPD broth supplemented with 0.1% L-tryptophan. Growth conditions, such as the pH and temperature of the medium, influenced yeast IAA production. Our results also suggested the existence of a tryptophan-independent IAA biosynthetic pathway. We evaluated the effects of various concentrations of exogenous IAA on yeast growth and observed that IAA produced by wild yeasts modifies auxin-inducible gene expression in Arabidopsis. Our data suggest that yeasts can promote plant growth and support ongoing prospecting of yeast strains for inclusion into biofertilizer for sustainable agriculture. PMID:25464336

Phylogenetic classification of yeasts and related taxa within Pucciniomycotina.

PubMed

Wang, Q-M; Yurkov, A M; Göker, M; Lumbsch, H T; Leavitt, S D; Groenewald, M; Theelen, B; Liu, X-Z; Boekhout, T; Bai, F-Y

2015-06-01

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Ectomycorrhizal diversity and community structure in stands of Quercus oleoides in the seasonally dry tropical forests of Costa Rica

NASA Astrophysics Data System (ADS)

Desai, Nikhilesh S.; Wilson, Andrew W.; Powers, Jennifer S.; Mueller, Gregory M.; Egerton-Warburton, Louise M.

2016-12-01

Most conservation efforts in seasonally dry tropical forests have overlooked less obvious targets for conservation, such as mycorrhizal fungi, that are critical to plant growth and ecosystem structure. We documented the diversity of ectomycorrhizal (EMF) and arbuscular mycorrhizal (AMF) fungal communities in Quercus oleoides (Fagaceae) in Guanacaste province, Costa Rica. Soil cores and sporocarps were collected from regenerating Q. oleoides plots differing in stand age (early vs late regeneration) during the wet season. Sequencing of the nuclear ribosomal ITS region in EMF root tips and sporocarps identified 37 taxa in the Basidiomycota; EMF Ascomycota were uncommon. The EMF community was dominated by one species (Thelephora sp. 1; 70% of soil cores), more than half of all EMF species were found only once in an individual soil core, and there were few conspecific taxa. Most EMF taxa were also restricted to either Early or Late plots. Levels of EMF species richness and diversity, and AMF root colonization were similar between plots. Our results highlight the need for comprehensive spatiotemporal samplings of EMF communities in Q. oleoides to identify and prioritize rare EMF for conservation, and document their genetic and functional diversity.

Antioxidant and Antimycotic Activities of Two Native Lavandula Species from Portugal

PubMed Central

Baptista, Rafael; Madureira, Ana Margarida; Jorge, Rita; Adão, Rita; Duarte, Aida; Duarte, Noélia; Lopes, Maria Manuel; Teixeira, Generosa

2015-01-01

The antioxidant and antimycotic activities of the essential oils and extracts of two native Portuguese Lavandula species, L. stoechas subsp. luisieri and L. pedunculata, were evaluated by in vitro assays. The total phenolics and flavonoids content were also determined. The antioxidant potential was assessed through DPPH radical scavenging, inhibition of lipid peroxidation (ILP), and DNA protection assays. All samples displayed a high DPPH scavenging activity, some of them showing concentration dependence. The majority of the samples were also able to inhibit lipid peroxidation. A strong correlation was observed between the results of DPPH and ILP assays and the flavonoids content of the samples. In the DNA protection assay, all the extracts were able to preserve DNA integrity. The antimycotic activity was performed against twelve fungi belonging to Basidiomycota and Ascomycota Divisions. L. stoechas subsp. luisieri exhibited the broadest activity spectra. L. pedunculata extracts were active against five fungi. Cryptococcus neoformans was the most sensitive, being inhibited by all the extracts. Our results led to the conclusion that L. stoechas subsp. luisieri and L. pedunculata can be useful as new sources of natural antioxidants and antimycotic agents, providing a possible valorization of the existing biodiversity and resources of Portuguese flora. PMID:25922611

Specialized proteinine rove beetles shed light on insect-fungal associations in the Cretaceous.

PubMed

Cai, Chenyang; Newton, Alfred F; Thayer, Margaret K; Leschen, Richard A B; Huang, Diying

2016-12-28

Insects and fungi have a long history of association in shared habitats. Fungus-feeding, or mycophagy, is remarkably widespread in beetles (Coleoptera) and appears to be a primitive feeding habit that preceded feeding on plant tissues. Numerous Mesozoic beetles belonging to extant fungus-associated families are known, but direct fossil evidence elucidating mycophagy in insects has remained elusive. Here, we report a remarkable genus and species, Vetuproteinus cretaceus gen. et sp. nov., belonging to a new tribe (Vetuproteinini trib. nov.) of the extant rove beetle subfamily Proteininae (Staphylinidae) in Mid-Cretaceous Burmese amber. The mouthparts of this beetle have a markedly enlarged protruding galea bearing an apparent spore brush, a specialized structure we infer was used to scrape spores off surfaces and direct them into the mouth, as in multiple modern spore-feeding beetles. Considering the long evolutionary history of Fungi, the Mid-Cretaceous beetles likely fed on ancient Basidiomycota and/or Ascomycota fungi or spore-producing organisms such as slime moulds (Myxomycetes). The discovery of the first Mesozoic proteinine illustrates the antiquity of the subfamily, and suggests that ancestral Proteininae were already diverse and widespread in Pangaea before the supercontinent broke up. © 2016 The Author(s).

Phylogenetic analyses and nitrate-reducing activity of fungal cultures isolated from the permanent, oceanic oxygen minimum zone of the Arabian Sea.

PubMed

Manohar, Cathrine Sumathi; Menezes, Larissa Danielle; Ramasamy, Kesava Priyan; Meena, Ram M

2015-03-01

Reports on the active role of fungi as denitrifiers in terrestrial ecosystems have stimulated an interest in the study of the role of fungi in oxygen-deficient marine systems. In this study, the culturable diversity of fungi was investigated from 4 stations within the permanent, oceanic, oxygen minimum zone of the Arabian Sea. The isolated cultures grouped within the 2 major fungal phyla Ascomycota and Basidiomycota; diversity estimates in the stations sampled indicated that the diversity of the oxygen-depleted environments is less than that of mangrove regions and deep-sea habitats. Phylogenetic analyses of 18S rRNA sequences revealed a few divergent isolates that clustered with environmental sequences previously obtained by others. This is significant, as these isolates represent phylotypes that so far were known only from metagenomic studies and are of phylogenetic importance. Nitrate reduction activity, the first step in the denitrification process, was recorded for isolates under simulated anoxic, deep-sea conditions showing ecological significance of fungi in the oxygen-depleted habitats. This report increases our understanding of fungal diversity in unique, poorly studied habitats and underlines the importance of fungi in the oxygen-depleted environments.

Sarcodon in the Neotropics II: four new species from Colombia and a key to the regional species.

PubMed

Grupe, Arthur C; Vasco-Palacios, Aída Marcela; Smith, Matthew E; Boekhout, Teun; Henkel, Terry W

2016-01-01

This work reports on four species of the ectomycorrhizal (ECM) tooth fungus genus Sarcodon (Bankeraceae, Thelephorales, Basidiomycota) recently discovered in the Colombian Amazon. Sarcodon colombiensis sp. nov., Sarcodon rufobrunneus sp. nov., Sarcodon pallidogriseus sp. nov. and Sarcodon bairdii sp. nov. are described as new to science. These fungi occur in forests dominated by ECM trees in the genera Pseudomonotes (Dipterocarpaceae), Dicymbe (Fabaceae subfam. Caesalpinioideae) and Aldina (Fabaceae subfam. Papilionoideae). These records bring the number of Sarcodon species known from the Neotropics to 10. Each of the new species possesses the accepted diagnostic characters for the genus: pileate-stipitate stature, a dentate hymenophore, determinate basidiomata development, fleshy, non-zonate context, and brown, tuberculate basidiospores. Molecular phylogenetic analysis corroborated the generic placement of the species, and, in combination with morphological characters, confirmed that they are new to science. Macromorphological, micromorphological, habitat and DNA sequence data from the nuc rDNA internal transcribed spacer region (ITS) are provided for each of the new species. A key is provided that allows identification of all known Neotropical Sarcodon species and similar extralimital taxa. © 2016 by The Mycological Society of America.

Specialized proteinine rove beetles shed light on insect–fungal associations in the Cretaceous

PubMed Central

Leschen, Richard A. B.; Huang, Diying

2016-01-01

Insects and fungi have a long history of association in shared habitats. Fungus-feeding, or mycophagy, is remarkably widespread in beetles (Coleoptera) and appears to be a primitive feeding habit that preceded feeding on plant tissues. Numerous Mesozoic beetles belonging to extant fungus-associated families are known, but direct fossil evidence elucidating mycophagy in insects has remained elusive. Here, we report a remarkable genus and species, Vetuproteinus cretaceus gen. et sp. nov., belonging to a new tribe (Vetuproteinini trib. nov.) of the extant rove beetle subfamily Proteininae (Staphylinidae) in Mid-Cretaceous Burmese amber. The mouthparts of this beetle have a markedly enlarged protruding galea bearing an apparent spore brush, a specialized structure we infer was used to scrape spores off surfaces and direct them into the mouth, as in multiple modern spore-feeding beetles. Considering the long evolutionary history of Fungi, the Mid-Cretaceous beetles likely fed on ancient Basidiomycota and/or Ascomycota fungi or spore-producing organisms such as slime moulds (Myxomycetes). The discovery of the first Mesozoic proteinine illustrates the antiquity of the subfamily, and suggests that ancestral Proteininae were already diverse and widespread in Pangaea before the supercontinent broke up. PMID:28003444

[Microeukaryotic biodiversity in the waste ore samples surrounding an acid mine drainage lake].

PubMed

Li, Si-Yuan; Hao, Chun-Bo; Wang, Li-Hua; Lü, Zheng; Zhang, Li-Na; Liu, Ying; Feng, Chuan-Ping

2013-10-01

The abandoned mineral samples were collected in an acid mine drainage area in Anhui Province. Molecular ecological methods were used to construct 18S rDNA clone libraries after analyzing the main physicochemical parameters, and then the microeukaryotic diversity and community structure in the acid mine drainage area were studied. The results showed that the region was strongly acidic (pH <3), and the concentrations of Fe, SO2-(4), P, NO-(3) -N showed the same trend, all higher in the bare waste ore samples PD and 1 M than in the vegetation covered samples LW and XC. Four eukaryotic phyla were detected in the abandoned mineral samples: Ascomycota, Basidiomycota, Glomeromycota and Arthropoda. Glomeromycota can form an absolute symbiotic relationship with the plant, and it was a key factor for early plant to adapt the terrestrial environment. The biodiversity of the vegetation covered samples LW and XC, which contained Glomeromycota, was much higher than that of the bare abandoned rock samples PD and 1 M. Moreover, many sequences in the libraries were closely related to some isolated strains, which are tolerant to low pH and heavy metals, such as Penicillium purpurogenum, Chaetothyriales sp. and Staninwardia suttonii.

Fomitopsis betulina (formerly Piptoporus betulinus): the Iceman's polypore fungus with modern biotechnological potential.

PubMed

Pleszczyńska, Małgorzata; Lemieszek, Marta K; Siwulski, Marek; Wiater, Adrian; Rzeski, Wojciech; Szczodrak, Janusz

2017-05-01

Higher Basidiomycota have been used in natural medicine throughout the world for centuries. One of such fungi is Fomitopsis betulina (formerly Piptoporus betulinus), which causes brown rot of birch wood. Annual white to brownish fruiting bodies of the species can be found on trees in the northern hemisphere but F. betulina can also be cultured as a mycelium and fruiting body. The fungus has a long tradition of being applied in folk medicine as an antimicrobial, anticancer, and anti-inflammatory agent. Probably due to the curative properties, pieces of its fruiting body were carried by Ötzi the Iceman. Modern research confirms the health-promoting benefits of F. betulina. Pharmacological studies have provided evidence supporting the antibacterial, anti-parasitic, antiviral, anti-inflammatory, anticancer, neuroprotective, and immunomodulating activities of F. betulina preparations. Biologically active compounds such as triterpenoids have been isolated. The mushroom is also a reservoir of valuable enzymes and other substances such as cell wall (1→3)-α-D-glucan which can be used for induction of microbial enzymes degrading cariogenic dental biofilm. In conclusion, F. betulina can be considered as a promising source for the development of new products for healthcare and other biotechnological uses.

Ethanol Production from Various Sugars and Cellulosic Biomass by White Rot Fungus Lenzites betulinus.

PubMed

Im, Kyung Hoan; Nguyen, Trung Kien; Choi, Jaehyuk; Lee, Tae Soo

2016-03-01

Lenzites betulinus, known as gilled polypore belongs to Basidiomycota was isolated from fruiting body on broadleaf dead trees. It was found that the mycelia of white rot fungus Lenzites betulinus IUM 5468 produced ethanol from various sugars, including glucose, mannose, galactose, and cellobiose with a yield of 0.38, 0.26, 0.07, and 0.26 g of ethanol per gram of sugar consumed, respectively. This fungus relatively exhibited a good ethanol production from xylose at 0.26 g of ethanol per gram of sugar consumed. However, the ethanol conversion rate of arabinose was relatively low (at 0.07 g of ethanol per gram sugar). L. betulinus was capable of producing ethanol directly from rice straw and corn stalks at 0.22 g and 0.16 g of ethanol per gram of substrates, respectively, when this fungus was cultured in a basal medium containing 20 g/L rice straw or corn stalks. These results indicate that L. betulinus can produce ethanol efficiently from glucose, mannose, and cellobiose and produce ethanol very poorly from galactose and arabinose. Therefore, it is suggested that this fungus can ferment ethanol from various sugars and hydrolyze cellulosic materials to sugars and convert them to ethanol simultaneously.

Oligonucleotide fingerprinting of rRNA genes for analysis of fungal community composition.

PubMed

Valinsky, Lea; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

2002-12-01

Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with average sequence identities of 99.2% were grouped into the same cluster. To examine the accuracy of the taxonomic identities produced by this OFRG experiment, we determined the nucleotide sequences for 117 clones distributed throughout the tree. For all but two of these clones, the taxonomic identities generated by this OFRG experiment were consistent with those generated by a nucleotide sequence analysis. Eighty-eight percent of the clones were affiliated with Ascomycota, while 12% belonged to BASIDIOMYCOTA: A large fraction of the clones were affiliated with the genera Fusarium (404 clones) and Raciborskiomyces (176 clones). Smaller assemblages of clones had high sequence identities to the Alternaria, Ascobolus, Chaetomium, Cryptococcus, and Rhizoctonia clades.

Influence of Peanut Cultivars and Environmental Conditions on the Diversity and Community Composition of Pod Rot Soil Fungi in China.

PubMed

Wang, Mian; Chen, Mingna; Yang, Zhen; Chen, Na; Chi, Xiaoyuan; Pan, Lijuan; Wang, Tong; Yu, Shanlin; Guo, Xingqi

2017-12-01

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium , Chaetomium , Alternaria , and Sordariomycetes , followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

Phylogenomic Relationships between Amylolytic Enzymes from 85 Strains of Fungi

PubMed Central

Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

2012-01-01

Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions. PMID:23166747

Comparison of bacterial and fungal communities between natural and planted pine forests in subtropical China.

PubMed

Nie, Ming; Meng, Han; Li, Ke; Wan, Jia-Rong; Quan, Zhe-Xue; Fang, Chang-Ming; Chen, Jia-Kuan; Li, Bo

2012-01-01

To improve our understanding of the changes in bacterial and fungal diversity in natural pine and planted forests in subtropical region of China, we examined bacterial and fungal communities from a native and a nearby planted pine forest of the Mt. Lushan by constructing clone libraries of 16S and 18S rRNA genes. For bacterial communities, Proteobacteria and Acidobacteria were dominant bacterial taxa in both two types of forest soils. The Shannon-Wiener diversity index, rarefaction curve analysis, and LibShuff analysis suggest that these two forests contained similar diversity of bacterial communities. Low soil acidity (pH ≈ 4) of our study forests might be one of the most important selection factors determining growth of acidophilic Acidobacteria and Proteobacteria. However, the natural forest harbored greater level of fungal diversity than the planted forest according to the Shannon-Wiener diversity index and rarefaction curve analysis. Basidiomycota and Ascomycota were dominant fungal taxa in the soils of natural and planted forests, respectively. Our results suggest that fungal community was more sensitive than the bacterial community in characterizing the differences in plant cover impacts on the microbial flora in the natural and planted forests. The natural and planted forests may function differently due to the differences in soil fungal diversity and relative abundance.

Diversity of endolithic fungal communities in dolomite and limestone rocks from Nanjiang Canyon in Guizhou karst area, China.

PubMed

Tang, Yuan; Lian, Bin

2012-06-01

The endolithic environment, the tiny pores and cracks in rocks, buffer microbial communities from a number of physical stresses, such as desiccation, rapid temperature variations, and UV radiation. Considerable knowledge has been acquired about the diversity of microorganisms in these ecosystems, but few culture-independent studies have been carried out on the diversity of fungi to date. Scanning electron microscopy of carbonate rock fragments has revealed that the rock samples contain certain kinds of filamentous fungi. We evaluated endolithic fungal communities from bare dolomite and limestone rocks collected from Nanjiang Canyon (a typical karst canyon in China) using culture-independent methods. Results showed that Ascomycota was absolutely dominant both in the dolomite and limestone fungal clone libraries. Basidiomycota and other eukaryotic groups (Bryophyta and Chlorophyta) were only detected occasionally or at low frequencies. The most common genus in the investigated carbonate rocks was Verrucaria. Some other lichen-forming fungi (e.g., Caloplaca, Exophiala, and Botryolepraria), Aspergillus, and Penicillium were also identified from the rock samples. The results provide a cross-section of the endolithic fungal communities in carbonate rocks and help us understand more about the role of microbes (fungi and other rock-inhabiting microorganisms) in rock weathering and pedogenesis.

Lignin-degrading peroxidases in white-rot fungus Trametes hirsuta 072. Absolute expression quantification of full multigene family

PubMed Central

Vasina, Daria V.; Moiseenko, Konstantin V.; Fedorova, Tatiana V.; Tyazhelova, Tatiana V.

2017-01-01

Ligninolytic heme peroxidases comprise an extensive family of enzymes, which production is characteristic for white-rot Basidiomycota. The majority of fungal heme peroxidases are encoded by multigene families that differentially express closely related proteins. Currently, there were very few attempts to characterize the complete multigene family of heme peroxidases in a single fungus. Here we are focusing on identification and characterization of peroxidase genes, which are transcribed and secreted by basidiomycete Trametes hirsuta 072, an efficient lignin degrader. The T. hirsuta genome contains 18 ligninolytic peroxidase genes encoding 9 putative lignin peroxidases (LiP), 7 putative short manganese peroxidases (MnP) and 2 putative versatile peroxidases (VP). Using ddPCR method we have quantified the absolute expression of the 18 peroxidase genes under different culture conditions and on different growth stages of basidiomycete. It was shown that only two genes (one MnP and one VP) were prevalently expressed as well as secreted into cultural broth under all conditions investigated. However their transcriptome and protein profiles differed in time depending on the effector used. The expression of other peroxidase genes revealed a significant variability, so one can propose the specific roles of these enzymes in fungal development and lifestyle. PMID:28301519

Does the Agaricus blazei Murill mushroom have properties that affect the immune system? An integrative review.

PubMed

Lima, Cristiane Urcina Joanna Oliveira; Cordova, Cláudio Olavo de Almeida; Nóbrega, Otávio de Tolêdo; Funghetto, Silvana Schwerz; Karnikowski, Margô Gomes de Oliveira

2011-01-01

There has been a significant increase in the use of mushrooms for therapeutic and medicinal purposes, in particular, use of the species Agaricus blazei Murrill, a basidiomycota of Brazilian origin. The objective of this study was to identify scientific evidence regarding the influence of A. blazei Murrill on the immune system. We undertook an integrative review of indexed publications published between 2000 and 2009, using the following question as a guideline: "What evidence can be found in the literature regarding the influence of A. blazei Murrill on the immune system?" Fourteen studies verified that there is in vitro and in vivo research demonstrating this mushroom's influence on the immune system. All research was characterized as evidence level 7 (preclinical study [animals/in vitro]). The research shows that A. blazei Murrill functions through bioactive compounds via mechanisms that are not yet entirely clear, although it has been shown that they promote action on the innate and adaptive immunological response, activation of the complement system, and synthesis of pro- and anti-inflammatory cytokines and even aid in diapedesis. Despite broad scientific evidence demonstrating relevant immunomodulatory properties of A. blazei Murrill, randomized clinical trials with human subjects are still needed in order for the mushroom to be put into clinical practice.

Expanding genomics of mycorrhizal symbiosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuo, Alan; Kohler, Annegret; Martin, Francis M.

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolvemore » through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.« less

Expanding genomics of mycorrhizal symbiosis

DOE PAGES

Kuo, Alan; Kohler, Annegret; Martin, Francis M.; ...

2014-11-04

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant nutrition, soil health, and carbon cycling. The symbiosis evolved repeatedly and independently as multiple morphotypes [e.g., arbuscular mycorrhizae (AM), ectomycorrhizal (ECM)] in multiple fungal clades (e.g., phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and cultivability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first three mycorrhizal fungal genomes, representing two morphotypes and three phyla. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolvemore » through loss of plant cell wall-degrading enzymes (PCWDEs) and expansion of lineage-specific gene families such as short secreted protein (SSP) effectors. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of families as in Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other two fungi, symbiosis can involve similar solutions as symbiosis-induced SSPs and loss of PCWDEs. The three genomes provide a solid base for addressing fundamental questions about the nature and role of a vital mutualism.« less

Phylogenetic Analysis and Classification of the Fungal bHLH Domain

PubMed Central

Sailsbery, Joshua K.; Atchley, William R.; Dean, Ralph A.

2012-01-01

The basic Helix-Loop-Helix (bHLH) domain is an essential highly conserved DNA-binding domain found in many transcription factors in all eukaryotic organisms. The bHLH domain has been well studied in the Animal and Plant Kingdoms but has yet to be characterized within Fungi. Herein, we obtained and evaluated the phylogenetic relationship of 490 fungal-specific bHLH containing proteins from 55 whole genome projects composed of 49 Ascomycota and 6 Basidiomycota organisms. We identified 12 major groupings within Fungi (F1–F12); identifying conserved motifs and functions specific to each group. Several classification models were built to distinguish the 12 groups and elucidate the most discerning sites in the domain. Performance testing on these models, for correct group classification, resulted in a maximum sensitivity and specificity of 98.5% and 99.8%, respectively. We identified 12 highly discerning sites and incorporated those into a set of rules (simplified model) to classify sequences into the correct group. Conservation of amino acid sites and phylogenetic analyses established that like plant bHLH proteins, fungal bHLH–containing proteins are most closely related to animal Group B. The models used in these analyses were incorporated into a software package, the source code for which is available at www.fungalgenomics.ncsu.edu. PMID:22114358

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

PubMed Central

Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

2016-01-01

The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere. PMID:27080869

Diversity and distribution of lichen-associated fungi in the Ny-Ålesund Region (Svalbard, High Arctic) as revealed by 454 pyrosequencing

PubMed Central

Zhang, Tao; Wei, Xin-Li; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2015-01-01

This study assessed the diversity and distribution of fungal communities associated with seven lichen species in the Ny-Ålesund Region (Svalbard, High Arctic) using Roche 454 pyrosequencing with fungal-specific primers targeting the internal transcribed spacer (ITS) region of the ribosomal rRNA gene. Lichen-associated fungal communities showed high diversity, with a total of 42,259 reads belonging to 370 operational taxonomic units (OTUs) being found. Of these OTUs, 294 belonged to Ascomycota, 54 to Basidiomycota, 2 to Zygomycota, and 20 to unknown fungi. Leotiomycetes, Dothideomycetes, and Eurotiomycetes were the major classes, whereas the dominant orders were Helotiales, Capnodiales, and Chaetothyriales. Interestingly, most fungal OTUs were closely related to fungi from various habitats (e.g., soil, rock, plant tissues) in the Arctic, Antarctic and alpine regions, which suggests that living in association with lichen thalli may be a transient stage of life cycle for these fungi and that long-distance dispersal may be important to the fungi in the Arctic. In addition, host-related factors shaped the lichen-associated fungal communities in this region. Taken together, these results suggest that lichens thalli act as reservoirs of diverse fungi from various niches, which may improve our understanding of fungal evolution and ecology in the Arctic. PMID:26463847

Diversity and biotransformative potential of endophytic fungi associated with the medicinal plant Kadsura angustifolia.

PubMed

Huang, Qian; An, Hongmei; Song, Hongchuan; Mao, Hongqiang; Shen, Weiyun; Dong, Jinyan

2015-01-01

This study investigated the diversity and host component-transforming activity of endophytic fungi in medicinal plant Kadsura angustifolia. A total of 426 isolates obtained were grouped into 42 taxa belonging to Fungi Imperfecti (65.96%), Ascomycota (27.00%), Zygomycota (1.64%), Basidiomycota (0.47%) and Mycelia Sterilia (4.93%). The abundance, richness, and species composition of endophytic assemblages were significantly dependent on the tissue and the sampling site. Many phytopathogenic species associated with healthy K. angustifolia were found prevalent. Among them, Verticillium dahliae was dominant with 16.43% abundance. From 134 morphospecies selected, 39 showed remarkable biocatalytic activity and were further identified as species belonging to the genera Colletotrichum, Eupenicillium, Fusarium, Hypoxylon, Penicillium, Phomopsis, Trametes, Trichoderma, Umbelopsis, Verticillium and Xylaria on the basis of the sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2). The results obtained in this work show that K. angustifolia is an interesting reservoir of pathogenic fungal species, and could be a community model for further ecological and evolutionary studies. Additionally, the converting potency screening of some endophytic fungi from this specific medicinal plant may provide an interesting niche on the search for novel biocatalysts. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Metagenomic Analysis of Fungal Diversity on Strawberry Plants and the Effect of Management Practices on the Fungal Community Structure of Aerial Organs

PubMed Central

Abdelfattah, Ahmed; Wisniewski, Michael; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga

2016-01-01

An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to identify the composition of fungal communities associated with different strawberry organs (leaves, flowers, immature and mature fruits), grown on a farm using management practices that entailed the routine use of various chemical pesticides. ITS2 sequences clustered into 316 OTUs and Ascomycota was the dominant phyla (95.6%) followed by Basidiomycota (3.9%). Strawberry plants supported a high diversity of microbial organisms, but two genera, Botrytis and Cladosporium, were the most abundant, representing 70–99% of the relative abundance (RA) of all detected sequences. According to alpha and beta diversity analyses, strawberry organs displayed significantly different fungal communities with leaves having the most diverse fungal community, followed by flowers, and fruit. The interruption of chemical treatments for one month resulted in a significant modification in the structure of the fungal community of leaves and flowers while immature and mature fruit were not significantly affected. Several plant pathogens of other plant species, that would not be intuitively expected to be present on strawberry plants such as Erysiphe, were detected, while some common strawberry pathogens, such as Rhizoctonia, were less evident or absent. PMID:27490110

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

PubMed Central

Pent, Mari; Põldmaa, Kadri; Bahram, Mohammad

2017-01-01

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales—the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements. PMID:28539921

Molecular phylogeny of Rigidoporus microporus isolates associated with white rot disease of rubber trees (Hevea brasiliensis).

PubMed

Oghenekaro, Abbot O; Miettinen, Otto; Omorusi, Victor I; Evueh, Grace A; Farid, Mohd A; Gazis, Romina; Asiegbu, Fred O

2014-01-01

Rigidoporus microporus (Polyporales, Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen of rubber plantations distributed in tropical and sub-tropical regions. Our primary objective was to characterize Nigerian isolates from rubber tree and compare them with other West African, Southeast Asian and American isolates. To characterize the 20 isolates from Nigeria, we used sequence data of the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) gene sequences. Altogether, 40 isolates of R. microporus were included in the analyses. Isolates from Africa, Asia and South/Central America formed three distinctive clades corresponding to at least three species. No phylogeographic pattern was detected among R. microporus collected from West and Central African rubber plantations suggesting continuous gene flow among these populations. Our molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analyses placed R. microporus in the Hymenochaetales in the vicinity of Oxyporus. This is the first study to characterize R. microporus isolates from Nigeria through molecular phylogenetic techniques, and also the first to compare isolates from rubber plantations in Africa and Asia. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Phylogenetic congruence between subtropical trees and their associated fungi.

PubMed

Liu, Xubing; Liang, Minxia; Etienne, Rampal S; Gilbert, Gregory S; Yu, Shixiao

2016-12-01

Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next-generation high-throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK , rbcL , atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host-fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant-fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant-fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method.

PubMed

Nasanit, Rujikan; Tangwong-O-Thai, Apirat; Tantirungkij, Manee; Limtong, Savitree

2015-12-01

The diversity of epiphytic yeasts from sugarcane (Saccharum officinarum Linn.) phyllospheres in Thailand was investigated by culture-independent method based on the analysis of the D1/D2 domains of the large subunit rRNA gene sequences. Forty-five samples of sugarcane leaf were collected randomly from ten provinces in Thailand. A total of 1342 clones were obtained from 45 clone libraries. 426 clones (31.7 %) were closely related to yeast strains in the GenBank database, and they were clustered into 31 operational taxonomic units (OTUs) with a similarity threshold of 99 %. All OTU sequences were classified in phylum Basidiomycota which were closely related to 11 yeast species in seven genera including Cryptococcus flavus, Hannaella coprosmaensis, Rhodotorula taiwanensis, Jaminaea angkoreiensis, Malassezia restricta, Pseudozyma antarctica, Pseudozyma aphidis, Pseudozyma hubeiensis, Pseudozyma prolifica, Pseudozyma shanxiensis, and Sporobolomyces vermiculatus. The most predominant yeasts detected belonged to Ustilaginales with 89.4 % relative frequency and the prevalent yeast genus was Pseudozyma. However, the majority were unable to be identified as known yeast species and these sequences may represent the sequences of new yeast taxa. In addition, The OTU that closely related to P. prolifica was commonly detected in sugarcane phyllosphere. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts.

PubMed

Long, Hongan; Behringer, Megan G; Williams, Emily; Te, Ronald; Lynch, Michael

2016-12-01

Yeast species are extremely diverse and not monophyletic. Because the majority of yeast research focuses on ascomycetes, the mutational determinants of genetic diversity across yeast species are not well understood. By combining mutation-accumulation techniques with whole-genome sequencing, we resolved the genomic mutation rate and spectrum of the oleaginous (oil-producing) ‘red yeast’ Rhodotorula toruloides, the first such study in the fungal phylum Basidiomycota. We find that the mutation spectrum is quite different from what has been observed in all other studied unicellular eukaryotes, but similar to that in most bacteria—a predominance of transitions relative to transversions. Rhodotorula toruloides has a significantly higher A:T→G:C transition rate—possibly elevated by the abundant flanking G/C nucleotides in the GC-rich genome, as well as a much lower G:C→T:A transversion rate. In spite of these striking differences, there are substantial consistencies between R. toruloides and the ascomycete model yeasts: a spontaneous base-substitution mutation rate of 1.90 × 10 −10 per site per cell division as well as an elevated mutation rate at non-methylated 5'CpG3' sites. These results imply the evolution of variable mutation spectra in the face of similar mutation rates in yeasts.

Aneuraceae (Metzgeriales) and tulasnelloid fungi (Basidiomycota): a model for early steps in fungal symbiosis.

PubMed

Krause, Cornelia; Garnica, Sigisfredo; Bauer, Robert; Nebel, Martin

2011-09-01

A total of 35 population samples of the liverwort genera Aneura (A. pinguis) and Riccardia (R. latifrons, R. multifida, and R. palmata) were sampled from diverse habitats and geographical provenances in Germany, Austria, and Switzerland. Light and transmission electron microscopy were used to characterise the morphological features of the associations, and phylogenetic analyses based on internal transcribed spacers (ITS) and the D1/D2 regions of the fungal 28S rDNA were used to address diversity and phylogenetic relationships. By comparing the cellular structures of the plant-fungus interactions, we recognised the following states of fungal colonisation within the thalli: fungus-free, epiphytic, intercellular, and intracellular. Colonising hyphae showed dolipores with imperforate parenthesomes, slime bodies, and multilayered walls. Colonised liverwort cells had pleomorphic nuclei and elongated starch-free chloroplasts with distinctive grana. Our analyses revealed six phylogenetic groups of tulasnelloid fungi associated with liverworts, where major lineages mostly share similar host and/or ecological specialisations. The mode of colonisation of the tulasnelloid mycobionts in Aneura and Riccardia sharing identical fungal sequences is different. Consequently, the mode of colonisation may be host-dependent. Finally, our findings demonstrate that Aneuraceae are model organisms for evolutionary studies of symbiotic associations between liverworts and fungi. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

PubMed Central

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-01-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi.

PubMed

Chen, Ko-Hsuan; Liao, Hui-Ling; Arnold, A Elizabeth; Bonito, Gregory; Lutzoni, François

2018-06-01

Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Investigations of biodeterioration by fungi in historic wooden churches of Chiloé, Chile.

PubMed

Ortiz, Rodrigo; Párraga, Mario; Navarrete, José; Carrasco, Ivo; de la Vega, Eduardo; Ortiz, Manuel; Herrera, Paula; Jurgens, Joel A; Held, Benjamin W; Blanchette, Robert A

2014-04-01

The use of wood in construction has had a long history and Chile has a rich cultural heritage of using native woods for building churches and other important structures. In 2000, UNESCO designated a number of the historic churches of Chiloé, built entirely of native woods, as World Heritage Sites. These unique churches were built in the late 1700 s and throughout the 1800 s, and because of their age and exposure to the environment, they have been found to have serious deterioration problems. Efforts are underway to better understand these decay processes and to carryout conservation efforts for the long-term preservation of these important structures. This study characterized the types of degradation taking place and identified the wood decay fungi obtained from eight historic churches in Chiloé, seven of them designated as UNESCO World Heritage sites. Micromorphological observations identified white, brown and soft rot in the structural woods and isolations provided pure cultures of fungi that were identified by sequencing of the internal transcribed region of rDNA. Twenty-nine Basidiomycota and 18 Ascomycota were found. These diverse groups of fungi represent several genera and species not previously reported from Chile and demonstrates a varied microflora is causing decay in these historic buildings.

An endophytic Basidiomycete, Grammothele lineata, isolated from Corchorus olitorius, produces paclitaxel that shows cytotoxicity

PubMed Central

Das, Avizit; Rahman, Mohammad Imtiazur; Ferdous, Ahlan Sabah; Amin, Al-; Rahman, Mohammad Mahbubur; Nahar, Nilufar; Uddin, Md. Aftab; Islam, Mohammad Riazul; Khan, Haseena

2017-01-01

Grammothele lineata, an endophyte isolated in our laboratory from jute (Corchorus olitorius acc. 2015) was found to be a substantial paclitaxel producer. Taxol and its related compounds, produced by this endophyte were extracted by growing the fungus in simple nutrient media (potato dextrose broth, PDB). Taxol was identified and characterized by different analytical techniques (TLC, HPLC, FTIR, LC-ESI-MS/MS) following its extraction by ethyl acetate. In PDB media, this fungus was found to produce 382.2 μgL-1 of taxol which is about 7.6 x103 fold higher than the first reported endophytic fungi, Taxomyces andreanae. The extracted taxol exhibited cytotoxic activity in an in vitro culture of HeLa cancer cell line. The fungal extract also exhibited antifungal and antibacterial activities against different pathogenic strains. This is the first report of a jute endophytic fungus harboring the capacity to produce taxol and also the first reported taxol producing species that belongs to the Basidiomycota phylum, so far unknown to be a taxol producer. These findings suggest that the fungal endophyte, Grammothele lineata can be an excellent source of taxol and can also serve as a potential species for chemical and genetic engineering to enhance further the production of taxol. PMID:28636663

An endophytic Basidiomycete, Grammothele lineata, isolated from Corchorus olitorius, produces paclitaxel that shows cytotoxicity.

PubMed

Das, Avizit; Rahman, Mohammad Imtiazur; Ferdous, Ahlan Sabah; Amin, Al-; Rahman, Mohammad Mahbubur; Nahar, Nilufar; Uddin, Md Aftab; Islam, Mohammad Riazul; Khan, Haseena

2017-01-01

Grammothele lineata, an endophyte isolated in our laboratory from jute (Corchorus olitorius acc. 2015) was found to be a substantial paclitaxel producer. Taxol and its related compounds, produced by this endophyte were extracted by growing the fungus in simple nutrient media (potato dextrose broth, PDB). Taxol was identified and characterized by different analytical techniques (TLC, HPLC, FTIR, LC-ESI-MS/MS) following its extraction by ethyl acetate. In PDB media, this fungus was found to produce 382.2 μgL-1 of taxol which is about 7.6 x103 fold higher than the first reported endophytic fungi, Taxomyces andreanae. The extracted taxol exhibited cytotoxic activity in an in vitro culture of HeLa cancer cell line. The fungal extract also exhibited antifungal and antibacterial activities against different pathogenic strains. This is the first report of a jute endophytic fungus harboring the capacity to produce taxol and also the first reported taxol producing species that belongs to the Basidiomycota phylum, so far unknown to be a taxol producer. These findings suggest that the fungal endophyte, Grammothele lineata can be an excellent source of taxol and can also serve as a potential species for chemical and genetic engineering to enhance further the production of taxol.

Large variability of bathypelagic microbial eukaryotic communities across the world's oceans.

PubMed

Pernice, Massimo C; Giner, Caterina R; Logares, Ramiro; Perera-Bel, Júlia; Acinas, Silvia G; Duarte, Carlos M; Gasol, Josep M; Massana, Ramon

2016-04-01

In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8-20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

Ethanol Production from Various Sugars and Cellulosic Biomass by White Rot Fungus Lenzites betulinus

PubMed Central

Im, Kyung Hoan; Nguyen, Trung Kien; Choi, Jaehyuk

2016-01-01

Lenzites betulinus, known as gilled polypore belongs to Basidiomycota was isolated from fruiting body on broadleaf dead trees. It was found that the mycelia of white rot fungus Lenzites betulinus IUM 5468 produced ethanol from various sugars, including glucose, mannose, galactose, and cellobiose with a yield of 0.38, 0.26, 0.07, and 0.26 g of ethanol per gram of sugar consumed, respectively. This fungus relatively exhibited a good ethanol production from xylose at 0.26 g of ethanol per gram of sugar consumed. However, the ethanol conversion rate of arabinose was relatively low (at 0.07 g of ethanol per gram sugar). L. betulinus was capable of producing ethanol directly from rice straw and corn stalks at 0.22 g and 0.16 g of ethanol per gram of substrates, respectively, when this fungus was cultured in a basal medium containing 20 g/L rice straw or corn stalks. These results indicate that L. betulinus can produce ethanol efficiently from glucose, mannose, and cellobiose and produce ethanol very poorly from galactose and arabinose. Therefore, it is suggested that this fungus can ferment ethanol from various sugars and hydrolyze cellulosic materials to sugars and convert them to ethanol simultaneously. PMID:27103854

Lactarius subgenus Russularia (Basidiomycota, Russulales): novel Asian species, worldwide phylogeny and evolutionary relationships.

PubMed

Wisitrassameewong, Komsit; Looney, Brian P; Le, Huyen T; De Crop, Eske; Das, Kanad; Van de Putte, Kobeke; Eberhardt, Ursula; Jiayu, Guo; Stubbe, Dirk; Hyde, Kevin D; Verbeken, Annemieke; Nuytinck, Jorinde

2016-12-01

Lactarius subg. Russularia is a large group of milkcaps occurring almost worldwide and dominant in many ecosystems. In this study we focus on new diversity, evolutionary relationships, divergence time, and origin of the subgenus. Six conifer symbionts are described as new to science: Lactarius atrii, L. aurantionitidus, L. dombangensis, L. flavigalactus, L. lachungensis, and L. sikkimensis. Species delimitation is assessed based on the concordance between morphological characteristics and an ITS phylogeny. Infrageneric relationships were studied using a phylogeny constructed from concatenated ITS-rpb2 data using Maximum Likelihood and Bayesian inference. Results show that species in this subgenus do not cluster together according to their geographic origin. Intercontinental sister relationships between Europe/Asia/North America are common but actual conspecificity is rare. This result suggests that allopatric speciation has played an important role within this subgenus. Only few morphological characteristics tend to be phylogenetically informative, with the most important being presence or absence of true cystidia and the pileipellis structure. Two datasets were generated in order to estimate the age of L. subg. Russularia. The results suggest the origin of L. subg. Russularia to be in the Mid Miocene period. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

NASA Astrophysics Data System (ADS)

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-03-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

NASA Astrophysics Data System (ADS)

Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

2016-04-01

The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

PubMed

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon.

PubMed

Frank, Jonathan L; Coffan, Robert A; Southworth, Darlene

2010-01-01

A species of Psathyrella (Basidiomycota) with true gills has been observed fruiting underwater in the clear, cold, flowing waters of the upper Rogue River in Oregon. Fruiting bodies develop and mature in the main channel, where they are constantly submerged, and were observed fruiting over 11 wk. These mushrooms develop underwater, not on wood recently washed into the river. Substrates include water-logged wood, gravel and the silty riverbed. DNA sequences of the ITS region and a portion of the ribosomal large subunit gene place this fungus in Psathyrella sensu stricto near P. atomata, P. fontinalis and P. superiorensis. Morphological characters distinguish the underwater mushroom from previously described species. Fruiting bodies have long fibrillose stipes with small diameter caps. Immature stages have a thin veil that is soon lost. Gills lack reddish edges. Cystidia are ventricose with subacute apices. Spores were observed as wedge-shape rafts released into gas pockets below the caps. Underwater gills and ballistospores indicate a recent adaptation to the stream environment. This particular river habitat combines the characteristics of spring-fed flows and cold, aerated water with woody debris in shallow depths on a fine volcanic substrate. Based on molecular and morphological evidence we conclude that the underwater mushrooms are a new species, Psathyrella aquatica. This report adds to the biodiversity of stream fungi that degrade woody substrates. The underwater environment is a new habitat for gilled mushrooms.

Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments.

PubMed

Bernhard, Joan M; Kormas, Konstantinos; Pachiadaki, Maria G; Rocke, Emma; Beaudoin, David J; Morrison, Colin; Visscher, Pieter T; Cobban, Alec; Starczak, Victoria R; Edgcomb, Virginia P

2014-01-01

Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L' Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers.

Benthic protists and fungi of Mediterranean deep hypsersaline anoxic basin redoxcline sediments

PubMed Central

Bernhard, Joan M.; Kormas, Konstantinos; Pachiadaki, Maria G.; Rocke, Emma; Beaudoin, David J.; Morrison, Colin; Visscher, Pieter T.; Cobban, Alec; Starczak, Victoria R.; Edgcomb, Virginia P.

2014-01-01

Some of the most extreme marine habitats known are the Mediterranean deep hypersaline anoxic basins (DHABs; water depth ∼3500 m). Brines of DHABs are nearly saturated with salt, leading many to suspect they are uninhabitable for eukaryotes. While diverse bacterial and protistan communities are reported from some DHAB water-column haloclines and brines, the existence and activity of benthic DHAB protists have rarely been explored. Here, we report findings regarding protists and fungi recovered from sediments of three DHAB (Discovery, Urania, L’ Atalante) haloclines, and compare these to communities from sediments underlying normoxic waters of typical Mediterranean salinity. Halocline sediments, where the redoxcline impinges the seafloor, were studied from all three DHABs. Microscopic cell counts suggested that halocline sediments supported denser protist populations than those in adjacent control sediments. Pyrosequencing analysis based on ribosomal RNA detected eukaryotic ribotypes in the halocline sediments from each of the three DHABs, most of which were fungi. Sequences affiliated with Ustilaginomycotina Basidiomycota were the most abundant eukaryotic signatures detected. Benthic communities in these DHABs appeared to differ, as expected, due to differing brine chemistries. Microscopy indicated that only a low proportion of protists appeared to bear associated putative symbionts. In a considerable number of cases, when prokaryotes were associated with a protist, DAPI staining did not reveal presence of any nuclei, suggesting that at least some protists were carcasses inhabited by prokaryotic scavengers. PMID:25452749

Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem.

PubMed

Veach, Allison M; Dodds, Walter K; Jumpponen, Ari

2015-10-01

Woody plant encroachment has become a global threat to grasslands and has caused declines in aboveground richness and changes in ecosystem function; yet we have a limited understanding on the effects of these phenomena on belowground microbial communities. We completed riparian woody plant removals at Konza Prairie Biological Station, Kansas and collected soils spanning land-water interfaces in removal and woody vegetation impacted areas. We measured stream sediments and soils for edaphic variables (C and N pools, soil water content, pH) and bacterial (16S rRNA genes) and fungal (ITS2 rRNA gene repeat) communities using Illumina MiSeq metabarcoding. Bacterial richness and diversity decreased with distance from streams. Fungal richness decreased with distance from the stream in wooded areas, but was similar across landscape position while Planctomycetes and Basidiomycota relative abundance was lower in removal areas. Cyanobacteria, Ascomycota, Chytridiomycota and Glomeromycota relative abundance was greater in removal areas. Ordination analyses indicated that bacterial community composition shifted more across land-water interfaces than fungi yet both were marginally influenced by treatment. This study highlights the impacts of woody encroachment restoration on grassland bacterial and fungal communities which likely subsequently affects belowground processes and plant health in this ecosystem. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Pumpkin powdery mildew disease severity influences the fungal diversity of the phyllosphere.

PubMed

Zhang, Zhuo; Luo, Luyun; Tan, Xinqiu; Kong, Xiao; Yang, Jianguo; Wang, Duanhua; Zhang, Deyong; Jin, Decai; Liu, Yong

2018-01-01

Phyllosphere microbiota play a crucial role in plant-environment interactions and their microbial community and function are influenced by biotic and abiotic factors. However, there is little research on how pathogens affect the microbial community of phyllosphere fungi. In this study, we collected 16 pumpkin ( Cucurbita moschata ) leaf samples which exhibited powdery mildew disease, with a severity ranging from L1 (least severe) to L4 (most severe). The fungal community structure and diversity was examined by Illumina MiSeq sequencing of the internal transcribed spacer (ITS) region of ribosomal RNA genes. The results showed that the fungal communities were dominated by members of the Basidiomycota and Ascomycota. The Podosphaera was the most dominant genus on these infected leaves, which was the key pathogen responsible for the pumpkin powdery mildew. The abundance of Ascomycota and Podosphaera increased as disease severity increased from L1 to L4, and was significantly higher at disease severity L4 ( P < 0.05). The richness and diversity of the fungal community increased from L1 to L2, and then declined from L2 to L4, likely due to the biotic pressure (i.e., symbiotic and competitive stresses among microbial species) at disease severity L4. Our results could give new perspectives on the changes of the leaf microbiome at different pumpkin powdery mildew disease severity.

Made for Each Other: Ascomycete Yeasts and Insects.

PubMed

Blackwell, Meredith

2017-06-01

Fungi and insects live together in the same habitats, and many species of both groups rely on each other for success. Insects, the most successful animals on Earth, cannot produce sterols, essential vitamins, and many enzymes; fungi, often yeast-like in growth form, make up for these deficits. Fungi, however, require constantly replenished substrates because they consume the previous ones, and insects, sometimes lured by volatile fungal compounds, carry fungi directly to a similar, but fresh, habitat. Yeasts associated with insects include Ascomycota (Saccharomycotina, Pezizomycotina) and a few Basidiomycota. Beetles, homopterans, and flies are important associates of fungi, and in turn the insects carry yeasts in pits, specialized external pouches, and modified gut pockets. Some yeasts undergo sexual reproduction within the insect gut, where the genetic diversity of the population is increased, while others, well suited to their stable environment, may never mate. The range of interactions extends from dispersal of yeasts on the surface of insects (e.g., cactus- Drosophila -yeast and ephemeral flower communities, ambrosia beetles, yeasts with holdfasts) to extremely specialized associations of organisms that can no longer exist independently, as in the case of yeast-like symbionts of planthoppers. In a few cases yeast-like fungus-insect associations threaten butterflies and other species with extinction. Technical advances improve discovery and identification of the fungi but also inform our understanding of the evolution of yeast-insect symbioses, although there is much more to learn.

Microbial hitchhikers on intercontinental dust: catching a lift in Chad

PubMed Central

Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A

2013-01-01

Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes—Bacillaceae, (b) Actinobacteria—Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria—Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes—Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516

Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

PubMed Central

Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

2014-01-01

The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species. PMID:24710002

Root-associated fungi of Vaccinium carlesii in subtropical forests of China: intra- and inter-annual variability and impacts of human disturbances

PubMed Central

Zhang, Yanhua; Ni, Jian; Tang, Fangping; Pei, Kequan; Luo, Yiqi; Jiang, Lifen; Sun, Lifu; Liang, Yu

2016-01-01

Ericoid mycorrhiza (ERM) are expected to facilitate establishment of ericaceous plants in harsh habitats. However, diversity and driving factors of the root-associated fungi of ericaceous plants are poorly understood. In this study, hair-root samples of Vaccinium carlesii were taken from four forest types: old growth forests (OGF), secondary forests with once or twice cutting (SEC I and SEC II), and Cunninghamia lanceolata plantation (PLF). Fungal communities were determined using high-throughput sequencing, and impacts of human disturbances and the intra- and inter-annual variability of root-associated fungal community were evaluated. Diverse fungal taxa were observed and our results showed that (1) Intra- and inter-annual changes in root-associated fungal community were found, and the Basidiomycota to Ascomycota ratio was related to mean temperature of the sampling month; (2) Human disturbances significantly affected structure of root-associated fungal community of V. carlesii, and two secondary forest types were similar in root-associated fungal community and were closer to that of the old growth forest; (3) Plant community composition, edaphic parameters, and geographic factors significantly affected root-associated fungal communities of V. carlesii. These results may be helpful in better understanding the maintenance mechanisms of fungal diversity associated with hair roots of ERM plants under human disturbances. PMID:26928608

The diversity and antimicrobial activity of endophytic fungi associated with medicinal plant Baccharis trimera (Asteraceae) from the Brazilian savannah.

PubMed

Vieira, Mariana L A; Johann, Susana; Hughes, Frederic M; Rosa, Carlos A; Rosa, Luiz H

2014-12-01

The fungal endophyte community associated with Baccharis trimera, a Brazilian medicinal plant, was characterized and screened for its ability to present antimicrobial activity. By using molecular methods, we identified and classified the endophytic fungi obtained into 25 different taxa from the phyla Ascomycota and Basidiomycota. The most abundant species were closely related to Diaporthe phaseolorum, Pestalotiopsis sp. 1, and Preussia pseudominima. The differences observed in endophytic assemblages from different B. trimera specimens might be associated with their crude extract activities. Plants that had higher α-biodiversity were also those that contributed more to the regional (γ) diversity. All fungal isolates were cultured and their crude extracts screened to examine the antimicrobial activities. Twenty-three extracts (12.8%) displayed antimicrobial activities against at least one target microorganism. Among these extracts, those obtained from Epicoccum sp., Pestalotiopsis sp. 1, Cochliobolus lunatus, and Nigrospora sp. presented the best minimum inhibitory concentration values. Our results show that the endophytic fungal community associated with the medicinal plant B. trimera included few dominant bioactive taxa, which may represent sources of compounds with antifungal activity. Additionally, the discovery of these bioactive fungi in association with B. trimera suggests that Brazilian plants used as folk medicine may shelter a rich fungal diversity as well as taxa able to produce bioactive metabolites with antimicrobial activities.

Endophytic fungi harbored in the root of Sophora tonkinensis Gapnep: Diversity and biocontrol potential against phytopathogens.

PubMed

Yao, Yu Qun; Lan, Fang; Qiao, Yun Ming; Wei, Ji Guang; Huang, Rong Shao; Li, Liang Bo

2017-06-01

This work, for the first time, investigated the diversity of endophytic fungi harbored in the xylem and phloem of the root of Sophora tonkinensis Gapnep from three geographic localities with emphasis on the influence of the tissue type and geographic locality on endophytic fungal communities and their potential as biocontrol agents against phytopathogens of Panax notoginseng. A total of 655 fungal strains representing 47 taxa were isolated. Forty-two taxa (89.4%) were identified but not five taxa (10.6%) according to morphology and molecular phylogenetics. Out of identifiable taxa, the majority of endophyte taxa were Ascomycota (76.6%), followed by Basidiomycota (8.5%) and Zygomycota (4.3%). The alpha-diversity indices indicated that the species diversity of endophytic fungal community harbored in the root of S. tonkinensis was very high. The colonization and species diversity of endophytic fungal communities were significantly influenced by the geographic locality but not tissue type. The geographic locality and tissue type had great effects on the species composition of endophytic fungal communities. Forty-seven respective strains were challenged by three fungal phytopathogens of P. notoginseng and six strains exhibited significant inhibitory activity. It was noteworthy that endophytic Rhexocercosporidium sp. and F. solani strongly inhibited pathogenic F. solani and other fungal phytopathogens of P. notoginseng. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Exploring the potential of fungi isolated from PAH-polluted soil as a source of xenobiotics-degrading fungi.

PubMed

Godoy, Patricia; Reina, Rocío; Calderón, Andrea; Wittich, Regina-Michaela; García-Romera, Inmaculada; Aranda, Elisabet

2016-10-01

The aim of this study was to find polycyclic aromatic hydrocarbon (PAH)-degrading fungi adapted to polluted environments for further application in bioremediation processes. In this study, a total of 23 fungal species were isolated from a historically pyrogenic PAH-polluted soil in Spain and taxonomically identified. The dominant groups in these samples were the ones associated with fungi belonging to the Ascomycota phylum and two isolates belonging to the Mucoromycotina subphylum and Basiodiomycota phylum. We tested their ability to convert the three-ring PAH anthracene in a 42-day time course and analysed their ability to secrete extracellular oxidoreductase enzymes. Among the 23 fungal species screened, 12 were able to oxidize anthracene, leading to the formation of 9,10-anthraquinone as the main metabolite, a less toxic one than the parent compound. The complete removal of anthracene was achieved by three fungal species. In the case of Scopulariopsis brevicaulis, extracellular enzyme independent degradation of the initial 100 μM anthracene occurred, whilst in the case of the ligninolytic fungus Fomes (Basidiomycota), the same result was obtained with extracellular enzyme-dependent transformation. The yield of accumulated 9,10-anthraquinone was 80 and 91 %, respectively, and Fomes sp. could slowly deplete it from the growth medium when offered alone. These results are indicative for the effectiveness of these fungi for pollutant removal. Graphical abstract ᅟ.

Seasonal Succession of Fungi Associated with Ips typographus Beetles and Their Phoretic Mites in an Outbreak Region of Finland.

PubMed

Linnakoski, Riikka; Mahilainen, Saila; Harrington, Alison; Vanhanen, Henri; Eriksson, Miikka; Mehtätalo, Lauri; Pappinen, Ari; Wingfield, Michael J

2016-01-01

The ophiostomatoid fungi (Microascales and Ophiostomatales, Ascomycota) are common associates of Ips typographus, and include tree pathogens and species responsible for blue-stain of timber. Fungal assemblages associated with I. typographus have varied considerably between studies but few investigations have attempted to explain this variation. For this reason, we assessed the overall cultivable fungal diversity associated with I. typographus in a storm-felled spruce forest in south-eastern Finland. Fungi were isolated from the individually collected beetles as well as their phoretic mites in spring, summer and autumn, including different life stages of the beetle (hibernation, dispersal flight and first generation). The internal transcribed spacer (ITS) gene region was used to identify the fungi. A total of 32 operational taxonomic units (OTUs) were found and these resided in four fungal phyla/subphyla (24 Ascomycota, 2 Basidiomycota, 5 Mucoromycotina, 1 Mortierellomycotina) in association with adult bark beetles. Ophiostomatoid species were the most commonly detected fungal associates. A generalized linear model analysis showed a clear association between fungal communities and season, indicating seasonal succession among I. typographus-associated fungi. The season of sampling appears to be an important factor that has resulted in inconsistencies between results in previous studies. Many of these fungi were also found on phoretic mites and their presence or absence could have influenced variation in patterns of association.

Seasonal Succession of Fungi Associated with Ips typographus Beetles and Their Phoretic Mites in an Outbreak Region of Finland

PubMed Central

Mahilainen, Saila; Harrington, Alison; Vanhanen, Henri; Eriksson, Miikka; Mehtätalo, Lauri; Pappinen, Ari; Wingfield, Michael J.

2016-01-01

The ophiostomatoid fungi (Microascales and Ophiostomatales, Ascomycota) are common associates of Ips typographus, and include tree pathogens and species responsible for blue-stain of timber. Fungal assemblages associated with I. typographus have varied considerably between studies but few investigations have attempted to explain this variation. For this reason, we assessed the overall cultivable fungal diversity associated with I. typographus in a storm-felled spruce forest in south-eastern Finland. Fungi were isolated from the individually collected beetles as well as their phoretic mites in spring, summer and autumn, including different life stages of the beetle (hibernation, dispersal flight and first generation). The internal transcribed spacer (ITS) gene region was used to identify the fungi. A total of 32 operational taxonomic units (OTUs) were found and these resided in four fungal phyla/subphyla (24 Ascomycota, 2 Basidiomycota, 5 Mucoromycotina, 1 Mortierellomycotina) in association with adult bark beetles. Ophiostomatoid species were the most commonly detected fungal associates. A generalized linear model analysis showed a clear association between fungal communities and season, indicating seasonal succession among I. typographus-associated fungi. The season of sampling appears to be an important factor that has resulted in inconsistencies between results in previous studies. Many of these fungi were also found on phoretic mites and their presence or absence could have influenced variation in patterns of association. PMID:27187192

Bacterial selection by mycospheres of Atlantic Rainforest mushrooms.

PubMed

Halsey, Joshua Andrew; de Cássia Pereira E Silva, Michele; Andreote, Fernando Dini

2016-10-01

This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.

Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

PubMed

Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

2014-01-01

The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

[Evaluation of Psilocybe cubensis (Agaricales, Basidiomycota) toxicity over Artemia franciscana (Crustacea, Anostraca)].

PubMed

Vega-Villasante, Fernando; Ruiz-González, Luis Eduardo; Guerrero-Galván, Saúl Rogelio; Guzmán-Dávalos, Laura

2013-01-03

Psilocybe cubensis is a species with psychodysleptic action that grows on cattle dung in pastures in the tropics and subtropics. This fungus has been widely used in Mexico since ancient times both for ceremonies and rituals, as well as for healing or medicinal purposes. Artemia franciscana is a crustacean frequently used as a model organism for toxicity testing. With the objective of determining the toxicity of P. cubensis, the results of a study with the extract of P. cubensis on nauplii and adults of the brine shrimp A. franciscana are presented. Specimens were collected at Bahía de Banderas, Jalisco, Mexico, and were dried and homogenized in artificial sea water. Bioassays were carried out on crystal vials filled with different concentrations of the extract of P. cubensis (EAP), and with potassium dichromate as reference toxic compound. The median lethal concentration (LC(50)) in nauplii and adults and the inhibition of cysts hatching in A. franciscana were calculated. Nauplii showed a LC(50) = 135 μg/ml, while adults a LC(50) = 172 μg/ml. Cysts' hatching was inhibited by the EAP at all tested concentrations. Under the conditions of this study, the extract of P. cubensis was toxic for nauplii and adults of A. franciscana. Copyright © 2011 Revista Iberoamericana de Micología. Published by Elsevier España, S.L. All rights reserved.

The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China

PubMed Central

He, Dongpeng; Gu, Ji-Dong; Feng, Huyuan; Chen, Tuo; Liu, Guangxiu; An, Lizhe

2017-01-01

In this study, a culture-independent Illumina MiSeq sequencing strategy was applied to investigate the microbial communities colonizing the ancient painted sculptures of the Maijishan Grottoes, a famous World Cultural Heritage site listed by UNESCO in China. Four mixed samples were collected from Cave 4–4 of the Maijishan Grottoes, the so-called Upper Seven Buddha Pavilion, which was built during the Northern Zhou Dynasty (557-581AD). The 16/18S rRNA gene-based sequences revealed a rich bacterial diversity and a relatively low fungal abundance, including the bacterial groups Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes, Proteobacteria and Verrucomicrobia and the fungal groups Ascomycota, Basidiomycota and Chytridiomycota. Among them, the bacteria genera of Pseudonocardia and Rubrobacter and unclassified fungi in the order of Capnodiales were dominant. The relative abundance of Pseudonocardia in the painted layer samples was higher than that in the dust sample, while Cyanobacteria dominated in the dust sample. Many of them have been discovered at other cultural heritage sites and associated with the biodeterioration of cultural relics. The presence and activity of these pioneering microorganisms may lead to an unexpected deterioration of the painted sculptures that are preserved in this heritage site. Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures. PMID:28678844

Isolation of oligotrophic yeasts from supraglacial environments of different altitude on the Gulkana Glacier (Alaska).

PubMed

Uetake, Jun; Yoshimura, Yoshitaka; Nagatsuka, Naoko; Kanda, Hiroshi

2012-11-01

Psychrophilic yeasts have been isolated from supra- and subglacial ice at many sites worldwide. To understand the ecology of psychrophilic yeasts on glaciers, we focused on their adaptation to wide range of nutrient concentrations and their distribution with altitude on the Gulkana Glacier in Alaska. We found various culturable psychrophilic yeasts on the ice surfaces of the glacier, and 11 species were isolated with incubation at 4 °C in four different dilutions of agar medium. Some of our isolated species (Rhodotorula psychrophenolica, Rhodotorula aff. psychrophenolica, Rhodotorula glacialis, and Basidiomycota sp. 1) can grow on the low dissolved organic matter (DOC) concentrations medium (7.6 mg L(-1)) which is close to the typical level of supraglacial melt water, suggesting that these species can inhabit in any supraglacial meltwater. Otherwise, most of other species were isolated only from higher DOC concentration medium (183 mg L(-1) -18.3 g L(-1)), suggesting that these are inhabitant around the cryoconite, because DOC concentrations in melted surface-ice contained cryoconite is much higher than in melted water. Similarity of altitudinal distribution between culturable yeast and algal biomass suggests that the ecological role played by the cold-adapted yeasts is as organic matter decomposers and nutrient cyclers in glacier ecosystem. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor

Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012more » alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.« less

Biodegradation and detoxification of olive mill wastewater by selected strains of the mushroom genera Ganoderma and Pleurotus.

PubMed

Ntougias, Spyridon; Baldrian, Petr; Ehaliotis, Constantinos; Nerud, Frantisek; Antoniou, Theodoros; Merhautová, Věra; Zervakis, Georgios I

2012-07-01

Thirty-nine white-rot fungi belonging to nine species of Agaricomycotina (Basidiomycota) were initially screened for their ability to decrease olive-mill wastewater (OMW) phenolics. Four strains of Ganoderma australe, Ganoderma carnosum, Pleurotus eryngii and Pleurotus ostreatus, were selected and further examined for key-aspects of the OMW biodegradation process. Fungal growth in OMW-containing batch cultures resulted in significant decolorization (by 40-46% and 60-65% for Ganoderma and Pleurotus spp. respectively) and reduction of phenolics (by 64-67% and 74-81% for Ganoderma and Pleurotus spp. respectively). COD decrease was less pronounced (12-29%). Cress-seeds germination increased by 30-40% when OMW was treated by Pleurotus strains. Toxicity expressed as inhibition of Aliivibrio fischeri luminescence was reduced in fungal-treated OMW samples by approximately 5-15 times compared to the control. As regards the pertinent enzyme activities, laccase and Mn-independent peroxidase were detected for Ganoderma spp. during the entire incubation period. In contrast, Pleurotus spp. did not exhibit any enzyme activities at early growth stages; instead, high laccase (five times greater than those of Ganoderma spp.) and Mn peroxidases activities were determined at the end of treatment. OMW decolorization by Ganoderma strains was strongly correlated to the reduction of phenolics, whereas P. eryngii laccase activity was correlated with the effluent's decolorization. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers.

PubMed

Stursová, Martina; Zifčáková, Lucia; Leigh, Mary Beth; Burgess, Robert; Baldrian, Petr

2012-06-01

Organic matter decomposition in the globally widespread coniferous forests has an important role in the carbon cycle, and cellulose decomposition is especially important in this respect because cellulose is the most abundant polysaccharide in plant litter. Cellulose decomposition was 10 times faster in the fungi-dominated litter of Picea abies forest than in the bacteria-dominated soil. In the soil, the added (13)C-labelled cellulose was the main source of microbial respiration and was preferentially accumulated in the fungal biomass and cellulose induced fungal proliferation. In contrast, in the litter, bacterial biomass showed higher labelling after (13)C-cellulose addition and bacterial biomass increased. While 80% of the total community was represented by 104-106 bacterial and 33-59 fungal operational taxonomic units (OTUs), 80% of the cellulolytic communities of bacteria and fungi were only composed of 8-18 highly abundant OTUs. Both the total and (13)C-labelled communities differed substantially between the litter and soil. Cellulolytic bacteria in the acidic topsoil included Betaproteobacteria, Bacteroidetes and Acidobacteria, whereas these typically found in neutral soils were absent. Most fungal cellulose decomposers belonged to Ascomycota; cellulolytic Basidiomycota were mainly represented by the yeasts Trichosporon and Cryptococcus. Several bacteria and fungi demonstrated here to derive their carbon from cellulose were previously not recognized as cellulolytic. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Fungi diversity in PM2. 5 and PM1 at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

NASA Astrophysics Data System (ADS)

Xu, Caihong; Wei, Min; Chen, Jianmin; Zhu, Chao; Li, Jiarong; Lv, Ganglin; Xu, Xianmang; Zheng, Lulu; Sui, Guodong; Li, Weijun; Chen, Bing; Wang, Wenxing; Zhang, Qingzhu; Ding, Aijun; Mellouki, Abdelwahid

2017-09-01

Fungi are ubiquitous throughout the near-surface atmosphere, where they represent an important component of primary biological aerosol particles. This study combined internal transcribed spacer region sequencing and quantitative real-time polymerase chain reaction (qPCR) to investigate the ambient fungi in fine (PM2. 5, 50 % cutoff aerodynamic diameter Da50 = 2.5 µm, geometric standard deviation of collection efficiency σg = 1.2) and submicron (PM1, Da50 = 1 µm, σg = 1.2) particles at the summit of Mt. Tai located in the North China Plain, China. Fungal abundance values were 9.4 × 104 and 1.3 × 105 copies m-3 in PM2. 5 and PM1, respectively. Most of the fungal sequences were from Ascomycota and Basidiomycota, which are known to actively discharge spores into the atmosphere. The fungal community showed a significant seasonal shift across different size fractions according to Metastats analysis and the Kruskal-Wallis rank sum test. The abundance of Glomerella and Zasmidium increased in larger particles in autumn, whereas Penicillium, Bullera, and Phaeosphaeria increased in smaller particles in winter. Environmental factors, namely Ca2+, humidity, and temperature, were found to be crucial for the seasonal variation in the fungal community. This study might serve as an important reference for fungal contribution to primary biological aerosol particles.

A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins

PubMed Central

Abba', Simona; Ghignone, Stefano; Bonfante, Paola

2006-01-01

Background The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage. Results Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration. Conclusion Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern. PMID:16512918

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

PubMed

Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

2017-08-31

The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

Metabolite analysis of endophytic fungi from cultivars of Zingiber officinale Rosc. identifies myriad of bioactive compounds including tyrosol.

PubMed

Anisha, C; Radhakrishnan, E K

2017-06-01

Endophytic fungi associated with rhizomes of four cultivars of Zingiber officinale were identified by molecular and morphological methods and evaluated for their activity against soft rot pathogen Pythium myriotylum and clinical pathogens. The volatile bioactive metabolites produced by these isolates were identified by GC-MS analysis of the fungal crude extracts. Understanding of the metabolites produced by endophytes is also important in the context of raw consumption of ginger as medicine and spice. A total of fifteen isolates were identified from the four varieties studied. The various genera identified were Acremonium sp., Gliocladiopsis sp., Fusarium sp., Colletotrichum sp., Aspergillus sp., Phlebia sp., Earliella sp., and Pseudolagarobasidium sp. The endophytic community was unique to each variety, which could be due to the varying host genotype. Fungi from phylum Basidiomycota were identified for the first time from ginger. Seven isolates showed activity against Pythium, while only two showed antibacterial activity. The bioactive metabolites identified in the fungal crude extracts include tyrosol, benzene acetic acid, ergone, dehydromevalonic lactone, N-aminopyrrolidine, and many bioactive fatty acids and their derivatives which included linoleic acid, oleic acid, myristic acid, n-hexadecanoic acid, palmitic acid methyl ester, and methyl linoleate. The presence of these varying bioactive endophytic fungi may be one of the reasons for the differences in the performance of the different ginger varieties.

Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation

PubMed Central

Young, Darcy; Rice, James; Martin, Rachael; Lindquist, Erika; Lipzen, Anna; Grigoriev, Igor; Hibbett, David

2015-01-01

Fungal lignocellulolytic enzymes are promising agents for oxidizing pollutants. This study investigated degradation of Number 6 “Bunker C” fuel oil compounds by the white-rot fungi Irpex lacteus, Trichaptum biforme, Phlebia radiata, Trametes versicolor, and Pleurotus ostreatus (Basidiomycota, Agaricomycetes). Averaging across all studied species, 98.1%, 48.6%, and 76.4% of the initial Bunker C C10 alkane, C14 alkane, and phenanthrene, respectively were degraded after 180 days of fungal growth on pine media. This study also investigated whether Bunker C oil induces changes in gene expression in the white-rot fungus Punctularia strigosozonata, for which a complete reference genome is available. After 20 days of growth, a monokaryon P. strigosozonata strain degraded 99% of the initial C10 alkane in both pine and aspen media but did not affect the amounts of the C14 alkane or phenanthrene. Differential gene expression analysis identified 119 genes with ≥ log2(2-fold) greater expression in one or more treatment comparisons. Six genes were significantly upregulated in media containing oil; these genes included three enzymes with potential roles in xenobiotic biotransformation. Carbohydrate metabolism genes showing differential expression significantly accumulated transcripts on aspen vs. pine substrates, perhaps reflecting white-rot adaptations to growth on hardwood substrates. The mechanisms by which P. strigosozonata may degrade complex oil compounds remain obscure, but degradation results of the 180-day cultures suggest that diverse white-rot fungi have promise for bioremediation of petroleum fuels. PMID:26111162

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils.

PubMed

Schwarz, Alexandra; Adetutu, Eric M; Juhasz, Albert L; Aburto-Medina, Arturo; Ball, Andrew S; Shahsavari, Esmaeil

2018-05-01

Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13 C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event ( 14 C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.

Comparative genome analysis of Basidiomycete fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Robert; Salamov, Asaf; Henrissat, Bernard

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism.more » Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.« less

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gacura, Matthew D.; Sprockett, Daniel D.; Heidenreich, Bess

Here, fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senescedmore » tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.« less

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

PubMed

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Mating type gene homologues and putative sex pheromone-sensing pathway in arbuscular mycorrhizal fungi, a presumably asexual plant root symbiont.

PubMed

Halary, Sébastien; Daubois, Laurence; Terrat, Yves; Ellenberger, Sabrina; Wöstemeyer, Johannes; Hijri, Mohamed

2013-01-01

The fungal kingdom displays a fascinating diversity of sex-determination systems. Recent advances in genomics provide insights into the molecular mechanisms of sex, mating type determination, and evolution of sexual reproduction in many fungal species in both ancient and modern phylogenetic lineages. All major fungal groups have evolved sexual differentiation and recombination pathways. However, sexuality is unknown in arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota, an ecologically vital group of obligate plant root symbionts. AMF are commonly considered an ancient asexual lineage dating back to the Ordovician, approximately 460 M years ago. In this study, we used genomic and transcriptomic surveys of several AMF species to demonstrate the presence of conserved putative sex pheromone-sensing mitogen-activated protein (MAP) kinases, comparable to those described in Ascomycota and Basidiomycota. We also find genes for high mobility group (HMG) transcription factors, homologous to SexM and SexP genes in the Mucorales. The SexM genes show a remarkable sequence diversity among multiple copies in the genome, while only a single SexP sequence was detected in some isolates of Rhizophagus irregularis. In the Mucorales and Microsporidia, the sexM gene is flanked by genes for a triosephosphate transporter (TPT) and a RNA helicase, but we find no evidence for synteny in the vicinity of the Sex locus in AMF. Nonetheless, our results, together with previous observations on meiotic machinery, suggest that AMF could undergo a complete sexual reproduction cycle.

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier

PubMed Central

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2–188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 (Cryptococcus terricola) increased with successional distance, whereas that of OTU65 (Tolypocladium tundrense) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and NH4+–N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario. PMID:28649234

Ecological Succession Pattern of Fungal Community in Soil along a Retreating Glacier.

PubMed

Tian, Jianqing; Qiao, Yuchen; Wu, Bing; Chen, Huai; Li, Wei; Jiang, Na; Zhang, Xiaoling; Liu, Xingzhong

2017-01-01

Accelerated by global climate changing, retreating glaciers leave behind soil chronosequences of primary succession. Current knowledge of primary succession is mainly from studies of vegetation dynamics, whereas information about belowground microbes remains unclear. Here, we combined shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. We investigated fungal succession and community assembly via high-throughput sequencing along a well-established glacier forefront chronosequence that spans 2-188 years of deglaciation. Shannon diversity and evenness peaked at a distance of 370 m and declined afterwards. The response of fungal diversity to distance varied in different phyla. Basidiomycota Shannon diversity significantly decreased with distance, while the pattern of Rozellomycota Shannon diversity was unimodal. Abundance of most frequencies OTU2 ( Cryptococcus terricola ) increased with successional distance, whereas that of OTU65 ( Tolypocladium tundrense ) decreased. Based on null deviation analyses, composition of the fungal community was initially governed by deterministic processes strongly but later less deterministic processes. Our results revealed that distance, altitude, soil microbial biomass carbon, soil microbial biomass nitrogen and [Formula: see text]-N significantly correlated with fungal community composition along the chronosequence. These results suggest that the drivers of fungal community are dynamics in a glacier chronosequence, that may relate to fungal ecophysiological traits and adaptation in an evolving ecosystem. The information will provide understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession under different scales and scenario.

Recovery and phylogenetic diversity of culturable fungi associated with marine sponges Clathrina luteoculcitella and Holoxea sp. in the South China Sea.

PubMed

Ding, Bo; Yin, Ying; Zhang, Fengli; Li, Zhiyong

2011-08-01

Sponge-associated fungi represent an important source of marine natural products, but little is known about the fungal diversity and the relationship of sponge-fungal association, especially no research on the fungal diversity in the South China Sea sponge has been reported. In this study, a total of 111 cultivable fungi strains were isolated from two South China Sea sponges Clathrina luteoculcitella and Holoxea sp. using eight different media. Thirty-two independent representatives were selected for analysis of phylogenetic diversity according to ARDRA and morphological characteristics. The culturable fungal communities consisted of at least 17 genera within ten taxonomic orders of two phyla (nine orders of the phylum Ascomycota and one order of the phylum Basidiomycota) including some potential novel marine fungi. Particularly, eight genera of Apiospora, Botryosphaeria, Davidiella, Didymocrea, Lentomitella, Marasmius, Pestalotiopsis, and Rhizomucor were isolated from sponge for the first time. Sponge C. luteoculcitella has greater culturable fungal diversity than sponge Holoxea sp. Five genera of Aspergillus, Davidiella, Fusarium, Paecilomyces, and Penicillium were isolated from both sponges, while 12 genera of Apiospora, Botryosphaeria, Candida, Marasmius, Cladosporium, Didymocrea, Hypocrea, Lentomitella, Nigrospora, Pestalotiopsis, Rhizomucor, and Scopulariopsis were isolated from sponge C. luteoculcitella only. Order Eurotiales especially genera Penicillium, Aspergillus, and order Hypocreales represented the dominant culturable fungi in these two South China Sea sponges. Nigrospora oryzae strain PF18 isolated from sponge C. luteoculcitella showed a strong and broad spectrum antimicrobial activities suggesting the potential for antimicrobial compounds production.

Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jasrotia, Puja; Green, Stefan; Canion, Andy

2014-01-01

The objective of this study was to characterize fungal communities in a subsurface environment co-contaminated with uranium and nitrate at the watershed scale, and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution and diversity of fungi in subsurface groundwater samples were determined using quantitative and semi-quantitative molecular techniques, including quantitative PCR of eukaryotic SSU rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from subsurface. Our results demonstrate that subsurface fungalmore » communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH < 4.5) conditions. Fungal isolates recovered from subsurface sediments were shown to reduce nitrate to nitrous oxide, including cultures of the genus Coniochaeta that were detected in abundance in pyrosequence libraries of site groundwater samples. Denitrifying fungal isolates recovered from the site were classified, and found to be distributed broadly within the phylum Ascomycota, and within a single genus within the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.« less

Evidence for biological shaping of hair ice

NASA Astrophysics Data System (ADS)

Hofmann, D.; Preuss, G.; Mätzler, C.

2015-07-01

An unusual ice type, called hair ice, grows on the surface of dead wood of broad-leaf trees at temperatures slightly below 0 °C. We describe this phenomenon and present physical, chemical, and biological investigations to gain insight in the properties and processes related to hair ice. Tests revealed that the biological activity of a winter-active fungus is required in the wood for enabling the growth of hair ice. We confirmed the fungus hypothesis originally suggested by Wegener (1918) by reproducing hair ice on wood samples. Treatment by heat and fungicide suppresses the formation of hair ice. Fruiting bodies of Asco- and Basidiomycota are identified on hair-ice-carrying wood. One species, Exidiopsis effusa (Ee), was present on all investigated samples. Both hair-ice-producing wood samples and those with killed fungus show essentially the same temperature variation, indicating that the heat produced by fungal metabolism is very small, that the freezing rate is not influenced by the fungus activity, and that ice segregation is the common mechanism of ice growth on the wood surface. The fungus plays the role of shaping the ice hairs and preventing them from recrystallisation. Melted hair ice indicates the presence of organic matter. Chemical analyses show a complex mixture of several thousand CHO(N,S) compounds similar to fulvic acids in dissolved organic matter (DOM). The evaluation reveals decomposed lignin as being the main constituent. Further work is needed to clarify its role in hair-ice growth and to identify the recrystallisation inhibitor.

Evidence for biological shaping of hair ice

NASA Astrophysics Data System (ADS)

Hofmann, D.; Preuss, G.; Mätzler, C.

2015-04-01

An unusual ice type, called hair ice, grows on the surface of dead wood of broad-leaf trees at temperatures slightly below 0 °C. We describe this phenomenon and present physical, chemical, and biological investigations to gain insight in the properties and processes related to hair ice. Tests revealed that the biological activity of a winter-active fungus is required in the wood for enabling the growth of hair ice. We confirmed the fungus hypothesis originally suggested by Wegener (1918) by reproducing hair ice on wood samples. Treatment by heat and fungicide, respectively, suppresses the formation of hair ice. Fruiting bodies of Asco- and Basidiomycota are identified on hair-ice carrying wood. One species, Exidiopsis effusa (Ee), has been present on all investigated samples. Both hair-ice producing wood samples and those with killed fungus show essentially the same temperature variation, indicating that the heat produced by fungal metabolism is very small, that the freezing rate is not influenced by the fungus activity and that ice segregation is the common mechanism of ice growth at the wood surface. The fungus plays the role of shaping the ice hairs and to prevent them from recrystallisation. Melted hair ice indicates the presence of organic matter. Chemical analyses show a complex mixture of several thousand CHO(N,S)-compounds similar to fulvic acids in dissolved organic matter (DOM). The evaluation reveals decomposed lignin as the main constituent. Further work is needed to clarify its role in hair-ice growth and to identify the recrystallisation inhibitor.

Fungi that Infect Humans.

PubMed

Köhler, Julia R; Hube, Bernhard; Puccia, Rosana; Casadevall, Arturo; Perfect, John R

2017-06-01

Fungi must meet four criteria to infect humans: growth at human body temperatures, circumvention or penetration of surface barriers, lysis and absorption of tissue, and resistance to immune defenses, including elevated body temperatures. Morphogenesis between small round, detachable cells and long, connected cells is the mechanism by which fungi solve problems of locomotion around or through host barriers. Secretion of lytic enzymes, and uptake systems for the released nutrients, are necessary if a fungus is to nutritionally utilize human tissue. Last, the potent human immune system evolved in the interaction with potential fungal pathogens, so few fungi meet all four conditions for a healthy human host. Paradoxically, the advances of modern medicine have made millions of people newly susceptible to fungal infections by disrupting immune defenses. This article explores how different members of four fungal phyla use different strategies to fulfill the four criteria to infect humans: the Entomophthorales, the Mucorales, the Ascomycota, and the Basidiomycota. Unique traits confer human pathogenic potential on various important members of these phyla: pathogenic Onygenales comprising thermal dimorphs such as Histoplasma and Coccidioides ; the Cryptococcus spp. that infect immunocompromised as well as healthy humans; and important pathogens of immunocompromised patients- Candida , Pneumocystis , and Aspergillus spp. Also discussed are agents of neglected tropical diseases important in global health such as mycetoma and paracoccidiomycosis and common pathogens rarely implicated in serious illness such as dermatophytes. Commensalism is considered, as well as parasitism, in shaping genomes and physiological systems of hosts and fungi during evolution.

Ligninolytic Activity at 0 °C of Fungi on Oak Leaves Under Snow Cover in a Mixed Forest in Japan.

PubMed

Miyamoto, Toshizumi; Koda, Keiichi; Kawaguchi, Arata; Uraki, Yasumitsu

2017-08-01

Despite the importance of litter decomposition under snow cover in boreal forests and tundra, very little is known regarding the characteristics and functions of litter-decomposing fungi adapted to the cold climate. We investigated the decomposition of oak leaves in a heavy snowfall forest region of Japan. The rate of litter weight loss reached 26.5% during the snow cover period for 7 months and accounted for 64.6% of the annual loss (41.1%). Although no statistically significant lignin loss was detected, decolourization portions of oak leaf litter, which was attributable to the activities of ligninolytic fungi, were observed during snow cover period. This suggests that fungi involved in litter decomposition can produce extracellular enzymes to degrade lignin that remain active at 0 °C. Fungi were isolated from oak leaves collected from the forest floor under the snow layer. One hundred and sixty-six strains were isolated and classified into 33 operational taxonomic units (OTUs) based on culture characteristics and nuclear rDNA internal transcribed spacer (ITS) region sequences. To test the ability to degrade lignin, the production of extracellular phenoloxidases by isolates was quantified at 0 °C. Ten OTUs (9 Ascomycota and 1 Basidiomycota) of fungi exhibited mycelial growth and ligninolytic activity. These results suggested that some litter-decomposing fungi that had the potential to degrade lignin at 0 °C significantly contribute to litter decomposition under snow cover.

Defects in Mitochondrial and Peroxisomal β-Oxidation Influence Virulence in the Maize Pathogen Ustilago maydis

PubMed Central

Kretschmer, Matthias; Klose, Jana

2012-01-01

An understanding of metabolic adaptation during the colonization of plants by phytopathogenic fungi is critical for developing strategies to protect crops. Lipids are abundant in plant tissues, and fungal phytopathogens in the phylum basidiomycota possess both peroxisomal and mitochondrial β-oxidation pathways to utilize this potential carbon source. Previously, we demonstrated a role for the peroxisomal β-oxidation enzyme Mfe2 in the filamentous growth, virulence, and sporulation of the maize pathogen Ustilago maydis. However, mfe2 mutants still caused disease symptoms, thus prompting a more detailed investigation of β-oxidation. We now demonstrate that a defect in the had1 gene encoding hydroxyacyl coenzyme A dehydrogenase for mitochondrial β-oxidation also influences virulence, although its paralog, had2, makes only a minor contribution. Additionally, we identified a gene encoding a polypeptide with similarity to the C terminus of Mfe2 and designated it Mfe2b; this gene makes a contribution to virulence only in the background of an mfe2Δ mutant. We also show that short-chain fatty acids induce cell death in U. maydis and that a block in β-oxidation leads to toxicity, likely because of the accumulation of toxic intermediates. Overall, this study reveals that β-oxidation has a complex influence on the formation of disease symptoms by U. maydis that includes potential metabolic contributions to proliferation in planta and an effect on virulence-related morphogenesis. PMID:22707484

Intercropped Silviculture Systems, a Key to Achieving Soil Fungal Community Management in Eucalyptus Plantations

PubMed Central

Rachid, Caio T. C. C.; Balieiro, Fabiano C.; Fonseca, Eduardo S.; Peixoto, Raquel Silva; Chaer, Guilherme M.; Tiedje, James M.; Rosado, Alexandre S.

2015-01-01

Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that. PMID:25706388

Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Yong; Wang, Guang-Hua; Xu, Xin-Ya; Nong, Xu-Hua; Wang, Jie; Amin, Muhammad; Qi, Shu-Hua

2016-10-01

The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

PubMed Central

Jasrotia, Puja; Green, Stefan J.; Canion, Andy; Overholt, Will A.; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2014-01-01

The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions. PMID:24389927

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

DOE PAGES

Gacura, Matthew D.; Sprockett, Daniel D.; Heidenreich, Bess; ...

2016-02-17

Here, fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senescedmore » tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.« less

Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China

PubMed Central

Tian, Lei; Ma, Lina; Luo, Shasha; Zhang, Jianfeng; Li, Xiujun

2017-01-01

Peatlands in the Sanjiang Plain could be more vulnerable to global warming because they are located at the southernmost boundary of northern peatlands. Unlike bacteria, fungi are often overlooked, even though they play important roles in substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding of fungal community structure and diversity in the peatlands. In this study, high-throughput Illumina sequencing was used to study the fungal communities in three fens in the Sanjiang Plain, located at the southern edge of northern peatlands. Peat soil was collected from the three fens which developed during different periods. A total of 463,198 fungal ITS sequences were obtained, and these sequences were classified into at least six phyla, 21 classes, more than 60 orders and over 200 genera. The fungal community structures were distinct in the three sites and were dominated by Ascomycota and Basidiomycota. However, there were no significant differences between these three fens in any α-diversity index (p > 0.05). Soil age and the carbon (C) accumulation rate, as well as total carbon (TC), total nitrogen (TN), C/N ratio, and bulk density were found to be closely related to the abundance of several dominant fungal taxa. We captured a rich fungal community and confirmed that the dominant taxa were those which were frequently detected in other northern peatlands. Soil age and the C accumulation rate were found to play important roles in shaping the fungal community structure. PMID:29236715

Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

PubMed

Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

2015-07-01

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

NASA Astrophysics Data System (ADS)

Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Fröhlich-Nowoisky, J.; Grothe, H.

2013-12-01

Fungal spores are ubiquitous biological aerosols, which are considered to act as ice nuclei. In this study the ice nucleation (IN) activity of spores harvested from 29 fungal strains belonging to 21 different species was tested in the immersion freezing mode by microscopic observation of water-in-oil emulsions. Spores of 8 of these strains were also investigated in a microdroplet freezing array instrument. The focus was laid on species of economical, ecological or sanitary significance. Besides common molds (Ascomycota), some representatives of the widespread group of mushrooms (Basidiomycota) were also investigated. Fusarium avenaceum was the only sample showing IN activity at relatively high temperatures (about 264 K), while the other investigated fungal spores showed no freezing above 248 K. Many of the samples indeed froze at homogeneous ice nucleation temperatures (about 237 K). In combination with other studies, this suggests that only a limited number of species may act as atmospheric ice nuclei. This would be analogous to what is already known for the bacterial ice nuclei. Apart from that, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during their cultivation. This was in order to test if the exposure to a cold environment encourages the expression of ice nuclei during growth as a way of adaptation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing.

PubMed

He, Liming; Liu, Fang; Karuppiah, Valliappan; Ren, Yi; Li, Zhiyong

2014-05-01

To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sponge holobionts were probably different. In order to test this hypothesis, the communities of eukaryota associated with 11 species of South China Sea sponges were compared with the V4 region of 18S ribosomal ribonucleic acid gene using 454 pyrosequencing. Consequently, 135 and 721 unique operational taxonomic units (OTUs) of fungi and protists were obtained at 97 % sequence similarity, respectively. These sequences were assigned to 2 phyla of fungi (Ascomycota and Basidiomycota) and 9 phyla of protists including 5 algal phyla (Chlorophyta, Haptophyta, Streptophyta, Rhodophyta, and Stramenopiles) and 4 protozoal phyla (Alveolata, Cercozoa, Haplosporidia, and Radiolaria) including 47 orders (12 fungi, 35 protists). Entorrhizales of fungi and 18 orders of protists were detected in marine sponges for the first time. Particularly, Tilletiales of fungi and Chlorocystidales of protists were detected for the first time in marine habitats. Though Ascomycota, Alveolata, and Radiolaria were detected in all the 11 sponge species, sponge holobionts have different fungi and protistan communities according to OTU comparison and principal component analysis at the order level. This study provided the first insights into the fungal and protistan communities associated with different marine sponge holobionts using pyrosequencing, thus further extending the knowledge on sponge-associated eukaryotic diversity.

Fungal microbiota dysbiosis in IBD

PubMed Central

Sokol, Harry; Leducq, Valentin; Aschard, Hugues; Pham, Hang-Phuong; Jegou, Sarah; Landman, Cecilia; Cohen, David; Liguori, Giuseppina; Bourrier, Anne; Nion-Larmurier, Isabelle; Cosnes, Jacques; Seksik, Philippe; Langella, Philippe; Skurnik, David; Richard, Mathias L; Beaugerie, Laurent

2017-01-01

Objective The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. Design Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. Results We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. Conclusions Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis. PMID:26843508

Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations.

PubMed

Rachid, Caio T C C; Balieiro, Fabiano C; Fonseca, Eduardo S; Peixoto, Raquel Silva; Chaer, Guilherme M; Tiedje, James M; Rosado, Alexandre S

2015-01-01

Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments: monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.

Extraordinary proliferation of microorganisms in aposymbiotic pea aphids, Acyrthosiphon pisum.

PubMed

Nakabachi, Atsushi; Ishikawa, Hajime; Kudo, Toshiaki

2003-03-01

Aposymbiotic pea aphids, which were deprived of their intracellular symbiotic bacterium, Buchnera, exhibit growth retardation and no fecundity. High performance liquid chromatographic (HPLC) analysis revealed that these aposymbiotic aphids, when reared on broad bean plants, accumulated a large amount of histamine. To assess the possibility of extraordinary proliferation of microorganisms other than Buchnera, we enumerated eubacteria and fungi in aphids using the real-time quantitative PCR method that targets genes encoding small-subunit rRNAs. The result showed that these microorganisms were extremely abundant in the aposymbiotic aphids reared on plants. Microbial communities in aposymbiotic aphids were further profiled by phylogenetic analysis of small-subunit rDNAs. Of 172 nonchimeric sequences of fungal 18S rDNAs, 138 (80.2%) belonged to the phylum Ascomycota. Among them, 21 clustered within a monophyletic group consisting of insect-pathogenic fungi and yeast-like symbionts of homopteran insects. Thirty-one (18.0%), two (1.2%), and one (0.6%) clones were clustered within the Basidiomycota, Zygomycota, and Oomycota, respectively. Of 167 nonchimeric sequences of eubacterial 16S rDNAs, 84 (50.3%) belonged to the gamma-subdivision of Proteobacteria to which most primary endosymbionts of insects and prolific histamine producers belong. Forty (24.0%), 25 (15.0%), 10 (6.0%), and five (3.0%) clones were clustered within alpha-Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB) group, Actinobacteria, and beta-Proteobacteria, respectively. Three had no phylogenetic association with known taxonomic divisions. None of the sequences studied in this study coincided exactly with those deposited in GenBank.

Intercropped silviculture systems, a key to achieving soil fungal community management in eucalyptus plantations

DOE PAGES

Caio T.C.C. Rachid; Balieiro, Fabiano C.; Fonseca, Eduardo S.; ...

2015-02-23

Fungi are ubiquitous and important contributors to soil nutrient cycling, playing a vital role in C, N and P turnover, with many fungi having direct beneficial relationships with plants. However, the factors that modulate the soil fungal community are poorly understood. We studied the degree to which the composition of tree species affected the soil fungal community structure and diversity by pyrosequencing the 28S rRNA gene in soil DNA. We were also interested in whether intercropping (mixed plantation of two plant species) could be used to select fungal species. More than 50,000 high quality sequences were analyzed from three treatments:more » monoculture of Eucalyptus; monoculture of Acacia mangium; and a mixed plantation with both species sampled 2 and 3 years after planting. We found that the plant type had a major effect on the soil fungal community structure, with 75% of the sequences from the Eucalyptus soil belonging to Basidiomycota and 19% to Ascomycota, and the Acacia soil having a sequence distribution of 28% and 62%, respectively. The intercropping of Acacia mangium in a Eucalyptus plantation significantly increased the number of fungal genera and the diversity indices and introduced or increased the frequency of several genera that were not found in the monoculture cultivation samples. Our results suggest that management of soil fungi is possible by manipulating the composition of the plant community, and intercropped systems can be a means to achieve that.« less

Crystal Structure and Computational Characterization of the Lytic Polysaccharide Monooxygenase GH61D from the Basidiomycota Fungus Phanerochaete chrysosporium*

PubMed Central

Wu, Miao; Beckham, Gregg T.; Larsson, Anna M.; Ishida, Takuya; Kim, Seonah; Payne, Christina M.; Himmel, Michael E.; Crowley, Michael F.; Horn, Svein J.; Westereng, Bjørge; Igarashi, Kiyohiko; Samejima, Masahiro; Ståhlberg, Jerry; Eijsink, Vincent G. H.; Sandgren, Mats

2013-01-01

Carbohydrate structures are modified and degraded in the biosphere by a myriad of mostly hydrolytic enzymes. Recently, lytic polysaccharide mono-oxygenases (LPMOs) were discovered as a new class of enzymes for cleavage of recalcitrant polysaccharides that instead employ an oxidative mechanism. LPMOs employ copper as the catalytic metal and are dependent on oxygen and reducing agents for activity. LPMOs are found in many fungi and bacteria, but to date no basidiomycete LPMO has been structurally characterized. Here we present the three-dimensional crystal structure of the basidiomycete Phanerochaete chrysosporium GH61D LPMO, and, for the first time, measure the product distribution of LPMO action on a lignocellulosic substrate. The structure reveals a copper-bound active site common to LPMOs, a collection of aromatic and polar residues near the binding surface that may be responsible for regio-selectivity, and substantial differences in loop structures near the binding face compared with other LPMO structures. The activity assays indicate that this LPMO primarily produces aldonic acids. Last, molecular simulations reveal conformational changes, including the binding of several regions to the cellulose surface, leading to alignment of three tyrosine residues on the binding face of the enzyme with individual cellulose chains, similar to what has been observed for family 1 carbohydrate-binding modules. A calculated potential energy surface for surface translation indicates that P. chrysosporium GH61D exhibits energy wells whose spacing seems adapted to the spacing of cellobiose units along a cellulose chain. PMID:23525113

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition.

PubMed

Li, Wei; Wang, Mengmeng; Bian, Xiaomeng; Guo, Jiajia; Cai, Lei

2016-01-01

The intertidal region is one of the most dynamic environments in the biosphere, which potentially supports vast biodiversity. Fungi have been found to play important roles in marine ecosystems, e.g., as parasites or symbionts of plants and animals, and as decomposers of organic materials. The fungal diversity in intertidal region, however, remains poorly understood. In this study, sediment samples from various intertidal habitats of Chinese seas were collected and investigated for determination of fungal community and spatial distribution. Through ribosomal RNA internal transcribed spacer-2 (ITS2) metabarcoding, a high-level fungal diversity was revealed, as represented by 6,013 OTUs that spanned six phyla, 23 classes, 84 orders and 526 genera. The presence of typical decomposers (e.g., Corollospora in Ascomycota and Lepiota in Basidiomycota) and pathogens (e.g., Olpidium in Chytriomycota, Actinomucor in Zygomycota and unidentified Rozellomycota spp.), and even mycorrhizal fungi (e.g., Glomus in Glomeromycota) indicated a complicated origin of intertidal fungi. Interestingly, a small proportion of sequences were classified to obligate marine fungi (e.g., Corollospora, Lignincola, Remispora, Sigmoidea ). Our data also showed that the East China Sea significantly differed from other regions in terms of species richness and community composition, indicating a profound effect of the huge discharge of the Yangtze River. No significant difference in fungal communities was detected, however, among habitat types (i.e., aquaculture, dock, plant, river mouth and tourism). These observations raise further questions on adaptation of these members to environments and the ecological functions they probably perform.

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment

PubMed Central

Siles, José A.; Rachid, Caio T. C. C.; Sampedro, Inmaculada; García-Romera, Inmaculada; Tiedje, James M.

2014-01-01

The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR), a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR) and C. floccosa-transformed DOR (CORDOR) on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR. PMID:25058610

Fungal monitoring of the indoor air of the Museo de La Plata Herbarium, Argentina.

PubMed

Mallo, Andrea C; Elíades, Lorena A; Nitiu, Daniela S; Saparrat, Mario C N

Biological agents, such as fungal spores in the air in places where scientific collections are stored, can attack and deteriorate them. The aim of this study was to gather information on the indoor air quality of the Herbarium of Vascular Plants of the Museo de Ciencias Naturales de La Plata, Argentina, in relation to fungal propagules and inert particles. This study was made using a volumetric system and two complementary sampling methods: (1) a non-viable method for direct evaluation, and (2) a viable method by culture for viable fungal propagules. The non-viable method led to ten spore morphotypes being found from related fungal sources. A total of 4401.88spores/m 3 and 32135.18 inert suspended particles/m 3 were recorded. The viable method led to the finding of nine fungal taxa as viable spores that mostly belonged to anamorphic forms of Ascomycota, although the pigmented yeast Rhodotorula F.C. Harrison (Basidiomycota) was also found. A total count of 40,500fungal CFU/m 3 air was estimated for all the sites sampled. Both the non-viable and viable sampling methods were necessary to monitor the bio-aerosol load in the La Plata Herbarium. The indoor air of this institution seems to be reasonably adequate for the conservation of vascular plants due to the low indoor/outdoor index, low concentrations of air spores, and/or lack of indicators of moisture problems. Copyright © 2016 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

PubMed

Yordanova, Martina M; Wu, Cheng; Andreev, Dmitry E; Sachs, Matthew S; Atkins, John F

2015-07-17

The protein antizyme is a negative regulator of cellular polyamine concentrations from yeast to mammals. Synthesis of functional antizyme requires programmed +1 ribosomal frameshifting at the 3' end of the first of two partially overlapping ORFs. The frameshift is the sensor and effector in an autoregulatory circuit. Except for Saccharomyces cerevisiae antizyme mRNA, the frameshift site alone only supports low levels of frameshifting. The high levels usually observed depend on the presence of cis-acting stimulatory elements located 5' and 3' of the frameshift site. Antizyme genes from different evolutionary branches have evolved different stimulatory elements. Prior and new multiple alignments of fungal antizyme mRNA sequences from the Agaricomycetes class of Basidiomycota show a distinct pattern of conservation 5' of the frameshift site consistent with a function at the amino acid level. As shown here when tested in Schizosaccharomyces pombe and mammalian HEK293T cells, the 5' part of this conserved sequence acts at the nascent peptide level to stimulate the frameshifting, without involving stalling detectable by toe-printing. However, the peptide is only part of the signal. The 3' part of the stimulator functions largely independently and acts at least mostly at the nucleotide level. When polyamine levels were varied, the stimulatory effect was seen to be especially responsive in the endogenous polyamine concentration range, and this effect may be more general. A conserved RNA secondary structure 3' of the frameshift site has weaker stimulatory and polyamine sensitizing effects on frameshifting. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterization of fungal spores in ambient particulate matter: A study from the Himalayan region

NASA Astrophysics Data System (ADS)

Kumar, Ajay; Attri, Arun K.

2016-10-01

Fungal spores as a constituent of ambient particulate matter (PM) is of concern; they not only display the physical traits of a particle, but are also potential allergens and health risk. An investigation over fourteen month was undertaken at a rural site located in the Western Himalayan region, to evaluate the PM associated fungal spores' concentration and diversity. The season-wise change in the fungal spores concentration in the Coarse Particulate Matter (CPM) fraction (aerodynamic diameter > 10 μm) varied from 500 to 3899 spores m-3. Their average concentration over 14 months was 1517 spores m-3. Significant diversity of fungal spores in the CPM samples was observed; 27 individual genera of fungal spores were identified, of which many were known allergens. Presence of Ascomycota and Basidiomycota fungal spores was dominant in the samples; ∼20% of the spores were un-characterized. The season-wise variability in fungal spores showed a statistically significant high correlation with CPM load. Maximum number concentration of the spores in CPM was recorded in the summer, while minimum in the winter. The high diversity of spores occurred during monsoon and post monsoon months. The meteorological factors played an important role in the fungal spores' distribution profile. The temporal profile of the spores showed significant correlation with the ambient temperature (T), relative humidity (RH), wind speed (WS) and planetary boundary layer (PBL) height. Strong correlation of WS with fungal spores and CPM, and wind back trajectories suggest that re-suspension and wind assisted transport of PM contributes to ambient CPM associated fungal spores.

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition

PubMed Central

Li, Wei; Wang, Mengmeng; Bian, Xiaomeng; Guo, Jiajia; Cai, Lei

2016-01-01

The intertidal region is one of the most dynamic environments in the biosphere, which potentially supports vast biodiversity. Fungi have been found to play important roles in marine ecosystems, e.g., as parasites or symbionts of plants and animals, and as decomposers of organic materials. The fungal diversity in intertidal region, however, remains poorly understood. In this study, sediment samples from various intertidal habitats of Chinese seas were collected and investigated for determination of fungal community and spatial distribution. Through ribosomal RNA internal transcribed spacer-2 (ITS2) metabarcoding, a high-level fungal diversity was revealed, as represented by 6,013 OTUs that spanned six phyla, 23 classes, 84 orders and 526 genera. The presence of typical decomposers (e.g., Corollospora in Ascomycota and Lepiota in Basidiomycota) and pathogens (e.g., Olpidium in Chytriomycota, Actinomucor in Zygomycota and unidentified Rozellomycota spp.), and even mycorrhizal fungi (e.g., Glomus in Glomeromycota) indicated a complicated origin of intertidal fungi. Interestingly, a small proportion of sequences were classified to obligate marine fungi (e.g., Corollospora, Lignincola, Remispora, Sigmoidea). Our data also showed that the East China Sea significantly differed from other regions in terms of species richness and community composition, indicating a profound effect of the huge discharge of the Yangtze River. No significant difference in fungal communities was detected, however, among habitat types (i.e., aquaculture, dock, plant, river mouth and tourism). These observations raise further questions on adaptation of these members to environments and the ecological functions they probably perform. PMID:28066402

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes▿ †

PubMed Central

Hoffman, Michele T.; Arnold, A. Elizabeth

2010-01-01

Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the Proteobacteria, but a small number of Bacillaceae also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur. PMID:20435775

Characterizing Aeroallergens by Infrared Spectroscopy of Fungal Spores and Pollen

PubMed Central

Zimmermann, Boris; Tkalčec, Zdenko; Mešić, Armin; Kohler, Achim

2015-01-01

Background Fungal spores and plant pollen cause respiratory diseases in susceptible individuals, such as asthma, allergic rhinitis and hypersensitivity pneumonitis. Aeroallergen monitoring networks are an important part of treatment strategies, but unfortunately traditional analysis is time consuming and expensive. We have explored the use of infrared spectroscopy of pollen and spores for an inexpensive and rapid characterization of aeroallergens. Methodology The study is based on measurement of spore and pollen samples by single reflectance attenuated total reflectance Fourier transform infrared spectroscopy (SR-ATR FTIR). The experimental set includes 71 spore (Basidiomycota) and 121 pollen (Pinales, Fagales and Poales) samples. Along with fresh basidiospores, the study has been conducted on the archived samples collected within the last 50 years. Results The spectroscopic-based methodology enables clear spectral differentiation between pollen and spores, as well as the separation of confamiliar and congeneric species. In addition, the analysis of the scattering signals inherent in the infrared spectra indicates that the FTIR methodology offers indirect estimation of morphology of pollen and spores. The analysis of fresh and archived spores shows that chemical composition of spores is well preserved even after decades of storage, including the characteristic taxonomy-related signals. Therefore, biochemical analysis of fungal spores by FTIR could provide economical, reliable and timely methodologies for improving fungal taxonomy, as well as for fungal identification and monitoring. This proof of principle study shows the potential for using FTIR as a rapid tool in aeroallergen studies. In addition, the presented method is ready to be immediately implemented in biological and ecological studies for direct measurement of pollen and spores from flowers and sporocarps. PMID:25867755

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes

PubMed Central

Mali, Tuulia; Kuuskeri, Jaana; Shah, Firoz

2017-01-01

Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter. PMID:28953947

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Robert; Salamov, Asaf; Brown, Daren W.

Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rotmore » classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.« less

Analysis of the influence of living environment and age on vaginal fungal microbiome in giant pandas (Ailuropoda melanoleuca) by high throughput sequencing.

PubMed

Chen, Danyu; Li, Caiwu; Feng, Lan; Zhang, Zhizhong; Zhang, Heming; Cheng, Guangyang; Li, Desheng; Zhang, Guiquan; Wang, Hongning; Chen, Yanxi; Feng, Mingfu; Wang, Chengdong; Wu, Honglin; Deng, Linhua; Ming, He; Yang, Xin

2018-02-01

A recent study has described the normal vaginal bacterial community in giant pandas, but there is a lack of knowledge of the fungal community residing in the vagina of giant pandas. In order to comprehensively understand the vaginal fungal microbial diversity and abundance in giant pandas, high throughput sequencing was used to analyse the ITS1 region, based on thirteen samples taken from the pandas' vaginas, which were grouped by sampling points and age. The results showed that the most abundant phyla were Basidiomycota (73.37%), followed by Ascomycota (20.04%), Zygomycota (5.23%), Glomeromycota (0.014%) and Chytridiomycota (0.006%). At the genus level, Guehomyces (37.92%) was the most abundant, followed by Cladosporium (9.072%), Trichosporon (6.2%) and Mucor (4.97%). Furthermore, Candida only accounted for a low percentage of the vaginal fungal community. With the saturation of rarefaction curves and fungal diversity indices, the samples from Dujiangyan and Chungking Safari Park (DC group) showed a higher fungal species richness and diversity than other living environments. Shannon diversity indices showed significant difference between group WL (Wolong nature reserve) and DC (P < .05). Additionally, a higher diversity was found in ten to fifteen years old (Group 2) than other groups. Group 2 and Group 3 displayed significant differences in the diversities of their vaginal fungal communities (P < .05). These data that has been collected from this research will be helpful for further study to improve the reproductive status of giant pandas. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

Fungal diversity from deep marine subsurface sediments (IODP 317, Canterbury Basin, New Zealand)

NASA Astrophysics Data System (ADS)

Redou, V.; Arzur, D.; Burgaud, G.; Barbier, G.

2012-12-01

Recent years have seen a growing interest regarding micro-eukaryotic communities in extreme environments as a third microbial domain after Bacteria and Archaea. However, knowledge is still scarce and the diversity of micro-eukaryotes in such environments remains hidden and their ecological role unknown. Our research program is based on the deep sedimentary layers of the Canterbury Basin in New Zealand (IODP 317) from the subsurface to the record depth of 1884 meters below seafloor. The objectives of our study are (i) to assess the genetic diversity of fungi in deep-sea sediments and (ii) identify the functional part in order to better understand the origin and the ecological role of fungal communities in this extreme ecosystem. Fingerprinting-based methods using capillary electrophoresis single-strand conformation polymorphism and denaturing high-performance liquid chromatography were used as a first step to raise our objectives. Molecular fungal diversity was assessed using amplification of ITS1 (Internal Transcribed Spacer 1) as a biomarker on 11 samples sediments from 3.76 to 1884 meters below seafloor. Fungal molecular signatures were detected throughout the sediment core. The phyla Ascomycota and Basidiomycota were revealed with DNA as well as cDNA. Most of the phylotypes are affiliated to environmental sequences and some to common fungal cultured species. The discovery of a present and metabolically active fungal component in this unique ecosystem allows some interesting first hypotheses that will be further combined to culture-based methods and deeper molecular methods (454 pyrosequencing) to highlight essential informations regarding physiology and ecological role of fungal communities in deep marine sediments.

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

PubMed Central

Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

2015-01-01

The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions. PMID:26132745

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea).

PubMed

Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

2015-01-01

The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions.

Microbial profiling of South African acid mine water samples using next generation sequencing platform.

PubMed

Kamika, I; Azizi, S; Tekere, M

2016-07-01

This study monitored changes in bacterial and fungal structure in a mine water in a monthly basis over 4 months. Over the 4-month study period, mine water samples contained more bacteria (91.06 %) compared to fungi (8.94 %). For bacteria, mine water samples were dominated by Proteobacteria (39.14 to 65.06 %) followed by Firmicutes (26.34 to 28.9 %) in summer, and Cyanobacteria (27.05 %) in winter. In the collected samples, 18 % of bacteria could not be assigned to a phylum and remained unclassified suggesting hitherto vast untapped microbial diversity especially during winter. The fungal domain was the sole eukaryotic microorganism found in the mine water samples with unclassified fungi (68.2 to 91 %) as the predominant group, followed by Basidiomycota (6.9 to 27.8 %). The time of collection, which was linked to the weather, had higher impact on bacterial community than fungal community. The bacterial operational taxonomic units (OTUs) ranged from 865 to 4052 over the 4-month sampling period, while fungal OTUs varied from 73 to 249. The diversity indices suggested that the bacterial community inhabiting the mine water samples were more diverse than the fungal community. The canonical correspondence analysis (CCA) results highlighted that the bacterial community variance had the strongest relationship with water temperature, conductivity, pH, and dissolved oxygen (DO) content, as compared to fungi and water characteristics, had the greatest contribution to both bacterial and fungal community variance. The results provided the relationships between microbial community and environmental variables in the studied mining sites.

The Impact of Selective-Logging and Forest Clearance for Oil Palm on Fungal Communities in Borneo

PubMed Central

Kerfahi, Dorsaf; Tripathi, Binu M.; Lee, Junghoon; Edwards, David P.; Adams, Jonathan M.

2014-01-01

Tropical forests are being rapidly altered by logging, and cleared for agriculture. Understanding the effects of these land use changes on soil fungi, which play vital roles in the soil ecosystem functioning and services, is a major conservation frontier. Using 454-pyrosequencing of the ITS1 region of extracted soil DNA, we compared communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, and areas cleared for oil palm, in Sabah, Malaysia. Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure. Such wholesale changes in fungal communities might impact the long-term sustainability of oil palm agriculture. Logging also has more subtle long term effects, on relative abundance of EcM fungi, which might affect tree recruitment and nutrient cycling. However, in general the logged forest retains most of the diversity and community composition of unlogged forest. PMID:25405609

Neuroprotective effects of Ganoderma lucidum polysaccharides against traumatic spinal cord injury in rats.

PubMed

Gokce, Emre Cemal; Kahveci, Ramazan; Atanur, Osman Malik; Gürer, Bora; Aksoy, Nurkan; Gokce, Aysun; Sargon, Mustafa Fevzi; Cemil, Berker; Erdogan, Bulent; Kahveci, Ozan

2015-11-01

Ganoderma lucidum (G. lucidum) is a mushroom belonging to the polyporaceae family of Basidiomycota and has widely been used as a traditional medicine for thousands of years. G. lucidum has never been studied in traumatic spinal cord injury. The aim of this study is to investigate whether G. lucidum polysaccharides (GLPS) can protect the spinal cord after experimental spinal cord injury. Rats were randomized into five groups of eight animals each: control, sham, trauma, GLPS, and methylprednisolone. In the control group, no surgical intervention was performed. In the sham group, only a laminectomy was performed. In all the other groups, the spinal cord trauma model was created by the occlusion of the spinal cord with an aneurysm clip. In the spinal cord tissue, caspase-3 activity, tumour necrosis factor-alpha levels, myeloperoxidase activity, malondialdehyde levels, nitric oxide levels, and superoxide dismutase levels were analysed. Histopathological and ultrastructural evaluations were also performed. Neurological evaluation was performed using the Basso, Beattie, and Bresnahan locomotor scale and the inclined-plane test. After traumatic spinal cord injury, increases in caspase-3 activity, tumour necrosis factor-alpha levels, myeloperoxidase activity, malondialdehyde levels, and nitric oxide levels were detected. After the administration of GLPS, decreases were observed in tissue caspase-3 activity, tumour necrosis factor-alpha levels, myeloperoxidase activity, malondialdehyde levels, and nitric oxide levels. Furthermore, GLPS treatment showed improved results in histopathological scores, ultrastructural scores, and functional tests. Biochemical, histopathological, and ultrastructural analyses and functional tests reveal that GLPS exhibits meaningful neuroprotective effects against spinal cord injury. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rust fungi on Annonaceae II: the genus Dasyspora Berk. & M.A. Curtis.

PubMed

Beenken, Ludwig; Zoller, Stefan; Berndt, Reinhard

2012-01-01

Dasyspora gregaria, the single species of the allegedly monotypic rust genus Dasyspora (Basidiomycota, Pucciniales), was investigated by light microscopy and DNA sequencing (ITS1-5.8S-ITS2 region, partial LSU and SSU of the nuclear rDNA, mt cytochrome oxidase subunit 3). Both methods indicated that D. gregaria is not a single species but can be split in 11 distinct taxa, each of which appear confined to a single Xylopia species (Annonaceae) host. Herein nine of these are described as new. Both the phylogenetic analyses and morphology show that the species are grouped into two main clades designated Dasyspora gregaria and D. winteri. The first comprises D. gregaria, the type species of the genus, which is restricted to X. cayennensis, two new species on X. aromatica, D. segregaria from northern South America and D. echinata from Brazil. The second clade is formed by D. winteri, recombined from Puccinia winteri on X. sericea, and the new species D. amazonica on X. amazonica, D. emarginatae on X. emarginata, D. frutescentis on X. frutescens, D. ferrugineae on X. frutescens var. ferruginea, D. guianensis on X. benthamii, D. mesoamericana on X. frutescens, and D. nitidae on X. nitida. Dasyspora frutescentis and D. mesoamericana were not clearly distinguishable by their morphology and host associations but differed from another in their sequences and geographic distributions. They are considered cryptic species. An identification key and the distributions are given for all recognized species. Along with molecular data we discuss the systematic position of Dasyspora in the Pucciniales.

The impact of selective-logging and forest clearance for oil palm on fungal communities in Borneo.

PubMed

Kerfahi, Dorsaf; Tripathi, Binu M; Lee, Junghoon; Edwards, David P; Adams, Jonathan M

2014-01-01

Tropical forests are being rapidly altered by logging, and cleared for agriculture. Understanding the effects of these land use changes on soil fungi, which play vital roles in the soil ecosystem functioning and services, is a major conservation frontier. Using 454-pyrosequencing of the ITS1 region of extracted soil DNA, we compared communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, and areas cleared for oil palm, in Sabah, Malaysia. Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure. Such wholesale changes in fungal communities might impact the long-term sustainability of oil palm agriculture. Logging also has more subtle long term effects, on relative abundance of EcM fungi, which might affect tree recruitment and nutrient cycling. However, in general the logged forest retains most of the diversity and community composition of unlogged forest.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing

PubMed Central

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas. PMID:26020967

Chemical and microbiological characterization of an aged PCB-contaminated soil.

PubMed

Stella, T; Covino, S; Burianová, E; Filipová, A; Křesinová, Z; Voříšková, J; Větrovský, T; Baldrian, P; Cajthaml, T

2015-11-15

This study was aimed at complex characterization of three soil samples (bulk soil, topsoil and rhizosphere soil) from a site historically contaminated with polychlorinated biphenyls (PCB). The bulk soil was the most highly contaminated, with a PCB concentration of 705.95 mg kg(-1), while the rhizosphere soil was the least contaminated (169.36 mg kg(-1)). PCB degradation intermediates, namely chlorobenzoic acids (CBAs), were detected in all the soil samples, suggesting the occurrence of microbial transformation processes over time. The higher content of organic carbon in the topsoil and rhizosphere soil than in the bulk soil could be linked to the reduced bioaccessibility (bioavailability) of these chlorinated pollutants. However, different proportions of the PCB congener contents and different bioaccessibility of the PCB homologues indicate microbial biotransformation of the compounds. The higher content of organic carbon probably also promoted the growth of microorganisms, as revealed by phospholipid fatty acid (PFLA) quantification. Tag-encoded pyrosequencing analysis showed that the bacterial community structure was significantly similar among the three soils and was predominated by Proteobacteria (44-48%) in all cases. Moreover, analysis at lower taxonomic levels pointed to the presence of genera (Sphingomonas, Bulkholderia, Arthrobacter, Bacillus) including members with reported PCB removal abilities. The fungal community was mostly represented by Basidiomycota and Ascomycota, which accounted for >80% of all the sequences detected in the three soils. Fungal taxa with biodegradation potential (Paxillus, Cryptococcus, Phoma, Mortierella) were also found. These results highlight the potential of the indigenous consortia present at the site as a starting point for PCB bioremediation processes. Copyright © 2015 Elsevier B.V. All rights reserved.

Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts

PubMed Central

Chenthamara, Komal; Zhang, Jian; Atanasova, Lea; Yang, Dongqing; Miao, Youzhi; Grujic, Marica; Pourmehdi, Shadi; Pretzer, Carina; Kopchinskiy, Alexey G.; Hundley, Hope; Wang, Mei; Aerts, Andrea; Salamov, Asaf; Lipzen, Anna; Barry, Kerrie; Grigoriev, Igor V.; Shen, Qirong; Kubicek, Christian P.

2018-01-01

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass. PMID:29630596

Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas-fir forest.

PubMed

Beiler, Kevin J; Simard, Suzanne W; Lemay, Valerie; Durall, Daniel M

2012-12-01

Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and Rhizopogon vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas-fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. Rhizopogon vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared with xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes. © 2012 Blackwell Publishing Ltd.

Antimycobacterial and antimalarial activities of endophytic fungi associated with the ancient and narrowly endemic neotropical plant Vellozia gigantea from Brazil.

PubMed

Ferreira, Mariana C; Cantrell, Charles L; Wedge, David E; Gonçalves, Vívian N; Jacob, Melissa R; Khan, Shabana; Rosa, Carlos A; Rosa, Luiz H

2017-10-01

Endophytic fungi, present mainly in the Ascomycota and Basidiomycota phyla, are associated with different plants and represent important producers of bioactive natural products. Brazil has a rich biodiversity of plant species, including those reported as being endemic. Among the endemic Brazilian plant species, Vellozia gigantea (Velloziaceae) is threatened by extinction and is a promising target to recover endophytic fungi. The present study focused on bioprospecting of bioactive compounds of the endophytic fungi associated with V. gigantea, an endemic, ancient, and endangered plant species that occurs only in the rupestrian grasslands of Brazil. The capability of 285 fungal isolates to produce antimicrobial and antimalarial activities was examined. Fungi were grown at solid-state fermentation to recover their crude extracts in dichloromethane. Bioactive extracts were analysed by chromatographic fractionation and NMR and displayed compounds with antimicrobial, antimycobacterial, and antimalarial activities. Five fungi produced antimicrobial and antimalarial compounds. Extracts of Diaporthe miriciae showed antifungal, antibacterial, and antimalarial activities; Trichoderma effusum displayed selective antibacterial activity against methicillin-resistant Staphylococcus aureus and Mycobacterium intracellulare; and three Penicillium species showed antibacterial activity. D. miriciae extract contained highly functionalised secondary metabolites, yielding the compound epoxycytochalasin H with high antimalarial activity against the chloroquine-resistant strain of Plasmodium falciparum, with an IC50 approximately 3.5-fold lower than that with chloroquine. Our results indicate that V. gigantea may represent a microhabitat repository hotspot of potential fungi producers of bioactive compounds and suggest that endophytic fungal communities might be an important biological component contributing to the fitness of the plants living in the rupestrian grassland.

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi.

PubMed

Gacura, Matthew D; Sprockett, Daniel D; Heidenreich, Bess; Blackwood, Christopher B

2016-04-01

Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes. Copyright © 2016 Elsevier B.V. All rights reserved.

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom.

PubMed

Sun, Jing-Yun; Song, Yu; Ma, Zhi-Ping; Zhang, Huai-Jing; Yang, Zhong-Duo; Cai, Zhong-Hua; Zhou, Jin

2017-10-01

Contamination and eutrophication have caused serious ecological events (such as algal bloom) in coastal area. During this ecological process, microbial community structure is critical for algal bloom succession. The diversity and composition of bacteria and archaea communities in algal blooms have been widely investigated; however, those of fungi are poorly understood. To fill this gap, we used pyrosequencing and correlation approaches to assess fungal patterns and associations during a dinoflagellate (Noctiluca scintillans) bloom. Phylum level fungal types were predominated by Ascomycota, Chytridiomycota, Mucoromycotina, and Basidiomycota. At the genus level drastic changes were observed with Hysteropatella, Malassezia and Saitoella dominating during the initial bloom stage, while Malassezia was most abundant (>50%) during onset and peak-bloom stages. Saitoella and Lipomyces gradually became more abundant and, in the decline stage, contributed almost 70% of sequences. In the terminal stage of the bloom, Rozella increased rapidly to a maximum of 50-60%. Fungal population structure was significantly influenced by temperature and substrate (N and P) availability (P < 0.05). Inter-specific network analyses demonstrated that Rozella and Saitoella fungi strongly impacted the ecological trajectory of N. scintillans. The functional prediction show that symbiotrophic fungi was dominated in the onset stage; saprotroph type was the primary member present during the exponential growth period; whereas pathogentroph type fungi enriched in decline phase. Overall, fungal communities and functions correlated significantly with N. scintillans processes, suggesting that they may regulate dinoflagellate bloom fates. Our results will facilitate deeper understanding of the ecological importance of marine fungi and their roles in algal bloom formation and collapse. Copyright © 2017 Elsevier Ltd. All rights reserved.

Composted versus raw olive mill waste as substrates for the production of medicinal mushrooms: an assessment of selected cultivation and quality parameters.

PubMed

Zervakis, Georgios I; Koutrotsios, Georgios; Katsaris, Panagiotis

2013-01-01

Two-phase olive mill waste (TPOMW, "alperujo") is a highly biotoxic sludge-like effluent of the olive-oil milling process with a huge seasonal production. One of the treatment approaches that has so far received little attention is the use of TPOMW as substrate for the cultivation of edible mushrooms. Fifteen fungal strains belonging to five species (Basidiomycota), that is, Agrocybe cylindracea, Pleurotus cystidiosus, P. eryngii, P. ostreatus, and P. pulmonarius, were evaluated for their efficacy to colonize media composed of TPOMW, which was used either raw or composted in mixtures with wheat straw in various ratios. Qualified strains exhibited high values of biological efficiency (e.g., 120-135% for Pleurotus spp. and 125% for A. cylindracea) and productivity in subsequent cultivation experiments on substrates supplemented with 20-40% composted TPOMW or 20% raw TPOMW. Only when supplementation exceeded 60% for raw TPOMW, a negative impact was noted on mushroom yields which could be attributed to the effluent's toxicity (otherwise alleviated in the respective composted TPOMW medium). Earliness and mushroom size as well as quality parameters such as total phenolic content and antioxidant activity did not demonstrate significant differences versus the control wheat-straw substrate. The substrates hemicellulose content was negatively correlated with mycelium growth rates and yields and positively with earliness; in addition, cellulose: lignin ratio presented a positive correlation with mycelium growth and mushroom weight for A. cylindracea and with earliness for all species examined. TPOMW-based media revealed a great potential for the substitution of traditional cultivation substrates by valorizing environmentally hazardous agricultural waste.

Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox.

PubMed

Hildén, Kristiina; Mäkelä, Miia R; Steffen, Kari T; Hofrichter, Martin; Hatakka, Annele; Archer, David B; Lundell, Taina K

2014-11-01

Agrocybe praecox is a litter-decomposing Basidiomycota species of the order Agaricales, and is frequently found in forests and open woodlands. A. praecox grows in leaf-litter and the upper soil and is able to colonize bark mulch and wood chips. It produces extracellular manganese peroxidase (MnP) activities and mineralizes synthetic lignin. In this study, the A. praecox MnP1 isozyme was purified, cloned and enzymatically characterized. The enzyme catalysed the oxidation of Mn(2+) to Mn(3+), which is the specific reaction for manganese-dependent class II heme-peroxidases, in the presence of malonate as chelator with an activity maximum at pH 4.5; detectable activity was observed even at pH 7.0. The coding sequence of the mnp1 gene demonstrates a short-type of MnP protein with a slightly modified Mn(2+) binding site. Thus, A. praecox MnP1 may represent a novel group of atypical short-MnP enzymes. In lignocellulose-containing cultures composed of cereal bran or forest litter, transcription of mnp1 gene was followed by quantitative real-time RT-PCR. On spruce needle litter, mnp1 expression was more abundant than on leaf litter after three weeks cultivation. However, the expression was constitutive in wheat and rye bran cultures. Our data show that the atypical MnP of A. praecox is able to catalyse Mn(2+) oxidation, which suggests its involvement in lignocellulose decay by this litter-decomposer. Copyright © 2014 Elsevier Inc. All rights reserved.

[Isolation of wood-decaying fungi and evaluation of their enzymatic activity (Quindío, Colombia)].

PubMed

Chaparro, Deisy Fernanda; Rosas, Diana Carolina; Varela, Amanda

2009-12-31

White rot fungi (Ascomycota and Basidiomycota) were collected on fallen trunks with different decay stages, in a subandean forest (La Montaña del Ocaso nature reserve), and it was evaluated their ligninolitic activity. They were cultured on malt extract agar. Then it was performed semiquantitative tests for laccase and cellobiose dehydrogenase (CDH) activity using ABTS and DCPIP as enzymatic inducers. Based on the results of these tests, the fungi with higher activities from trunks with different decay stages were selected: Cookeina sulcipes (for stage 1), a fungus from the family Corticiaceae (for stage 2), Xylaria polymorpha (for stage 3) and Earliella sp. (for stage 4). A fermentation was performed at 28 degrees C, during 11 days, in a rotatory shaker at 150 rpm. Biomass, glucose, proteins and enzyme activities measurements were performed daily. The fungi that were in the trunks with decay states from 1 to 3, showed higher laccase activity as the state of decay increased. A higher DCH activity was also associated with a higher. Also, there was a positive relationship between both enzymes' activities. Erliella was the fungus which presented the highest biomass production (1140,19 g/l), laccase activity (157 UL(-1)) and CDH activity (43,50 UL(-1)). This work is the first report of laccase and CDH activity for Cookeina sulcipes and Earliella sp. Moreover, it gives basis for the use of these native fungi in biotechnological applications and the acknowledgment of their function in the wood decay process in native forest.

The phylogenetic position of poroid Hymenochaetaceae (Hymenochaetales, Basidiomycota) from Patagonia, Argentina.

PubMed

Rajchenberg, Mario; Pildain, María Belén; Bianchinotti, María V; Barroetaveña, Carolina

2015-01-01

Six poroid Hymenochaetaceae from Patagonia, Argentina, were studied phylogenetically with nuc rDNA internal transcribed spacer (ITS) and partial 28S rDNA sequences, together with morphological data. Two new genera and a new species are introduced as well as two new combinations proposed. Arambarria destruens gen. et sp. nov. is proposed for a taxon fruiting on fallen or standing, dead Diostea juncea and Lomatia hirsuta and previously recorded erroneously as Inocutis jamaicensis; it is distinguished by annual, effused to effused-reflexed basidiomes forming pilei, a monomitic hyphal system, thick-walled and yellowish basidiospores (brownish chestnut in potassium hydroxide solution), lack of a granular core in the context and lack of setoid elements. Nothophellinus gen. nov. is proposed to accommodate Phellinus andinopatagonicus, the main white wood-rotting polypore of standing Nothofagus pumilio and also an important wood-decayer of other Nothofagus species from southern Argentina and Chile. It is morphologically similar to Phellopilus (type species P. nigrolimitatus) but differs by lacking setae. The new combinations Pseudoinonotus crustosus and Phellinopsis andina are proposed for Inonotus crustosus and Phellinus andinus, respectively. Phellinus livescens, which decays the sapwood of several standing Nothofagus species, is closely related to Phellinus uncisetus, a Neotropical species related to Fomitiporia; for the time being P. livescens is retained in Phellinus sensu lato. An unidentified taxon responsible for a white heart-rot in living Austrocedrus chilensis grouped with Phellinus caryophyllii and Fulvifomes inermis, but its generic affinities remain ambiguous. Transmission electron microscopy studies confirm this unidentified taxon has an imperforate parenthesome, which is typical of the Hymenochaetaceae. © 2015 by The Mycological Society of America.

Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

PubMed Central

Andreakis, Nikos; Høj, Lone; Kearns, Philip; Hall, Michael R.; Ericson, Gavin; Cobb, Rose E.; Gordon, Benjamin R.; Evans-Illidge, Elizabeth

2015-01-01

Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS) provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290) of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS). Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs) by the automatic barcode gap finder (ABGD) method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters. PMID:26308620

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

PubMed Central

Riley, Robert; Salamov, Asaf A.; Brown, Daren W.; Nagy, Laszlo G.; Floudas, Dimitrios; Held, Benjamin W.; Levasseur, Anthony; Lombard, Vincent; Morin, Emmanuelle; Otillar, Robert; Lindquist, Erika A.; Sun, Hui; LaButti, Kurt M.; Schmutz, Jeremy; Jabbour, Dina; Luo, Hong; Baker, Scott E.; Pisabarro, Antonio G.; Walton, Jonathan D.; Blanchette, Robert A.; Henrissat, Bernard; Martin, Francis; Cullen, Dan; Hibbett, David S.; Grigoriev, Igor V.

2014-01-01

Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay. PMID:24958869

Unexpected diversity of basidiomycetous endophytes in sapwood and leaves of Hevea.

PubMed

Martin, Rachael; Gazis, Romina; Skaltsas, Demetra; Chaverri, Priscila; Hibbett, David

2015-01-01

Research on fungal endophytes has expanded dramatically in recent years, but little is known about the diversity and ecological roles of endophytic basidiomycetes. Here we report the analysis of 310 basidiomycetous endophytes isolated from wild and planted populations of the rubber tree genus, Hevea. Species accumulation curves were nonasymptotic, as in the majority of endophyte surveys, indicating that more sampling is needed to recover the true diversity of the community. One hundred eighteen OTUs were delimited, representing nine orders of Basidiomycota (Agaricales, Atheliales, Auriculariales, Cantharellales, Hymenochaetales, Polyporales, Russulales, Septobasidiales, Tremellales). The diversity of basidiomycetous endophytes found inhabiting wild populations of Hevea was comparable to that present in plantations. However, when samples were segregated by tissue type, sapwood of wild populations was found to contain a higher number of species than sapwood of planted trees. Seventy-five percent of isolates were members of the Polyporales, the majority in the phlebioid clade. Most of the species belong to clades known to cause a white-rot type of wood decay. Two species in the insect-associated genus Septobasidium were isolated. The most frequently isolated genera included Bjerkandera, Ceriporia, Phanerochaete, Phlebia, Rigidoporus, Tinctoporellus, Trametes (Polyporales), Peniophora, Stereum (Russulales) and Coprinellus (Agaricales), all of which have been reported as endophytes from a variety of hosts, across wide geographic locations. Literature records on the geographic distribution and host association of these genera revealed that their distribution and substrate affinity could be extended if the endophytic niche was investigated as part of fungal biodiversity surveys. © 2015 by The Mycological Society of America.

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes.

PubMed

Gomba, A; Chidamba, L; Korsten, L

2017-04-01

To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. Viable bacteria, yeast and fungi counts, and the pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extent of degreening effects varied between the citrus varieties. Pyrosequencing analysis showed a total of 4409 bacteria and 5792 fungi nonchimeric unique sequences with an average of 1102 bacteria and 1448 fungi reads per sample. Dominant phyla on the citrus carpoplane were Proteobacteria (53·5%), Actinobacteria (19·9%), Bacteroidetes (5·6%) and Deinococcus-Thermus (5·4%) for bacteria and Ascomycota (80·5%) and Basidiomycota (9·8%) for fungi. Beginning with freshly harvested fruit fungal diversity declined significantly after drenching, but had little effect on bacteria and populations recovered during degreening treatments, including those for Penicillium sp. Packhouse processing greatly influences microbial communities on the citrus carpoplane. A broad orange biome was described with pyrosequencing and gave insight into the likely survival and persistence of pathogens, especially as they may affect the quality and safety of the packed product. A close examination of the microbiota of fruit and the impact of intervention strategies on the ecological balance may provide a more durable approach to reduce losses and spoilage. © 2017 The Society for Applied Microbiology.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation.

PubMed

Campeão, Mariana E; Reis, Luciana; Leomil, Luciana; de Oliveira, Louisi; Otsuki, Koko; Gardinali, Piero; Pelz, Oliver; Valle, Rogerio; Thompson, Fabiano L; Thompson, Cristiane C

2017-01-01

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical-chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae , and Alcanivoracaceae ), archaea (e.g., Halobacteriaceae, Desulfurococcaceae , and Methanobacteriaceae ), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web.

Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield.

PubMed

Rime, Thomas; Hartmann, Martin; Brunner, Ivano; Widmer, Franco; Zeyer, Josef; Frey, Beat

2015-03-01

Spatial patterns of microbial communities have been extensively surveyed in well-developed soils, but few studies investigated the vertical distribution of micro-organisms in newly developed soils after glacier retreat. We used 454-pyrosequencing to assess whether bacterial and fungal community structures differed between stages of soil development (SSD) characterized by an increasing vegetation cover from barren (vegetation cover: 0%/age: 10 years), sparsely vegetated (13%/60 years), transient (60%/80 years) to vegetated (95%/110 years) and depths (surface, 5 and 20 cm) along the Damma glacier forefield (Switzerland). The SSD significantly influenced the bacterial and fungal communities. Based on indicator species analyses, metabolically versatile bacteria (e.g. Geobacter) and psychrophilic yeasts (e.g. Mrakia) characterized the barren soils. Vegetated soils with higher C, N and root biomass consisted of bacteria able to degrade complex organic compounds (e.g. Candidatus Solibacter), lignocellulolytic Ascomycota (e.g. Geoglossum) and ectomycorrhizal Basidiomycota (e.g. Laccaria). Soil depth only influenced bacterial and fungal communities in barren and sparsely vegetated soils. These changes were partly due to more silt and higher soil moisture in the surface. In both soil ages, the surface was characterized by OTUs affiliated to Phormidium and Sphingobacteriales. In lower depths, however, bacterial and fungal communities differed between SSD. Lower depths of sparsely vegetated soils consisted of OTUs affiliated to Acidobacteria and Geoglossum, whereas depths of barren soils were characterized by OTUs related to Gemmatimonadetes. Overall, plant establishment drives the soil microbiota along the successional gradient but does not influence the vertical distribution of microbiota in recently deglaciated soils. © 2014 John Wiley & Sons Ltd.

The Deep-Sea Microbial Community from the Amazonian Basin Associated with Oil Degradation

PubMed Central

Campeão, Mariana E.; Reis, Luciana; Leomil, Luciana; de Oliveira, Louisi; Otsuki, Koko; Gardinali, Piero; Pelz, Oliver; Valle, Rogerio; Thompson, Fabiano L.; Thompson, Cristiane C.

2017-01-01

One consequence of oil production is the possibility of unplanned accidental oil spills; therefore, it is important to evaluate the potential of indigenous microorganisms (both prokaryotes and eukaryotes) from different oceanic basins to degrade oil. The aim of this study was to characterize the microbial response during the biodegradation process of Brazilian crude oil, both with and without the addition of the dispersant Corexit 9500, using deep-sea water samples from the Amazon equatorial margin basins, Foz do Amazonas and Barreirinhas, in the dark and at low temperatures (4°C). We collected deep-sea samples in the field (about 2570 m below the sea surface), transported the samples back to the laboratory under controlled environmental conditions (5°C in the dark) and subsequently performed two laboratory biodegradation experiments that used metagenomics supported by classical microbiological methods and chemical analysis to elucidate both taxonomic and functional microbial diversity. We also analyzed several physical–chemical and biological parameters related to oil biodegradation. The concomitant depletion of dissolved oxygen levels, oil droplet density characteristic to oil biodegradation, and BTEX concentration with an increase in microbial counts revealed that oil can be degraded by the autochthonous deep-sea microbial communities. Indigenous bacteria (e.g., Alteromonadaceae, Colwelliaceae, and Alcanivoracaceae), archaea (e.g., Halobacteriaceae, Desulfurococcaceae, and Methanobacteriaceae), and eukaryotic microbes (e.g., Microsporidia, Ascomycota, and Basidiomycota) from the Amazonian margin deep-sea water were involved in biodegradation of Brazilian crude oil within less than 48-days in both treatments, with and without dispersant, possibly transforming oil into microbial biomass that may fuel the marine food web. PMID:28659874

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

PubMed Central

Taylor, Joe D; Cunliffe, Michael

2016-01-01

Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623

Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants

NASA Astrophysics Data System (ADS)

Renard, Pascal; Canet, Isabelle; Sancelme, Martine; Wirgot, Nolwenn; Deguillaume, Laurent; Delort, Anne-Marie

2016-09-01

A total of 480 microorganisms collected from 39 clouds sampled at the Puy de Dôme station (alt. 1465 m; 45°46'19'' N, 2°57'52'' E; Massif Central, France) were isolated and identified. This unique collection was screened for biosurfactant (surfactants of microbial origin) production by measuring the surface tension (σ) of the crude extracts, comprising the supernatants of the pure cultures, using the pendant drop technique. The results showed that 41 % of the tested strains were active producers (σ < 55 mN m-1), with 7 % being extremely active (σ < 30 mN m-1). The most efficient biosurfactant producers (σ < 45 mN m-1) belong to a few bacterial genera (Pseudomonas and Xanthomonas) from the Υ-Proteobacteria class (78 %) and a yeast genus (Udeniomyces) from the Basidiomycota phylum (11 %). Some Bacillus strains from the Firmicutes phylum were also active but represented a small fraction of the collected population. Strains from the Actinobacteria phylum in the collection examined in the present study showed moderate biosurfactant production (45<σ < 55 mN m-1). Pseudomonas (Υ-Proteobacteria), the most frequently detected genus in clouds, with some species issued from the phyllosphere, was the dominant group for the production of biosurfactants. We observed some correlations between the chemical composition of cloud water and the presence of biosurfactant-producing microorganisms, suggesting the "biogeography" of this production. Moreover, the potential impact of the production of biosurfactants by cloud microorganisms on atmospheric processes is discussed.

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes.

PubMed

Mali, Tuulia; Kuuskeri, Jaana; Shah, Firoz; Lundell, Taina Kristina

2017-01-01

Fomitopsis pinicola is a species of Polyporales frequently encountered in Nordic temperate and boreal forests. In nature, the fungus causes destructive brown rot in wood, colonizing tree trunks often occupied by other Basidiomycota species. We mimicked these species-species interactions by introducing F. pinicola to five white rot species, all common saprotrophs of Norway spruce. Hyphal interactions and mycelial growth in various combinations were recorded, while activities of lignocellulose-acting CAZymes and oxidoreductases were followed in co-cultures on two different carbon-source media. Of the species, Phlebia radiata and Trichaptum abietinum were the strongest producers of lignin-modifying oxidoreductases (laccase, manganese peroxidase) when evaluated alone, as well as in co-cultures, on the two different growth media (low-nitrogen liquid medium containing ground coniferous wood, and malt extract broth). F. pinicola was an outstanding producer of oxalic acid (up to 61 mM), whereas presence of P. radiata prevented acidification of the growth environment in the liquid malt-extract cultures. When enzyme profiles of the species combinations were clustered, time-dependent changes were observed on wood-supplemented medium during the eight weeks of growth. End-point acidity and production of mycelium, oxalic acid and oxidoreductase activities, in turn clustered the fungal combinations into three distinct functional groups, determined by the presence of F. pinicola and P. radiata, by principal component analysis. Our findings indicate that combinations of wood-decay fungi have dramatic dynamic effects on the production of lignocellulose-active enzymes, which may lead to divergent degradative processes of dead wood and forest litter.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota).

PubMed

Bellanger, J-M; Moreau, P-A; Corriol, G; Bidaud, A; Chalange, R; Dudova, Z; Richard, F

2015-04-01

During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.

The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils.

PubMed

Winder, Richard S; Lamarche, Josyanne; Constabel, C Peter; Hamelin, Richard C

2013-01-01

The impacts of leaf litter from genetically modified hybrid poplar accumulating high levels of condensed tannins (proanthocyanidins) were examined in soil microcosms consisting of moss growing on sieved soil. Moss preferentially proliferated in microcosms with lower tannin content; DGGE (denaturing gradient gel electrophoresis) detected increased fungal diversity in microcosms with low-tannin litter. The proportion of cloned rDNA sequences from Actinobacteria decreased with litter addition while Bacteroidetes, Chloroflexi, Cyanobacteria, and α-Proteobacteria significantly increased. β-Proteobacteria were proportionally more numerous at high-tannin levels. Tannins had no significant impact on overall diversity of bacterial communities analyzed with various estimators. There was an increased proportion of N-fixing bacteria corresponding to the addition of litter with low-tannin levels. The addition of litter increased the proportion of Ascomycota/Basidiomycota. Dothideomycetes, Pucciniomycetes, and Tremellomycetes also increased and Agaricomycetes decreased. Agaricomycetes and Sordariomycetes were significantly more abundant in controls, whereas Pucciniomycetes increased in soil with litter from transformed trees (P = 0.051). Richness estimators and diversity indices revealed no significant difference in the composition of fungal communities; PCoA (principal coordinate analyses) partitioned the fungal communities into three groups: (i) those with higher amounts of added tannin from both transformed and untransformed treatments, (ii) those corresponding to soils without litter, and (iii) those corresponding to microcosms with litter added from trees transformed only with a β-glucuronidase control vector. While the litter from transformed poplars had significant effects on soil microbe communities, the observed impacts reflected known impacts on soil processes associated with tannins, and were similar to changes that would be expected from natural variation in tannin levels.

Identity, diversity, and molecular phylogeny of the endophytic mycobiota in the roots of rare wild rice (Oryza granulate) from a nature reserve in Yunnan, China.

PubMed

Yuan, Zhi-Lin; Zhang, Chu-Long; Lin, Fu-Cheng; Kubicek, Christian P

2010-03-01

Rice (Oryza sativa L.) is, on a global scale, one of the most important food crops. Although endophytic fungi and bacteria associated with rice have been investigated, little is known about the endophytic fungi of wild rice (Oryza granulate) in China. Here we studied the root endophytic mycobiota residing in roots of O. granulate by the use of an integrated approach consisting of microscopy, cultivation, ecological indices, and direct PCR. Microscopy confirmed the ubiquitousness of dark septate endophytes (DSEs) and sclerotium-like structures in root tissues. Isolations from 204 root segments from 15 wild rice plants yielded 58 isolates, for which 31 internal transcribed spacer (ITS)-based genotypes were recorded. The best BLAST match indicated that 34.5% of all taxa encountered may represent hitherto undescribed species. Most of the fungi were isolated with a very low frequency. Calculation of ecological indices and estimation of taxon accumulation curves indicated a high diversity of fungal species. A culture-independent approach was also performed to analyze the endophytic fungal community. Three individual clone libraries were constructed. Using a threshold of 90% similarity, 35 potentially different sequences (phylotypes) were found among 186 positive clones. Phylogenetic analysis showed that frequently detected clones were classified as Basidiomycota, and 60.2% of total analyzed clones were affiliated with unknown taxa. Exophiala, Cladophialophora, Harpophora, Periconia macrospinosa, and the Ceratobasidium/Rhizoctonia complex may act as potential DSE groups. A comparison of the fungal communities characterized by the two approaches demonstrated distinctive fungal groups, and only a few taxa overlapped. Our findings indicate a complex and rich endophytic fungal consortium in wild rice roots, thus offering a potential bioresource for establishing a novel model of plant-fungal mutualistic interactions.

Terrestrial Macrofungal Diversity from the Tropical Dry Evergreen Biome of Southern India and Its Potential Role in Aerobiology

PubMed Central

Priyamvada, Hema; Akila, M.; Singh, Raj Kamal; Ravikrishna, R.; Verma, R. S.; Philip, Ligy; Marathe, R. R.; Sahu, L. K.; Sudheer, K. P.; Gunthe, S. S.

2017-01-01

Macrofungi have long been investigated for various scientific purposes including their food and medicinal characteristics. Their role in aerobiology as a fraction of the primary biological aerosol particles (PBAPs), however, has been poorly studied. In this study, we present a source of macrofungi with two different but interdependent objectives: (i) to characterize the macrofungi from a tropical dry evergreen biome in southern India using advanced molecular techniques to enrich the database from this region, and (ii) to assess whether identified species of macrofungi are a potential source of atmospheric PBAPs. From the DNA analysis, we report the diversity of the terrestrial macrofungi from a tropical dry evergreen biome robustly supported by the statistical analyses for diversity conclusions. A total of 113 macrofungal species belonging to 54 genera and 23 families were recorded, with Basidiomycota and Ascomycota constituting 96% and 4% of the species, respectively. The highest species richness was found in the family Agaricaceae (25.3%) followed by Polyporaceae (15.3%) and Marasmiaceae (10.8%). The difference in the distribution of commonly observed macrofungal families over this location was compared with other locations in India (Karnataka, Kerala, Maharashtra, and West Bengal) using two statistical tests. The distributions of the terrestrial macrofungi were distinctly different in each ecosystem. We further attempted to demonstrate the potential role of terrestrial macrofungi as a source of PBAPs in ambient air. In our opinion, the findings from this ecosystem of India will enhance our understanding of the distribution, diversity, ecology, and biological prospects of terrestrial macrofungi as well as their potential to contribute to airborne fungal aerosols. PMID:28072853

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase

PubMed Central

Abdelfattah, Ahmed; Wisniewski, Michael; Droby, Samir; Schena, Leonardo

2016-01-01

The fungal diversity in harvested apples from organic or conventional management practices was analyzed in different fruit locations (stem end, calyx end, peel, and wounded flesh) shortly after fruit purchase (T1) and after 2 weeks of storage (T5). A total of 5,760,162 high-quality fungal sequences were recovered and assigned to 8,504 Operational Taxonomic Units. Members of the phylum Ascomycota were dominant in all samples and accounted for 91.6% of the total number of detected sequences. This was followed by Basidiomycota (8%), Chytridiomycota (0.1%), and unidentified fungi (0.3%). Alpha and beta diversity analyses revealed the presence of significantly different fungal populations in the investigated fruit parts. Among detected fungi, the genus Penicillium prevailed in the peel and in the wounded flesh while Alternaria spp. prevailed in the calyx and stem end samples that included apple core tissues. Several taxonomic units that appear to be closely related to pathogenic fungi associated with secondary human infections were present in peel and wounds. Moreover, significantly different populations were revealed in organic and conventional apples and this result was consistent in all investigated fruit parts (calyx end, peel, stem end, and wounded flesh). Several unique taxa were exclusively detected in organic apples suggesting that management practices may have been a contributing factor in determining the taxa present. In contrast, little differences were revealed in the two assessment times (T1 and T5). Results of the present study represent an advancement of the current knowledge on the fungal microbiota in collected fruit tissues of apple. PMID:27766161

Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

PubMed Central

Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

2012-01-01

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

A survey of genes encoding H2O2-producing GMC oxidoreductases in 10 Polyporales genomes.

PubMed

Ferreira, Patricia; Carro, Juan; Serrano, Ana; Martínez, Angel T

2015-01-01

The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) recently were sequenced to expand our knowledge on the diversity and distribution of genes involved in degradation of plant polymers in this Basidiomycota order, which includes most wood-rotting fungi. Oxidases, including members of the glucose-methanol-choline (GMC) oxidoreductase superfamily, play a central role in the above degradative process because they generate extracellular H2O2 acting as the ultimate oxidizer in both white-rot and brown-rot decay. The survey was completed by analyzing the GMC genes in the available genomes of seven more species to cover the four Polyporales clades. First, an in silico search for sequences encoding members of the aryl-alcohol oxidase, glucose oxidase, methanol oxidase, pyranose oxidase, cellobiose dehydrogenase and pyranose dehydrogenase families was performed. The curated sequences were subjected to an analysis of their evolutionary relationships, followed by estimation of gene duplication/reduction history during fungal evolution. Second, the molecular structures of the near one hundred GMC oxidoreductases identified were modeled to gain insight into their structural variation and expected catalytic properties. In contrast to ligninolytic peroxidases, whose genes are present in all white-rot Polyporales genomes and absent from those of brown-rot species, the H2O2-generating oxidases are widely distributed in both fungal types. This indicates that the GMC oxidases provide H2O2 for both ligninolytic peroxidase activity (in white-rot decay) and Fenton attack on cellulose (in brown-rot decay), after the transition between both decay patterns in Polyporales occurred. © 2015 by The Mycological Society of America.

Yet More “Weeds” in the Garden: Fungal Novelties from Nests of Leaf-Cutting Ants

PubMed Central

Augustin, Juliana O.; Groenewald, Johannes Z.; Nascimento, Robson J.; Mizubuti, Eduardo S. G.; Barreto, Robert W.; Elliot, Simon L.; Evans, Harry C.

2013-01-01

Background Symbiotic relationships modulate the evolution of living organisms in all levels of biological organization. A notable example of symbiosis is that of attine ants (Attini; Formicidae: Hymenoptera) and their fungal cultivars (Lepiotaceae and Pterulaceae; Agaricales: Basidiomycota). In recent years, this mutualism has emerged as a model system for studying coevolution, speciation, and multitrophic interactions. Ubiquitous in this ant-fungal symbiosis is the “weedy” fungus Escovopsis (Hypocreales: Ascomycota), known only as a mycoparasite of attine fungal gardens. Despite interest in its biology, ecology and molecular phylogeny—noting, especially, the high genetic diversity encountered—which has led to a steady flow of publications over the past decade, only two species of Escovopsis have formally been described. Methods and Results We sampled from fungal gardens and garden waste (middens) of nests of the leaf-cutting ant genus Acromyrmex in a remnant of subtropical Atlantic rainforest in Minas Gerais, Brazil. In culture, distinct morphotypes of Escovopsis sensu lato were recognized. Using both morphological and molecular analyses, three new species of Escovopsis were identified. These are described and illustrated herein—E. lentecrescens, E. microspora, and E. moelleri—together with a re-description of the genus and the type species, E. weberi. The new genus Escovopsioides is erected for a fourth morphotype. We identify, for the first time, a mechanism for horizontal transmission via middens. Conclusions The present study makes a start at assigning names and formal descriptions to these specific fungal parasites of attine nests. Based on the results of this exploratory and geographically-restricted survey, we expect there to be many more species of the genus Escovopsis and its relatives associated with nests of both the lower and higher Attini throughout their neotropical range, as suggested in previous studies. PMID:24376525

Composted versus Raw Olive Mill Waste as Substrates for the Production of Medicinal Mushrooms: An Assessment of Selected Cultivation and Quality Parameters

PubMed Central

Zervakis, Georgios I.; Koutrotsios, Georgios; Katsaris, Panagiotis

2013-01-01

Two-phase olive mill waste (TPOMW, “alperujo”) is a highly biotoxic sludge-like effluent of the olive-oil milling process with a huge seasonal production. One of the treatment approaches that has so far received little attention is the use of TPOMW as substrate for the cultivation of edible mushrooms. Fifteen fungal strains belonging to five species (Basidiomycota), that is, Agrocybe cylindracea, Pleurotus cystidiosus, P. eryngii, P. ostreatus, and P. pulmonarius, were evaluated for their efficacy to colonize media composed of TPOMW, which was used either raw or composted in mixtures with wheat straw in various ratios. Qualified strains exhibited high values of biological efficiency (e.g., 120–135% for Pleurotus spp. and 125% for A. cylindracea) and productivity in subsequent cultivation experiments on substrates supplemented with 20–40% composted TPOMW or 20% raw TPOMW. Only when supplementation exceeded 60% for raw TPOMW, a negative impact was noted on mushroom yields which could be attributed to the effluent's toxicity (otherwise alleviated in the respective composted TPOMW medium). Earliness and mushroom size as well as quality parameters such as total phenolic content and antioxidant activity did not demonstrate significant differences versus the control wheat-straw substrate. The substrates hemicellulose content was negatively correlated with mycelium growth rates and yields and positively with earliness; in addition, cellulose: lignin ratio presented a positive correlation with mycelium growth and mushroom weight for A. cylindracea and with earliness for all species examined. TPOMW-based media revealed a great potential for the substitution of traditional cultivation substrates by valorizing environmentally hazardous agricultural waste. PMID:24027758

Bleaching of leaf litter and associated microfungi in subboreal and subalpine forests.

PubMed

Hagiwara, Yusuke; Matsuoka, Shunsuke; Hobara, Satoru; Mori, Akira S; Hirose, Dai; Osono, Takashi

2015-10-01

Fungal decomposition of lignin leads to the whitening, or bleaching, of leaf litter, especially in temperate and tropical forests, but less is known about such bleaching in forests of cooler regions, such as boreal and subalpine forests. The purposes of the present study were to examine the extent of bleached area on the surface of leaf litter and its variation with environmental conditions in subboreal and subalpine forests in Japan and to examine the microfungi associated with the bleaching of leaf litter by isolating fungi from the bleached portions of the litter. Bleached area accounted for 21.7%-32.7% and 2.0%-10.0% of total leaf area of Quercus crispula and Betula ermanii, respectively, in subboreal forests, and for 6.3% and 18.6% of total leaf area of B. ermanii and Picea jezoensis var. hondoensis, respectively, in a subalpine forest. In subboreal forests, elevation, C/N ratio and pH of the FH layer, and slope aspect were selected as predictor variables for the bleached leaf area. Leaf mass per area and lignin content were consistently lower in the bleached area than in the nonbleached area of the same leaves, indicating that the selective decomposition of acid unhydrolyzable residue (recalcitrant compounds such as lignin, tannins, and cutins) enhanced the mass loss of leaf tissues in the bleached portions. Isolates of a total of 11 fungal species (6 species of Ascomycota and 5 of Basidiomycota) exhibited leaf-litter-bleaching activity under pure culture conditions. Two fungal species (Coccomyces sp. and Mycena sp.) occurred in both subboreal and subalpine forests, which were separated from each other by approximately 1100 km.

Diversity and antioxidant activity of culturable endophytic fungi from alpine plants of Rhodiola crenulata, R. angusta, and R. sachalinensis.

PubMed

Cui, Jin-Long; Guo, Ting-Ting; Ren, Zhen-Xing; Zhang, Na-Sha; Wang, Meng-Liang

2015-01-01

Rhodiola spp. are rare and endangered alpine plants widely used as medicines and food additives by many civilizations since ancient times. Their main effective ingredients (such as salidroside and p-tyrosol) are praised to exhibit pharmacologic effects on high-altitude sickness and possess anti-aging and other adaptogenic capacities based on their antioxidant properties. In this study, 347 endophytic fungi were isolated from R. crenulata, R. angusta, and R. sachalinensis, and the molecular diversity and antioxidant activities of these fungi were investigated for the first time. These fungi were categorized into 180 morphotypes based on cultural characteristics, and their rRNA gene ITS sequences were analyzed by BLAST search in the GenBank database. Except for 12 unidentified fungi (6.67%), all others were affiliated to at least 57 genera in 20 orders of four phyla, namely, Ascomycota (88.89%), Basidiomycota (2.78%), Zygomycota (1.11%), and Glomeromycota (0.56%), which exhibited high abundance and diversity. Antioxidant assay showed that the DPPH radical-scavenging rates of 114 isolates (63.33%) were >50%, and those of five isolates (Rct45, Rct63, Rct64, Rac76, and Rsc57) were >90%. The EC50 values of five antioxidant assays suggested significant potential of these fungi on scavenging DPPH•, O2-•, and OH• radicals, as well as scavenging nitrite and chelating Fe2+, which showed preference and selection between endophytic fungi and their hosts. Further research also provided the first evidence that Rac12 could produce salidrosides and p-tyrosol. Results suggested that versatile endophytic fungi associated with Rhodiola known as antioxidants could be exploited as potential sources of novel antioxidant products.

Sequence-based methods for detecting and evaluating the human gut mycobiome.

PubMed

Suhr, M J; Banjara, N; Hallen-Adams, H E

2016-03-01

We surveyed the fungal microbiota in 16 faecal samples from healthy humans with a vegetarian diet. Fungi were identified using molecular cloning, 454 pyrosequencing and a Luminex analyte-specific reagent (ASR) assay, all targeting the ITS region of the rRNA genes. Fungi were detected in each faecal sample and at least 46 distinct fungal operational taxonomic units (OTUs) were detected, from two phyla - Ascomycota and Basidiomycota. Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus and Candida. Commonly detected fungi such as Aspergillus and Penicillium, as well as known dietary fungi Agaricus bisporus and Ophiocordyceps sinensis, are presumed to be transient, allochthonous members due to their abundance in the environment or dietary associations. No single method identified the full diversity of fungi in all samples; pyrosequencing detected more distinct OTUs than the other methods, but failed to detect OTUs in some samples that were detected by cloning and/or ASR assays. ASRs were limited by the commercially available assays, but the potential to design new, optimized assays, coupled with speed and cost, makes the ASR method worthy of further study. Fungi play a role in human gut ecology and health. The field lags immensely behind bacterial gut microbiota research, and studies continue to identify new fungi in faecal samples from healthy humans. However, many of these 'new' species are incapable of growth in the human GI tract, let alone making a meaningful contribution to the gut microbial community. Fungi actually inhabiting and impacting the gut likely constitute a small set of species, and an optimized, targeted, probe-based assay may prove to be the most sensible way of quantifying their abundances. © 2015 The Society for Applied Microbiology.

Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols.

PubMed

Ma, Mingchao; Jiang, Xin; Wang, Qingfeng; Ongena, Marc; Wei, Dan; Ding, Jianli; Guan, Dawei; Cao, Fengming; Zhao, Baisuo; Li, Jun

2018-03-23

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea--A Metagenomic Approach.

PubMed

Simões, Marta Filipa; Antunes, André; Ottoni, Cristiane A; Amini, Mohammad Shoaib; Alam, Intikhab; Alzubaidy, Hanin; Mokhtar, Noor-Azlin; Archer, John A C; Bajic, Vladimir B

2015-10-01

Covering a quarter of the world's tropical coastlines and being one of the most threatened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities. Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray mangroves (Avicennia marina) remain poorly characterized, and understanding of their fungal communities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum (76%-85%), while Basidiomycota was less abundant (14%-24%), yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial communities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous Panax notoginseng cropping practices.

PubMed

Tan, Yong; Cui, Yinshan; Li, Haoyu; Kuang, Anxiu; Li, Xiaoran; Wei, Yunlin; Ji, Xiuling

2017-01-01

Rhizosphere and endophytic fungal communities are considered critically important for plant health and soil fertility. In response to continuous cropping, Panax notoginseng becomes vulnerable to attack by fungal pathogens. In the present study, culture-independent Illumina MiSeq was used to investigate the rhizospheric and root endophytic fungi in response to continuous Panax notoginseng cropping practices. The results demonstrated that fungal diversity is increased inside the roots and in rhizospheric. Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota were the dominant phyla detected during the continuous cropping of Panax notoginseng. The fungal diversity in the rhizospheric soil and roots of root-rot P. notoginseng plants are less than that of healthy plants in the same cultivating year, thus showing that root-rot disease also affects the community structure and diversity of rhizospheric and root endophytic fungi. Similarities in the major fungal components show that endophytic fungal communities are similar to rhizospheric soil fungal community based on a specialized subset of organisms. Canonical correspondence analysis on the fungal communities in root-rot rhizospheric from both healthy plants and rotation soils reveals that the soil pH and organic matter have the greatest impact upon the microbial community composition during continuous cropping, whereas soil nutrition status does not significantly affect the fungal community composition in response to continuous cropping practices. In addition, the results suggest that the unclassified genera Leotiomycetes, Cylindrocarpon, Fusarium and Mycocentrospora are shown as the potential pathogens which are responsible for the obstacles in continuous cropping of P. notoginseng. Further exploration of these potential pathogens might be useful for the biological control of continuous cropping of P. notoginseng. Copyright © 2016 Elsevier GmbH. All rights reserved.

Diversity and antimicrobial activity of culturable fungi from fishscale bamboo (Phyllostachys heteroclada) in China.

PubMed

Zhou, Ying-Ke; Shen, Xiao-Ye; Hou, Cheng-Lin

2017-06-01

An important and useful bamboo species, fishscale bamboo (Phyllostachys heteroclada Oliver), is broadly distributed in Southeast China and has multiple purposes, including uses in cuisine, weaving, Chinese medicine and ecological protection. However, no previous studies have focused on the endophytes of this plant. In our article, a total of 127 fungal strains were first isolated from the healthy branches and leaves of common P. heteroclada. These endophytic fungi could be directly categorized into 50 morphotypes according to their culture characteristics, and their internal transcribed spacer (ITS) regions were analyzed for molecular identification. Using the BLAST search tool of the NCBI database and phylogenetic tree analysis, these isolates were divided into two phyla, Ascomycota (95.28%) and Basidiomycota (4.72%), including at least six orders (Xylariales, Capnodiales, Pleosporales, Hypocreales, Chaetothyriales and Polyporales) and fourteen genera (Arthrinium, Pestalotiopsis, Epicoccum, Cladosporium, Nigrospora, Setophoma, Didymella, Calcarisporium, Preussia, Nemania, Creosphaeria, Ophiobolus, Phialophora and Perenniporia). It is fascinating that four genera, Calcarisporium, Preussia, Creosphaeria and Phialophora were isolated from bamboos for the first time. The inhibitory effects against clinical pathogens were also preliminarily screened, and four isolates FB43 (Calcarisporium arbuscula), FB06 (Preussia minima), FB16 (Setophoma sp.) and FB21 (Perenniporia medulla-pains) among the candidate strains displayed broad-spectrum activities according to the agar diffusion method and the disk diffusion assay. Strain FB16 (Setophoma sp.) especially indicated high bioactivity against both clinical bacteria and yeast. This study is the first report on the diversity and antimicrobial activity of the endophytic fungi associated with P. heteroclada, which could be regarded as a potential source of drug precursors and could be used in biocontrol development.

Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen.

PubMed

Brar, Simren; Tsui, Clement K M; Dhillon, Braham; Bergeron, Marie-Josée; Joly, David L; Zambino, P J; El-Kassaby, Yousry A; Hamelin, Richard C

2015-01-01

White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola. We characterized 1,292 samples of C. ribicola from 66 geographic locations in North America using single nucleotide polymorphisms (SNPs) and evaluated the effect of landscape features, host distribution, and colonization history on the structure of these pathogen populations. We identified eastern and western genetic populations in North America that are strongly differentiated. Genetic diversity is two to five times higher in eastern populations than in western ones, which can be explained by the repeated accidental introductions of the pathogen into northeastern North America compared with a single documented introduction into western North America. These distinct genetic populations are maintained by a barrier to gene flow that corresponds to a region where host connectivity is interrupted. Furthermore, additional cryptic spatial differentiation was identified in western populations. This differentiation corresponds to landscape features, such as mountain ranges, and also to host connectivity. We also detected genetic differentiation between the pathogen populations in natural stands and plantations, an indication that anthropogenic movement of this pathogen still takes place. These results highlight the importance of monitoring this invasive alien tree pathogen to prevent admixture of eastern and western populations where different pathogen races occur.

Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

PubMed Central

Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties. PMID:24278144

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

PubMed

Neher, Deborah A; Weicht, Thomas R; Bates, Scott T; Leff, Jonathan W; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Terrestrial Macrofungal Diversity from the Tropical Dry Evergreen Biome of Southern India and Its Potential Role in Aerobiology.

PubMed

Priyamvada, Hema; Akila, M; Singh, Raj Kamal; Ravikrishna, R; Verma, R S; Philip, Ligy; Marathe, R R; Sahu, L K; Sudheer, K P; Gunthe, S S

2017-01-01

Macrofungi have long been investigated for various scientific purposes including their food and medicinal characteristics. Their role in aerobiology as a fraction of the primary biological aerosol particles (PBAPs), however, has been poorly studied. In this study, we present a source of macrofungi with two different but interdependent objectives: (i) to characterize the macrofungi from a tropical dry evergreen biome in southern India using advanced molecular techniques to enrich the database from this region, and (ii) to assess whether identified species of macrofungi are a potential source of atmospheric PBAPs. From the DNA analysis, we report the diversity of the terrestrial macrofungi from a tropical dry evergreen biome robustly supported by the statistical analyses for diversity conclusions. A total of 113 macrofungal species belonging to 54 genera and 23 families were recorded, with Basidiomycota and Ascomycota constituting 96% and 4% of the species, respectively. The highest species richness was found in the family Agaricaceae (25.3%) followed by Polyporaceae (15.3%) and Marasmiaceae (10.8%). The difference in the distribution of commonly observed macrofungal families over this location was compared with other locations in India (Karnataka, Kerala, Maharashtra, and West Bengal) using two statistical tests. The distributions of the terrestrial macrofungi were distinctly different in each ecosystem. We further attempted to demonstrate the potential role of terrestrial macrofungi as a source of PBAPs in ambient air. In our opinion, the findings from this ecosystem of India will enhance our understanding of the distribution, diversity, ecology, and biological prospects of terrestrial macrofungi as well as their potential to contribute to airborne fungal aerosols.

Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

PubMed

Wang, Q-M; Begerow, D; Groenewald, M; Liu, X-Z; Theelen, B; Bai, F-Y; Boekhout, T

2015-06-01

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota).

PubMed

Kuuskeri, Jaana; Mäkelä, Miia R; Isotalo, Jarkko; Oksanen, Ilona; Lundell, Taina

2015-10-19

The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1+5.8S+ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase.

PubMed

Abdelfattah, Ahmed; Wisniewski, Michael; Droby, Samir; Schena, Leonardo

2016-01-01

The fungal diversity in harvested apples from organic or conventional management practices was analyzed in different fruit locations (stem end, calyx end, peel, and wounded flesh) shortly after fruit purchase (T1) and after 2 weeks of storage (T5). A total of 5,760,162 high-quality fungal sequences were recovered and assigned to 8,504 Operational Taxonomic Units. Members of the phylum Ascomycota were dominant in all samples and accounted for 91.6% of the total number of detected sequences. This was followed by Basidiomycota (8%), Chytridiomycota (0.1%), and unidentified fungi (0.3%). Alpha and beta diversity analyses revealed the presence of significantly different fungal populations in the investigated fruit parts. Among detected fungi, the genus Penicillium prevailed in the peel and in the wounded flesh while Alternaria spp. prevailed in the calyx and stem end samples that included apple core tissues. Several taxonomic units that appear to be closely related to pathogenic fungi associated with secondary human infections were present in peel and wounds. Moreover, significantly different populations were revealed in organic and conventional apples and this result was consistent in all investigated fruit parts (calyx end, peel, stem end, and wounded flesh). Several unique taxa were exclusively detected in organic apples suggesting that management practices may have been a contributing factor in determining the taxa present. In contrast, little differences were revealed in the two assessment times (T1 and T5). Results of the present study represent an advancement of the current knowledge on the fungal microbiota in collected fruit tissues of apple.

Fungal Diversity and Community Composition of Culturable Fungi in Stanhopea trigrina Cast Gibberellin Producers

PubMed Central

Salazar-Cerezo, Sonia; Martinez-Montiel, Nancy; Cruz-Lopez, Maria del Carmen; Martinez-Contreras, Rebeca D.

2018-01-01

Stanhopea tigrina is a Mexican endemic orchid reported as a threatened species. The naturally occurring microorganisms present in S. tigrina are unknown. In this work, we analyzed the diversity of endophytic and epiphytic culturable fungi in S. tigrina according to morphological and molecular identification. Using this combined approach, in this study we retrieved a total of 634 fungal isolates that presented filamentous growth, which were grouped in 134 morphotypes that were associated to 63 genera, showing that S. tigrina harbors a rich diversity of both endophytic and epiphytic fungi. Among these, the majority of the isolates corresponded to Ascomycetes, with Trichoderma and Penicillium as the most frequent genera followed by Fusarium and Aspergillus. Non-ascomycetes isolated were associated only to the genus Mucor (Mucoromycota) and Schizophyllum (Basidiomycota). Identified genera showed a differential distribution considering their epiphytic or endophytic origin, the tissue from which they were isolated, and the ability of the orchid to grow on different substrates. To our knowledge, this work constitutes the first study of the mycobiome of S. tigrina. Interestingly, 21 fungal isolates showed the ability to produce gibberellins. Almost half of the isolates were related to the gibberellin-producer genus Penicillium based on morphological and molecular identification. However, the rest of the isolates were related to the following genera, which have not been reported as gibberellin producers so far: Bionectria, Macrophoma, Nectria, Neopestalotiopsis, Talaromyces, Trichoderma, and Diplodia. Taken together, we found that S. tigrina possess a significant fungal diversity that could be a rich source of fungal metabolites with the potential to develop biotechnological approaches oriented to revert the threatened state of this orchid in the near future. PMID:29670591

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing.

PubMed

Izuno, Ayako; Kanzaki, Mamoru; Artchawakom, Taksin; Wachrinrat, Chongrak; Isagi, Yuji

2016-01-01

Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%-92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica.

PubMed

Sanyal, Aritri; Antony, Runa; Samui, Gautami; Thamban, Meloth

2018-03-01

Cryoconite holes (cylindrical melt-holes on the glacier surface) are important hydrological and biological systems within glacial environments that support diverse microbial communities and biogeochemical processes. This study describes retrievable heterotrophic microbes in cryoconite hole water from three geographically distinct sites in Antarctica, and a Himalayan glacier, along with their potential to degrade organic compounds found in these environments. Microcosm experiments (22 days) show that 13-60% of the dissolved organic carbon in the water within cryoconite holes is bio-available to resident microbes. Biodegradation tests of organic compounds such as lactate, acetate, formate, propionate and oxalate that are present in cryoconite hole water show that microbes have good potential to metabolize the compounds tested. Substrate utilization tests on Biolog Ecoplate show that microbial communities in the Himalayan samples are able to oxidize a diverse array of organic substrates including carbohydrates, carboxylic acids, amino acids, amines/amides and polymers, while Antarctic communities generally utilized complex polymers. In addition, as determined by the extracellular enzyme activities, majority of the microbes (82%, total of 355) isolated in this study (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Basidiomycota) had ability to degrade a variety of compounds such as proteins, lipids, carbohydrates, cellulose and lignin that are documented to be present within cryoconite holes. Thus, microbial communities have good potential to metabolize organic compounds found in the cryoconite hole environment, thereby influencing the water chemistry in these holes. Moreover, microbes exported downstream during melting and flushing of cryoconite holes may participate in carbon cycling processes in recipient ecosystems. Copyright © 2018 Elsevier GmbH. All rights reserved.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

NASA Astrophysics Data System (ADS)

Nagano, Yuriko; Miura, Toshiko; Nishi, Shinro; Lima, Andre O.; Nakayama, Cristina; Pellizari, Vivian H.; Fujikura, Katsunori

2017-12-01

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Germination and seedling establishment in orchids: a complex of requirements

PubMed Central

Rasmussen, Hanne N.; Dixon, Kingsley W.; Jersáková, Jana; Těšitelová, Tamara

2015-01-01

Background Seedling recruitment is essential to the sustainability of any plant population. Due to the minute nature of seeds and early-stage seedlings, orchid germination in situ was for a long time practically impossible to observe, creating an obstacle towards understanding seedling site requirements and fluctuations in orchid populations. The introduction of seed packet techniques for sowing and retrieval in natural sites has brought with it important insights, but many aspects of orchid seed and germination biology remain largely unexplored. Key Considerations The germination niche for orchids is extremely complex, because it is defined by requirements not only for seed lodging and germination, but also for presence of a fungal host and its substrate. A mycobiont that the seedling can parasitize is considered an essential element, and a great diversity of Basidiomycota and Ascomycota have now been identified for their role in orchid seed germination, with fungi identifiable as imperfect Rhizoctonia species predominating. Specificity patterns vary from orchid species employing a single fungal lineage to species associating individually with a limited selection of distantly related fungi. A suitable organic carbon source for the mycobiont constitutes another key requirement. Orchid germination also relies on factors that generally influence the success of plant seeds, both abiotic, such as light/shade, moisture, substrate chemistry and texture, and biotic, such as competitors and antagonists. Complexity is furthermore increased when these factors influence seeds/seedling, fungi and fungal substrate differentially. Conclusions A better understanding of germination and seedling establishment is needed for conservation of orchid populations. Due to the obligate association with a mycobiont, the germination niches in orchid species are extremely complex and varied. Microsites suitable for germination can be small and transient, and direct observation is difficult. An experimental approach using several levels of environmental manipulation/control is recommended. PMID:26271118

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.

PubMed

Liu, Jia; Abdelfattah, Ahmed; Norelli, John; Burchard, Erik; Schena, Leonardo; Droby, Samir; Wisniewski, Michael

2018-01-27

High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component. Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9). The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.

Microbial composition and diversity are associated with plant performance: a case study on long-term fertilization effect on wheat growth in an Ultisol.

PubMed

Li, Lihua; Fan, Fenliang; Song, Alin; Yin, Chang; Cui, Peiyuan; Li, Zhaojun; Liang, Yongchao

2017-06-01

The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested. Changes in total bacterial and fungal community composition and structures using Ion Torrent sequencing were determined. The results show that the biomass of wheat was significantly higher in both sterilized soil inoculated with NPK (SNPK) and sterilized soil inoculated with MNPK (SMNPK) treatments than in other treatments (P < 0.05). The activities of β-1,4-N-acetylglucosaminidase (NAG) and cellobiohydrolase (CBH) were significantly correlated with wheat biomass. Among the microbial communities, the largest Ascomycota phylum in soils was negatively correlated with β-1,4-glucosidase (βG) (P < 0.05). The phylum Basidiomycota was negatively correlated with plant biomass (PB) and tillers per plant (TI) (P < 0.05). Nonmetric multidimensional scaling analysis shows that fungal community was strongly correlated with long-term fertilization strategy, while the bacterial community was strongly correlated with β-1,4-N-acetylglucosaminidase activity. According to the Mantel test, the growth of wheat was affected by fungal community. Taken together, microbial composition and diversity in soils could be a good player in predicting soil fertility and consequently plant growth.

Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation.

PubMed

Huang, Xinqi; Liu, Liangliang; Wen, Teng; Zhu, Rui; Zhang, Jinbo; Cai, Zucong

2015-12-01

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes, Acidobacteria, Planctomycetes increased as alternatives to the reducing Firmicutes. For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota. Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota. Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil. Copyright © 2015 Elsevier GmbH. All rights reserved.

Fungal Diversity and Community Composition of Culturable Fungi in Stanhopea trigrina Cast Gibberellin Producers.

PubMed

Salazar-Cerezo, Sonia; Martinez-Montiel, Nancy; Cruz-Lopez, Maria Del Carmen; Martinez-Contreras, Rebeca D

2018-01-01

Stanhopea tigrina is a Mexican endemic orchid reported as a threatened species. The naturally occurring microorganisms present in S. tigrina are unknown. In this work, we analyzed the diversity of endophytic and epiphytic culturable fungi in S. tigrina according to morphological and molecular identification. Using this combined approach, in this study we retrieved a total of 634 fungal isolates that presented filamentous growth, which were grouped in 134 morphotypes that were associated to 63 genera, showing that S. tigrina harbors a rich diversity of both endophytic and epiphytic fungi. Among these, the majority of the isolates corresponded to Ascomycetes, with Trichoderma and Penicillium as the most frequent genera followed by Fusarium and Aspergillus . Non-ascomycetes isolated were associated only to the genus Mucor (Mucoromycota) and Schizophyllum (Basidiomycota). Identified genera showed a differential distribution considering their epiphytic or endophytic origin, the tissue from which they were isolated, and the ability of the orchid to grow on different substrates. To our knowledge, this work constitutes the first study of the mycobiome of S. tigrina . Interestingly, 21 fungal isolates showed the ability to produce gibberellins. Almost half of the isolates were related to the gibberellin-producer genus Penicillium based on morphological and molecular identification. However, the rest of the isolates were related to the following genera, which have not been reported as gibberellin producers so far: Bionectria, Macrophoma, Nectria, Neopestalotiopsis, Talaromyces, Trichoderma , and Diplodia . Taken together, we found that S. tigrina possess a significant fungal diversity that could be a rich source of fungal metabolites with the potential to develop biotechnological approaches oriented to revert the threatened state of this orchid in the near future.

Overview on the Biochemical Potential of Filamentous Fungi to Degrade Pharmaceutical Compounds

PubMed Central

Olicón-Hernández, Darío R.; González-López, Jesús; Aranda, Elisabet

2017-01-01

Pharmaceuticals represent an immense business with increased demand due to intensive livestock raising and an aging human population, which guarantee the quality of human life and well-being. However, the development of removal technologies for these compounds is not keeping pace with the swift increase in their use. Pharmaceuticals constitute a potential risk group of multiclass chemicals of increasing concern since they are extremely frequent in all environments and have started to exhibit negative effects on micro- and macro-fauna as well as on human health. In this context, fungi are known to be extremely diverse and poorly studied microorganisms despite being well suited for bioremediation processes, taking into account their metabolic and physiological characteristics for the transformation of even highly toxic xenobiotic compounds. Increasing studies indicate that fungi can transform many structures of pharmaceutical compounds, including anti-inflammatories, β-blockers, and antibiotics. This is possible due to different mechanisms in combination with the extracellular and intracellular enzymes, which have broad of biotechnological applications. Thus, fungi and their enzymes could represent a promising tool to deal with this environmental problem. Here, we review the studies performed on pharmaceutical compounds biodegradation by the great diversity of these eukaryotes. We examine the state of the art of the current application of the Basidiomycota division, best known in this field, as well as the assembly of novel biodegradation pathways within the Ascomycota division and the Mucoromycotina subdivision from the standpoint of shared enzymatic systems, particularly for the cytochrome P450 superfamily of enzymes, which appear to be the key enzymes in these catabolic processes. Finally, we discuss the latest advances in the field of genetic engineering for their further application. PMID:28979245

Evaluation of the functional roles of fungal endophytes of Phragmites australis from high saline and low saline habitats

USGS Publications Warehouse

Soares, Marcos Antonio; Li, Hai-Yan; Kowalski, Kurt P.; Bergen, Marshall; Torres, Monica S.; White, James F.

2016-01-01

Non-native Phragmites australis decreases biodiversity and produces dense stands in North America. We surveyed the endophyte communities in the stems, leaves and roots of collections of P. australis obtained from two sites with a low and high salt concentration to determine differences in endophyte composition and assess differences in functional roles of microbes in plants from both sites. We found differences in the abundance, richness and diversity of endophytes between the low saline collections (18 species distributed in phyla Ascomycota, Basidiomycota and Stramenopiles (Oomycota); from orders Dothideales, Pleosporales, Hypocreales, Eurotiales, Cantharellales and Pythiales; Shannon H = 2.639; Fisher alpha = 7.335) and high saline collections (15 species from phylum Ascomycota; belonging to orders Pleosporales, Hypocreales, Diaporthales, Xylariales and Dothideales; Shannon H = 2.289; Fisher alpha = 4.181). Peyronellaea glomerata, Phoma macrostoma and Alternaria tenuissima were species obtained from both sites. The high salt endophyte community showed higher resistance to zinc, mercury and salt stress compared to fungal species from the low salt site. These endophytes also showed a greater propensity for growth promotion of rice seedlings (a model species) under salt stress. The results of this study are consistent with the ‘habitat-adapted symbiosis hypothesis’ that holds that endophytic microbes may help plants adapt to extreme habitats. The capacity of P. australis to establish symbiotic relationships with diverse endophytic microbes that enhance its tolerance to abiotic stresses could be a factor that contributes to its invasiveness in saline environments. Targeting the symbiotic associates of P. australis could lead to more sustainable control of non-native P. australis.

Optimization of the Liquid Culture Medium Composition to Obtain the Mycelium of Agaricus bisporus Rich in Essential Minerals.

PubMed

Krakowska, Agata; Reczyński, Witold; Muszyńska, Bożena

2016-09-01

Agaricus bisporus species (J.E. Lange) Imbach one of the most popular Basidiomycota species was chosen for the research because of its dietary and medicinal value. The presented herein studies included determination of essential mineral accumulation level in the mycelium of A. bisporus, cultivated on liquid cultures in the medium supplemented with addition of the chosen metals' salts. Quantitative analyses of Zn, Cu, Mg, and Fe in liquid cultures made it possible to determine the relationship between accumulation of the selected mineral in A. bisporus mycelium and the culture conditions. Monitoring of the liquid cultures and determination of the elements' concentrations in mycelium of A. bisporus were performed using the flame technique of AAS method. Concentration of Zn in the mycelium, maintained in the medium with the addition of its salt, was in a very wide range from 95.9 to 4462.0 mg/g DW. In the analyzed A. bisporus mycelium, cultured in the medium enriched with copper salt, this metal concentration changed from 89.79 to 7491.50 mg/g DW; considering Mg in liquid cultured mycelium (medium with Mg addition), its concentration has changed from 0.32 to 10.55 mg/g DW. The medium enriched with iron salts has led to bioaccumulation of Fe in mycelia of A. bisporus. Determined Fe concentration was in the range from 0.62 to 161.28 mg/g DW. The proposed method of liquid A. bisporus culturing on medium enriched with the selected macro- and microelements in proper concentrations ratio have led to obtaining maximal growth of biomass, characterized by high efficiency of the mineral accumulation. As a result, a dietary component of increased nutritive value was obtained.

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology

PubMed Central

Debode, Jane; De Tender, Caroline; Soltaninejad, Saman; Van Malderghem, Cinzia; Haegeman, Annelies; Van der Linden, Inge; Cottyn, Bart; Heyndrickx, Marc; Maes, Martine

2016-01-01

Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia coli O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves. PMID:27148242

Production of cyathane type secondary metabolites by submerged cultures of Hericium erinaceus and evaluation of their antibacterial activity by direct bioautography.

PubMed

Shen, T; Morlock, G; Zorn, H

2015-01-01

Fungi of the phylum Basidiomycota are well-known to form a broad spectrum of biologically active secondary metabolites, especially low molecular weight compounds such as terpenoids. Hericium erinaceus produces various cyathane type diterpenoids including erinacines. However, no quantitative data and production kinetics have been reported on the biosynthesis of the erinacines C and P in submerged cultures. In the present study, the production of erinacine C was optimized, and the product formation kinetics as well as the antimicrobial activity were studied by high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC) and direct bioautography. Oatmeal and Edamin ® K were identified to be crucial media components for an efficient production of erinacine C. The highest concentrations of erinacine C were obtained in the optimized culture medium on the 9 th culture day (approximately 260 mg L -1 ). The production of erinacine P was strongly time dependent. The maximum concentration of erinacine P of 184 mg L -1 was observed on the third culture day. Afterwards, the concentrations of erinacine P decreased while the concentrations of erinacine C steadily increased. Comparable results were obtained by HPTLC with UV detection and HPLC with diode-array detection (DAD) analyses. Direct bioautography allowed for an additional analysis of the antimicrobial activity of the secondary metabolites. The C and N sources oatmeal and Edamin ® K induced the formation of erinacine C. Detailed product formation kinetics of the erinacines C and P have been reported for the first time. HPTLC combined with the Aliivibrio fischeri bioassay allowed for an instant detection of cyathane diterpenoids in crude extracts and for an evaluation of the antimicrobial activity of the secondary metabolites directly on the plate.

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic)

PubMed Central

Zhang, Tao; Wang, Neng-Fei; Liu, Hong-Yu; Zhang, Yu-Qin; Yu, Li-Yan

2016-01-01

This study assessed the fungal community composition and its relationships with properties of surface soils in the Ny-Ålesund Region (Svalbard, High Arctic). A total of thirteen soil samples were collected and soil fungal community was analyzed by 454 pyrosequencing with fungi-specific primers targeting the rDNA internal transcribed spacer (ITS) region. The following eight soil properties were analyzed: pH, organic carbon (C), organic nitrogen (N), ammonium nitrogen (NH4+-N), silicate silicon (SiO42--Si), nitrite nitrogen (NO2--N), phosphate phosphorus (PO43--P), and nitrate nitrogen (NO3--N). A total of 57,952 reads belonging to 541 operational taxonomic units (OTUs) were found. of these OTUs, 343 belonged to Ascomycota, 100 to Basidiomycota, 31 to Chytridiomycota, 22 to Glomeromycota, 11 to Zygomycota, 10 to Rozellomycota, whereas 24 belonged to unknown fungi. The dominant orders were Helotiales, Verrucariales, Agaricales, Lecanorales, Chaetothyriales, Lecideales, and Capnodiales. The common genera (>eight soil samples) were Tetracladium, Mortierella, Fusarium, Cortinarius, and Atla. Distance-based redundancy analysis (db-rda) and analysis of similarities (ANOSIM) revealed that soil pH (p = 0.001) was the most significant factor in determining the soil fungal community composition. Members of Verrucariales were found to predominate in soils of pH 8–9, whereas Sordariales predominated in soils of pH 7–8 and Coniochaetales predominated in soils of pH 6–7. The results suggest the presence and distribution of diverse soil fungal communities in the High Arctic, which can provide reliable data for studying the ecological responses of soil fungal communities to climate changes in the Arctic. PMID:26955371

Fungal diversity, dominance, and community structure in the rhizosphere of clonal Picea mariana plants throughout nursery production chronosequences.

PubMed

Vujanovic, V; Hamelin, R C; Bernier, L; Vujanovic, G; St-Arnaud, M

2007-11-01

Fungal diversity in the rhizosphere of healthy and diseased clonal black spruce (Picea mariana) plants was analyzed with regard to nursery production chronosequences. The four key production stages were sampled: mother plants (MP), 8-week-old cuttings (B + 0), second-year cuttings (B + 1), and third-year cuttings (B + 2). A total of 45 fungal taxa were isolated and identified based on cultural, phenotypic, and molecular characters. Members of phylum Ascomycota dominated, followed by Basidiomycota and Zygomycota. Diagnosis characters and distance analysis of the internal transcribed spacer rDNA sequences allowed the identification of 39 ascomycetous taxa. Many belong to the order Hypocreales, families Hypocreaceae and Nectriaceae, which contain many clusters of potentially pathogenic taxa (Cylindrocladium, Fusarium, and Neonectria) and are also ecologically associated with antagonistic taxa (Chaetomium, Hypocrea, Microsphaeropsis, Penicillium, Paecilomyces, Verticillium, Trichoderma, and Sporothrix). This is also the first report of a Cylindrocladium canadense association with disease symptoms and relation with Pestalotiopsis, Fusarium, Exserochilum, Rhizoctonia, and Xenochalara fungal consortia. Both production chronosequence and plant health considerably influenced fungal taxa assemblages. Unweighted pair-group arithmetic average clustering showed that isolates from MP, B + 0, and B + 1 plant rhizospheres clustered together within healthy or diseased health classes, whereas isolates from healthy and diseased B + 2 plants clustered together. Canonical correspondence analysis revealed substantial alteration in community assemblages with regard to plant health and yielded a principal axis direction that regrouped taxa associated with diseased plant rhizosphere soil, whereas the opposite axis direction was associated with healthy plants. Two diversity indices were defined and applied to assess the fungal taxa contribution (Tc) and persistence (Pi) throughout the production.

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses

PubMed Central

Narendrula-Kotha, Ramya; Nkongolo, Kabwe K.

2017-01-01

Aims To assess the effects of dolomitic limestone applications on soil microbial communities’ dynamics and bacterial and fungal biomass, relative abundance, and diversity in metal reclaimed regions. Methods and Results The study was conducted in reclaimed mining sites and metal uncontaminated areas. The limestone applications were performed over 35 years ago. Total microbial biomass was determined by Phospholipid fatty acids. Bacterial and fungal relative abundance and diversity were assessed using 454 pyrosequencing. There was a significant increase of total microbial biomass in limed sites (342 ng/g) compared to unlimed areas (149 ng/g). Chao1 estimates followed the same trend. But the total number of OTUs (Operational Taxonomic Units) in limed (463 OTUs) and unlimed (473 OTUs) soil samples for bacteria were similar. For fungi, OTUs were 96 and 81 for limed and unlimed soil samples, respectively. Likewise, Simpson and Shannon diversity indices revealed no significant differences between limed and unlimed sites. Bacterial and fungal groups specific to either limed or unlimed sites were identified. Five major bacterial phyla including Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, and Proteobacteria were found. The latter was the most prevalent phylum in all the samples with a relative abundance of 50%. Bradyrhizobiaceae family with 12 genera including the nitrogen fixing Bradirhizobium genus was more abundant in limed sites compared to unlimed areas. For fungi, Ascomycota was the most predominant phylum in unlimed soils (46%) while Basidiomycota phylum represented 86% of all fungi in the limed areas. Conclusion Detailed analysis of the data revealed that although soil liming increases significantly the amount of microbial biomass, the level of species diversity remain statistically unchanged even though the microbial compositions of the damaged and restored sites are different. Significance and Impact of the study Soil liming still have a significant beneficial effects on soil microbial abundance and composition > 35 years after dolomitic limestone applications. PMID:28052072

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

Illumina sequencing of fungi associated with manganese oxide deposits in cave systems

NASA Astrophysics Data System (ADS)

Zorn, B. T.; Santelli, C. M.; Carmichael, S. K.; Pepe-Ranney, C. P.; Roble, L.; Carmichael, M.; Bräuer, S.

2013-12-01

The environmental cycling of manganese (Mn) remains relatively poorly characterized when compared with other metals such as iron. However, fungi have been observed to produce Mn(III/IV) oxides resembling buserite, birnessite, and todorokite on the periphery of vegetative hyphae, hyphal branching points and at the base of fruiting bodies. Recent studies indicate that some of these oxides may be generated by a two-stage reaction with soluble Mn(II) and biogenic reactive oxygen species for some groups of fungi, in particular the Ascomycota. These oxides can provide a versatile protective barrier or aid in the capture of trace metals in the environment, although the exact evolutionary function and trigger is unclear. In this study, two caves in the southern Appalachians, a pristine cave and an anthropogenically impacted cave, were compared by analyzing fungal community assemblages in manganese oxide rich deposits. Quantitative PCR data indicated that fungi are present in a low abundance (<1%) in all locations sampled within the caves. Among amplified DNA sequences retrieved in an 18S rDNA clone library, over 88% were representative of the phylum Basidiomycota (predominantly Agaricomycetes), 2.74% of Ascomycota, 2.28% of Blastocladiomycota and Chytridiomycota, 0.46% of Zygomycota, and 3.65% of Eukarya or Fungi incertae sedis. Using Illumina's MiSeq to sequence amplicons of the fungal ITS1 gene has yielded roughly 100,000-200,000 paired-end reads per sample. These data are currently being analyzed to compare fungal communities before and after induced Mn oxidation in the field. In addition, sites within the pristine cave are being compared with analogous sites in the impacted cave. Culturing efforts have thus far yielded Mn oxide producing members of the orders Glomerales and Pleosporales as well as two Genus incertae sedis (Fungal sp. YECT1, and Fungal sp. YECT3, growing on discarded electrical tape) that do not appear to be closely related to any other known Mn oxidizing fungi.

Diversity and Antimicrobial Activity of Culturable Endophytic Fungi Isolated from Moso Bamboo Seeds

PubMed Central

Cai, Chun-Ju; Fan, Li; Gao, Jian; Hou, Cheng-Lin

2014-01-01

Bamboos, regarded as therapeutic agents in ethnomedicine, have been used to inhibit inflammation and enhance natural immunity for a long time in Asia, and there are many bamboo associated fungi with medical and edible value. In the present study, a total of 350 fungal strains were isolated from the uncommon moso bamboo (Phyllostachys edulis) seeds for the first time. The molecular diversity of these endophytic fungi was investigated and bioactive compound producers were screened for the first time. All the fungal endophytes were categorized into 69 morphotypes according to culturable characteristics and their internal transcriber spacer (ITS) regions were analyzed by BLAST search with the NCBI database. The fungal isolates showed high diversity and were divided in Ascomycota (98.0%) and Basidiomycota (2.0%), including at least 19 genera in nine orders. Four particular genera were considered to be newly recorded bambusicolous fungi, including Leptosphaerulina, Simplicillium, Sebacina and an unknown genus in Basidiomycetes. Furthermore, inhibitory effects against clinical pathogens and phytopathogens were screened preliminarily and strains B09 (Cladosporium sp.), B34 (Curvularia sp.), B35 (undefined genus 1), B38 (Penicillium sp.) and zzz816 (Shiraia sp.) displayed broad-spectrum activity against clinical bacteria and yeasts by the agar diffusion method. The crude extracts of isolates B09, B34, B35, B38 and zzz816 under submerged fermentation, also demonstrated various levels of bioactivities against bambusicolous pathogenic fungi. This study is the first report on the antimicrobial activity of endophytic fungi associated with moso bamboo seeds, and the results show that they could be exploited as a potential source of bioactive compounds and plant defense activators. In addition, it is the first time that strains of Shiraia sp. have been isolated and cultured from moso bamboo seeds, and one of them (zzz816) could produce hypocrellin A at high yield, which is significantly different from the other strains published. PMID:24759896

Sugarcane smut: shedding light on the development of the whip-shaped sorus

PubMed Central

Marques, João Paulo R.; Appezzato-da-Glória, Beatriz; Piepenbring, Meike; Massola Jr, Nelson S.; Monteiro-Vitorello, Claudia B.

2017-01-01

Background and Aims Sugarcane smut is caused by the fungus Sporisorium scitamineum (Ustilaginales/Ustilaginomycotina/Basidiomycota), which is responsible for losses in sugarcane production worldwide. Infected plants show a profound metabolic modification resulting in the development of a whip-shaped structure (sorus) composed of a mixture of plant tissues and fungal hyphae. Within this structure, ustilospores develop and disseminate the disease. Despite the importance of this disease, a detailed histopathological analysis of the plant–pathogen interaction is lacking. Methods The whip-shaped sorus was investigated using light microscopy, scanning and transmission electron microscopy, histochemical tests and epifluorescence microscopy coupled with deconvolution. Key Results Sorus growth is mediated by intercalary meristem activity at the base of the sorus, where the fungus causes partial host cell wall degradation and formation of intercellular spaces. Sporogenesis in S. scitamineum is thallic, with ustilospore initials in intercalary or terminal positions, and mostly restricted to the base of the sorus. Ustilospore maturation is centrifugal in relation to the ground parenchyma and occurs throughout the sorus median region. At the apex of the sorus, the fungus produces sterile cells and promotes host cell detachment. Hyphae are present throughout the central axis of the sorus (columella). The plant cell produces callose around the intracellular hyphae as well as inside the papillae at the infection site. Conclusions The ontogeny of the whip-shaped sorus suggests that the fungus can cause the acropetal growth in the intercalary meristem. The sporogenesis of S. scitamineum was described in detail, demonstrating that the spores are formed exclusively at the base of the whip. Light was also shed on the nature of the sterile cells. The presence of the fungus alters the host cell wall composition, promotes its degradation and causes the release of some peripheral cells of the sorus. Finally, callose was observed around fungal hyphae in infected cells, suggesting that deposition of callose by the host may act as a structural response to fungal infection. PMID:27568298

Coupled Metagenomic and Chemical Analyses of Degrading Fungal Necromass and Implications for Fungal contributions to Stable Soil Organic Carbon

NASA Astrophysics Data System (ADS)

Egerton-Warburton, L. M.; Schreiner, K. M.; Morgan, B. S. T.; Schultz, J.; Blair, N. E.

2016-12-01

Fungi comprise a significant portion of total soil biomass, the turnover of which must represent a dominant flux within the soil carbon cycle. Fungal organic carbon (OC) can turn over on time scales of days to months, but this process is poorly understood. Here, we examined temporal changes in the chemical and microbial community composition of fungal necromass during a 2-month decomposition experiment in which Fusarium avenaceum (a common saprophyte) was exposed to a natural soil microbial community. Over the course of the experiment, residual fungal necromass was harvested and analyzed using FTIR and thermochemolysis-GCMS to examine chemical changes in the tissue. In addition, genomic DNA was extracted from tissues, amplified with barcoded ITS primers, and sequenced using the high-throughput Illumina platform to examine changes in microbial community composition. Up to 80% of the fungal necromass turned over in the first week. This rapid degradation phase corresponded to colonization of the necromass by known chitinolytic soil fungi including Mortierella species. Members of the Zygomycota and Ascomycota were among the dominant fungal groups involved in degradation with very small contributions from Basidiomycota. At the end of the 2-month degradation, only 15% of the original necromass remained. The residual material was rich in amide and C-O moieties which is consistent with previous work predicting that peptidoglycans are the main residual product from microbial tissue degradation. Straight-chain fatty acids exhibited varying degradation profiles, with some fatty acids (e.g. C16, C18:1) degrading more rapidly than bulk tissue while others maintained steady concentrations relative to bulk OC (C18) or increased in concentration throughout the degradation sequence (C24). These results indicate that the turnover of fungal necromass has the potential to rapidly and significantly influence a variety of soil OC properties including C/N ratios, lipid biomarker distributions, and OC turnover times.

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China

PubMed Central

Man, Baiying; Wang, Hongmei; Xiang, Xing; Wang, Ruicheng; Yun, Yuan; Gong, Linfeng

2015-01-01

Caves are nutrient-limited and dark subterranean ecosystems. To date, attention has been focused on geological research of caves in China, whilst indigenous microbial diversity has been insufficiently characterized. Here, we report the fungal diversity in the pristine, oligotrophic, karst Heshang Cave, central China, using a culture-dependent method coupled with the analysis of the fungal rRNA-ITS gene sequences. A total of 194 isolates were obtained with six different media from 14 sampling sites of sediments, weathered rocks, and bat guanos. Phylogenetic analysis clustered the 194 sequenced isolates into 33 genera within 15 orders of three phyla, Ascomycota, Basidiomycota, and Zygomycota, indicating a high degree of fungal diversity in the Heshang Cave. Notably, 16 out of the 36 fungal genera were also frequently observed in solution caves around the world and 23 genera were previously found in carbonate cave, indicating potential similarities among fungal communities in cave ecosystems. However, 10 genera in this study were not reported previously in any solution caves, thus expanding our knowledge about fungal diversity in cave ecosystems. Moreover, culturable fungal diversity varied from one habitat to another within the cave, being the highest in sediments, followed by weathered rocks and bat guanos as indicated by α-diversity indexes. At the genus level, Penicillium accounted for 40, 54, and 52% in three habitats of sediments, weathered rocks, and bat guanos, respectively. Trichoderma, Paecilomyces, and Aspergillus accounted for 9, 22, and 37% in the above habitats, correspondingly. Despite of the dominance of Penicillium in all samples, β-diversity index indicated significant differences between each two fungal communities in the three habitats in view of both the composition and abundance. Our study is the first report on fungal communities in a natural pristine solution cave system in central China and sheds light on fungal diversity and functions in cave ecosystems. PMID:26539184

Multigene assessment of the species boundaries and sexual status of the basidiomycetous yeasts Cryptococcus flavescens and C. terrestris (Tremellales).

PubMed

Yurkov, Andrey; Guerreiro, Marco A; Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful.

Introducing a novel mushroom from mycophagy community with emphasis on biomedical potency

PubMed Central

Khatua, Somanjana; Dutta, Arun Kumar; Chandra, Swarnendu; Paloi, Soumitra; Das, Kanad

2017-01-01

Mushrooms have been prized by humankind as medicine and culinary wonder since antiquity. Though several species are ethnically valued; many prospective species are still being discovered. One such wild macrofungus has recently been discovered during subsequent field surveys in West Bengal, India which in turn exposed as a traditionally consumed popular myco-food. The collected taxon was found to be unique with regard to its morphological as well as genetical features. After detailed characterizations, the fungus was identified as a novel taxon belonging to the genus Russula (Russulaceae, Basidiomycota). Besides, the investigation was further extended in search of new functional ingredients and in this context, a water soluble crude polysaccharide rich extract (Rusalan) was isolated from dried basidiocarps. Accumulating evidences from GC-MS, HPTLC, FT-IR along with several spectrophotometric methods postulated that the fraction consisted mainly of carbohydrate in triple helical conformation, where glucose was the major monosaccharide mostly with β-type glycosidic linkage. Conversely, Rusalan showed pronounced antioxidant activity in six in vitro assay systems with EC50 value ranging from 190–1328 μg/ml concentration. The crude polysaccharide was also evaluated against six bacterial strains using microdilution method and the growth of Staphylococcus aureus and Bacillus subtilis were found to be inhibited effectively. In addition, immune-stimulatory assays demonstrated that Rusalan could evidently promote proliferation, induce phagocytosis, release NO, produce intracellular ROS and upregulate mRNA expression of iNOS, TNF-α, COX-2, as well as IL-6 genes in in mouse macrophage cells. Therefore, aim of the present study was not only to describe a new taxon to the world mycoflora but also to introduce a potent therapeutic agent that could be explored for food and pharmaceutical purposes. However, isolation of active component and in vivo studies need to be designed further. PMID:28552988

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada.

PubMed

Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Sterflinger, Katja; Piñar, Guadalupe

2015-01-01

Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain). While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability. Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring), employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%), which decreased in the community (44.2%) after 5 months, and Gamma-proteobacteria (30.24%) and Chloroflexi (25.56%) appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1%) appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2%) and Cyanobacteria (57.8%) only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%), while, after five months, Basidiomycota (6.38%) appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33%) once again. Members of green algae (Chlorophyta, Viridiplantae) appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively. The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time. The molecular strategy employed here is suggested as an efficient monitoring tool to assess the impact on the stone-autochthonous microbiota of the application of biomineralization processes as a restoration/conservation procedure.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

PubMed Central

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

PubMed Central

Fuller, Michael P.

2017-01-01

A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota—99.31%, Basidiomycota—0.59%, Chytridiomycota—0.04%, Glomeromycota—0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota—74.26%, Basidiomycota—25.71%, Chytridiomycota—0.01%) and Thuwal (Ascomycota—99.59%, Basidiomycota—0.40%, Chytridiomycota—0.002%); while only Ascomycota—90.98% and Basidiomycota—9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road—59.88%, Khulais—68.26% and Thuwal—94.84%; while Pezizomycetes was dominant at Mecca old road—56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road—25.73%; while Tremellomycetes—5.77%, Malasseizomycetes—2.13% and Microbotryomycetes—1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais. PMID:28934322

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics.

PubMed

Ren, Chengjie; Zhang, Wei; Zhong, ZeKun; Han, Xinhui; Yang, Gaihe; Feng, Yongzhong; Ren, Guangxin

2018-01-01

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients. Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogenetic relationships and morphological evolution in Lentinus, Polyporellus and Neofavolus, emphasizing southeastern Asian taxa.

PubMed

Seelan, Jaya Seelan Sathiya; Justo, Alfredo; Nagy, Laszlo G; Grand, Edward A; Redhead, Scott A; Hibbett, David

2015-01-01

The genus Lentinus (Polyporaceae, Basidiomycota) is widely documented from tropical and temperate forests and is taxonomically controversial. Here we studied the relationships between Lentinus subg. Lentinus sensu Pegler (i.e. sections Lentinus, Tigrini, Dicholamellatae, Rigidi, Lentodiellum and Pleuroti and polypores that share similar morphological characters). We generated sequences of internal transcribed spacers (ITS) and partial 28S regions of nuc rDNA and genes encoding the largest subunit of RNA polymerase II (RPB1), focusing on Lentinus subg. Lentinus sensu Pegler and the Neofavolus group, combined these data with sequences from GenBank (including RPB2 gene sequences) and performed phylogenetic analyses with maximum likelihood and Bayesian methods. We also evaluated the transition in hymenophore morphology between Lentinus, Neofavolus and related polypores with ancestral state reconstruction. Single-gene phylogenies and phylogenies combining ITS and 28S with RPB1 and RPB2 genes all support existence of a Lentinus/Polyporellus clade and a separate Neofavolus clade. Polyporellus (represented by P. arcularius, P. ciliatus, P. brumalis) forms a clade with species representing Lentinus subg. Lentinus sensu Pegler (1983), excluding L. suavissimus. Lentinus tigrinus appears as the sister group of Polyporellus in the four-gene phylogeny, but this placement was weakly supported. All three multigene analyses and the single-gene analysis using ITS strongly supported Polyporus tricholoma as the sister group of the Lentinus/Polyporellus clade; only the 28S rRNA phylogeny failed to support this placement. Under parsimony the ancestral hymenophoral configuration for the Lentinus/Polyporellus clade is estimated to be circular pores, with independent transitions to angular pores and lamellae. The ancestral state for the Neofavolus clade is estimated to be angular pores, with a single transition to lamellae in L. suavissimus. We propose that Lentinus suavissimus (section Pleuroti) should be reclassified as Neofavolus suavissimus comb. nov. © 2015 by The Mycological Society of America.

Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete

PubMed Central

Sampaio, José Paulo; Gonçalves, Paula

2016-01-01

In fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system. PMID:27327578

Germination and seedling establishment in orchids: a complex of requirements.

PubMed

Rasmussen, Hanne N; Dixon, Kingsley W; Jersáková, Jana; Těšitelová, Tamara

2015-09-01

Seedling recruitment is essential to the sustainability of any plant population. Due to the minute nature of seeds and early-stage seedlings, orchid germination in situ was for a long time practically impossible to observe, creating an obstacle towards understanding seedling site requirements and fluctuations in orchid populations. The introduction of seed packet techniques for sowing and retrieval in natural sites has brought with it important insights, but many aspects of orchid seed and germination biology remain largely unexplored. The germination niche for orchids is extremely complex, because it is defined by requirements not only for seed lodging and germination, but also for presence of a fungal host and its substrate. A mycobiont that the seedling can parasitize is considered an essential element, and a great diversity of Basidiomycota and Ascomycota have now been identified for their role in orchid seed germination, with fungi identifiable as imperfect Rhizoctonia species predominating. Specificity patterns vary from orchid species employing a single fungal lineage to species associating individually with a limited selection of distantly related fungi. A suitable organic carbon source for the mycobiont constitutes another key requirement. Orchid germination also relies on factors that generally influence the success of plant seeds, both abiotic, such as light/shade, moisture, substrate chemistry and texture, and biotic, such as competitors and antagonists. Complexity is furthermore increased when these factors influence seeds/seedling, fungi and fungal substrate differentially. A better understanding of germination and seedling establishment is needed for conservation of orchid populations. Due to the obligate association with a mycobiont, the germination niches in orchid species are extremely complex and varied. Microsites suitable for germination can be small and transient, and direct observation is difficult. An experimental approach using several levels of environmental manipulation/control is recommended. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation

PubMed Central

Elliott, David R.; Caporn, Simon J. M.; Nwaishi, Felix; Nilsson, R. Henrik; Sen, Robin

2015-01-01

The UK hosts 15–19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration. PMID:25969988

Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation.

PubMed

Elliott, David R; Caporn, Simon J M; Nwaishi, Felix; Nilsson, R Henrik; Sen, Robin

2015-01-01

The UK hosts 15-19% of global upland ombrotrophic (rain fed) peatlands that are estimated to store 3.2 billion tonnes of carbon and represent a critical upland habitat with regard to biodiversity and ecosystem services provision. Net production is dependent on an imbalance between growth of peat-forming Sphagnum mosses and microbial decomposition by microorganisms that are limited by cold, acidic, and anaerobic conditions. In the Southern Pennines, land-use change, drainage, and over 200 years of anthropogenic N and heavy metal deposition have contributed to severe peatland degradation manifested as a loss of vegetation leaving bare peat susceptible to erosion and deep gullying. A restoration programme designed to regain peat hydrology, stability and functionality has involved re-vegetation through nurse grass, dwarf shrub and Sphagnum re-introduction. Our aim was to characterise bacterial and fungal communities, via high-throughput rRNA gene sequencing, in the surface acrotelm/mesotelm of degraded bare peat, long-term stable vegetated peat, and natural and managed restorations. Compared to long-term vegetated areas the bare peat microbiome had significantly higher levels of oligotrophic marker phyla (Acidobacteria, Verrucomicrobia, TM6) and lower Bacteroidetes and Actinobacteria, together with much higher ligninolytic Basidiomycota. Fewer distinct microbial sequences and significantly fewer cultivable microbes were detected in bare peat compared to other areas. Microbial community structure was linked to restoration activity and correlated with soil edaphic variables (e.g. moisture and heavy metals). Although rapid community changes were evident following restoration activity, restored bare peat did not approach a similar microbial community structure to non-eroded areas even after 25 years, which may be related to the stabilisation of historic deposited heavy metals pollution in long-term stable areas. These primary findings are discussed in relation to bare peat oligotrophy, re-vegetation recalcitrance, rhizosphere-microbe-soil interactions, C, N and P cycling, trajectory of restoration, and ecosystem service implications for peatland restoration.

Multigene Assessment of the Species Boundaries and Sexual Status of the Basidiomycetous Yeasts Cryptococcus flavescens and C. terrestris (Tremellales)

PubMed Central

Sharma, Lav; Carvalho, Cláudia; Fonseca, Álvaro

2015-01-01

Cryptococcus flavescens and C. terrestris are phenotypically indistinguishable sister species that belong to the order Tremellales (Tremellomycetes, Basidiomycota) and which may be mistaken for C. laurentii based on phenotype. Phylogenetic separation between C. flavescens and C. terrestris was based on rDNA sequence analyses, but very little is known on their intraspecific genetic variability or propensity for sexual reproduction. We studied 59 strains from different substrates and geographic locations, and used a multilocus sequencing (MLS) approach complemented with the sequencing of mating type (MAT) genes to assess genetic variation and reexamine the boundaries of the two species, as well as their sexual status. The following five loci were chosen for MLS: the rDNA ITS-LSU region, the rDNA IGS1 spacer, and fragments of the genes encoding the largest subunit of RNA polymerase II (RPB1), the translation elongation factor 1 alpha (TEF1) and the p21-activated protein kinase (STE20). Phylogenetic network analyses confirmed the genetic separation of the two species and revealed two additional cryptic species, for which the names Cryptococcus baii and C. ruineniae are proposed. Further analyses of the data revealed a high degree of genetic heterogeneity within C. flavescens as well as evidence for recombination between lineages detected for this species. Strains of C. terrestris displayed higher levels of similarity in all analysed genes and appear to make up a single recombining group. The two MAT genes (STE3 and SXI1/SXI2) sequenced for C. flavescens strains confirmed the potential for sexual reproduction and suggest the presence of a tetrapolar mating system with a biallelic pheromone/receptor locus and a multiallelic HD locus. In C. terrestris we could only sequence STE3, which revealed a biallelic P/R locus. In spite of the strong evidence for sexual recombination in the two species, attempts at mating compatible strains of both species on culture media were unsuccessful. PMID:25811603

Exploring the Antibacterial and Antifungal Potential of Jellyfish-Associated Marine Fungi by Cultivation-Dependent Approaches.

PubMed

Yue, Yang; Yu, Huahua; Li, Rongfeng; Xing, Ronge; Liu, Song; Li, Pengcheng

2015-01-01

Fungi isolated from marine invertebrates are of considerable importance as new promising sources of unique secondary metabolites with significant biomedical potential. However, the cultivable fungal community harbored in jellyfish was less investigated. In this work, we seek to recover symbiotic fungi from different tissues of jellyfish Nemopilema nomurai. A total of seven morphotypes were isolated, which were assigned into four genera (Aspergillus, Cladosporium, Purpureocillium, and Tilletiopsis) from two phyla (Ascomycota and Basidiomycota) by comparing the rDNA-ITS sequences with the reference sequences in GenBank. The most fungi were found in the inner tissues of subumbrella. Two of the cultivation-independent procedures, changing media type and co-cultivation, were employed to maximize the complexity of metabolites. Thus, thirteen EtOAc gum were obtained and fingerprinted by High Performance Liquid Chromatography (HPLC) equipped with a photodiode array (PDA) detector. Antibacterial and antifungal activities of these complex mixtures were tested against a panel of bacterial and fungal pathogens. The antimicrobial results showed that all of the 13 EtOAc extracts displayed different levels of antibacterial activity, three of which exhibited strong to significant antibacterial activity to the bacterial pathogens Staphylococcus aureus and Salmonella entrica. Antifungal activity indicated that the EtOAc extracts from pure culture of Aspergillus versicolor and co-culture of A. versicolor and Tilletiopsis sp. in rice media were promising for searching new compounds, with the maximal mycelial growth inhibition of 82.32% ± 0.61% for Rhizoctonia solani and 48.41% ± 11.02% for Botrytis cinerea at 200 μg/ml, respectively. This study is the first report on the antibacterial and antifungal activity of jellyfish-associated fungi and allows the first sight into cultivable fungal community residing in jellyfish. Induced metabolites by cultivation-dependent approaches provides a new reservoir for drug discovery from jellyfish-derived fungi.

Exploring the Antibacterial and Antifungal Potential of Jellyfish-Associated Marine Fungi by Cultivation-Dependent Approaches

PubMed Central

Yue, Yang; Yu, Huahua; Li, Rongfeng; Xing, Ronge; Liu, Song; Li, Pengcheng

2015-01-01

Fungi isolated from marine invertebrates are of considerable importance as new promising sources of unique secondary metabolites with significant biomedical potential. However, the cultivable fungal community harbored in jellyfish was less investigated. In this work, we seek to recover symbiotic fungi from different tissues of jellyfish Nemopilema nomurai. A total of seven morphotypes were isolated, which were assigned into four genera (Aspergillus, Cladosporium, Purpureocillium, and Tilletiopsis) from two phyla (Ascomycota and Basidiomycota) by comparing the rDNA-ITS sequences with the reference sequences in GenBank. The most fungi were found in the inner tissues of subumbrella. Two of the cultivation-independent procedures, changing media type and co-cultivation, were employed to maximize the complexity of metabolites. Thus, thirteen EtOAc gum were obtained and fingerprinted by High Performance Liquid Chromatography (HPLC) equipped with a photodiode array (PDA) detector. Antibacterial and antifungal activities of these complex mixtures were tested against a panel of bacterial and fungal pathogens. The antimicrobial results showed that all of the 13 EtOAc extracts displayed different levels of antibacterial activity, three of which exhibited strong to significant antibacterial activity to the bacterial pathogens Staphylococcus aureus and Salmonella entrica. Antifungal activity indicated that the EtOAc extracts from pure culture of Aspergillus versicolor and co-culture of A. versicolor and Tilletiopsis sp. in rice media were promising for searching new compounds, with the maximal mycelial growth inhibition of 82.32% ± 0.61% for Rhizoctonia solani and 48.41% ± 11.02% for Botrytis cinerea at 200 μg/ml, respectively. This study is the first report on the antibacterial and antifungal activity of jellyfish-associated fungi and allows the first sight into cultivable fungal community residing in jellyfish. Induced metabolites by cultivation-dependent approaches provides a new reservoir for drug discovery from jellyfish-derived fungi. PMID:26637162

[Structure and evolution of the eukaryotic FANCJ-like proteins].

PubMed

Wuhe, Jike; Zefeng, Wu; Sanhong, Fan; Xuguang, Xi

2015-02-01

The FANCJ-like protein family is a class of ATP-dependent helicases that can catalytically unwind duplex DNA along the 5'-3' direction. It is involved in the processes of DNA damage repair, homologous recombination and G-quadruplex DNA unwinding, and plays a critical role in maintaining genome integrity. In this study, we systemically analyzed FNACJ-like proteins from 47 eukaryotic species and discussed their sequences diversity, origin and evolution, motif organization patterns and spatial structure differences. Four members of FNACJ-like proteins, including XPD, CHL1, RTEL1 and FANCJ, were found in eukaryotes, but some of them were seriously deficient in most fungi and some insects. For example, the Zygomycota fungi lost RTEL1, Basidiomycota and Ascomycota fungi lost RTEL1 and FANCJ, and Diptera insect lost FANCJ. FANCJ-like proteins contain canonical motor domains HD1 and HD2, and the HD1 domain further integrates with three unique domains Fe-S, Arch and Extra-D. Fe-S and Arch domains are relatively conservative in all members of the family, but the Extra-D domain is lost in XPD and differs from one another in rest members. There are 7, 10 and 2 specific motifs found from the three unique domains respectively, while 5 and 12 specific motifs are found from HD1 and HD2 domains except the conserved motifs reported previously. By analyzing the arrangement pattern of these specific motifs, we found that RTEL1 and FANCJ are more closer and share two specific motifs Vb2 and Vc in HD2 domain, which are likely related with their G-quadruplex DNA unwinding activity. The evidence of evolution showed that FACNJ-like proteins were originated from a helicase, which has a HD1 domain inserted by extra Fe-S domain and Arch domain. By three continuous gene duplication events and followed specialization, eukaryotes finally possessed the current four members of FANCJ-like proteins.

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

PubMed Central

2013-01-01

Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity. PMID:23617724

A Phylogenetic Analysis of the Globins in Fungi

PubMed Central

Hoogewijs, David; Dewilde, Sylvia; Vierstraete, Andy; Moens, Luc; Vinogradov, Serge N.

2012-01-01

Background All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins. Results Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ∼60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota. Conclusion Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. PMID:22384087

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

PubMed

Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

2018-02-18

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

Isolation and characterization of a quinclorac-degrading Actinobacteria Streptomyces sp. strain AH-B and its implication on microecology in contaminated soil.

PubMed

Lang, Zhe; Qi, Dan; Dong, Jianjiang; Ren, Liwei; Zhu, Qifa; Huang, Weiwei; Liu, Yongmin; Lu, Diannan

2018-05-01

Quinclorac, a highly selective auxin herbicide, is widely used for controlling weeds in rice field. However, the residual quinclorac is toxic to many crops, vegetables, and aquatic animals, resulting in one of the major problems in crop rotation. Here, we investigated the degradation of quinclorac by strain AH-B, which was isolated from long-term quinclorac-contaminated soil using continuous circulating fluidized bed reactor and subjected to atmospheric and room temperature plasma mutation. Morphological examination, 16S rRNA gene sequencing, and phylogenetic analysis revealed that strain AH-B was Streptomyces sp. The quinclorac degradation efficiency of AH-B in liquid medium was 97.2% after 18 days when the initial quinclorac concentration was 20 mg L -1 . The degradation products were 3-chloro-7-methoxy-8-quinoline-carboxylic, 3-chloro-7-methyl-8-quinoline-carboxylic, 3-chloro-7-oxyethyl-8-quinoline-carboxylic, and 3,7-dichloro-6-methyl-8-quinoline-carboxylic. The inoculum size, initial quinclorac concentration, pH, and temperature were found to affect quinclorac degradation efficiency of AH-B. High-performance liquid chromatography-electrospray ionization tandem mass spectrometry analysis revealed that quinclorac degradation by AH-B produced many products. In soil with initial quinclorac content of 1 mg kg -1 dry soil, addition of AH-B resulted in 87.5% quinclorac degradation after 42 days, while that in the control (without AH-B) was 22.4%. Furthermore, microecological analysis using next-generation sequencing of 16S rRNA geneshowed that some bacterial species, such as Bacterioides and Proteobacteria, could survive in quinclorac-contaminated soil, while some bacteria, such as Firmicutes, were very sensitive to quinclorac. Besides, some fungal species, such as Basidiomycota, could also survive quinclorac-contamination. After 42 days, the diversity of bacteria and fungi in soil treated with AH-B was higher than that in the control, implying that bioaugmentation with strain AH-B could reduce quinclorac toxicity to microorganisms in soil. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparative Analysis of P450 Signature Motifs EXXR and CXG in the Large and Diverse Kingdom of Fungi: Identification of Evolutionarily Conserved Amino Acid Patterns Characteristic of P450 Family

PubMed Central

Syed, Khajamohiddin; Mashele, Samson Sitheni

2014-01-01

Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research. PMID:24743800

Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices.

PubMed

Corradi, Nicolas; Sanders, Ian R

2006-03-10

The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K+, Ca2+ and Na2+ concentrations. The presence of P-type II gene subfamilies that are specific for certain kingdoms has been reported but was sometimes contradicted by discovery of previously unknown homologous sequences in newly sequenced genomes. Members of this gene family have been sampled in all of the fungal phyla except the arbuscular mycorrhizal fungi (AMF; phylum Glomeromycota), which are known to play a key-role in terrestrial ecosystems and to be genetically highly variable within populations. Here we used highly degenerate primers on AMF genomic DNA to increase the sampling of fungal P-Type II ATPases and to test previous predictions about their evolution. In parallel, homologous sequences of the P-type II ATPases have been used to determine the nature and amount of polymorphism that is present at these loci among isolates of Glomus intraradices harvested from the same field. In this study, four P-type II ATPase sub-families have been isolated from three AMF species. We show that, contrary to previous predictions, P-type IIC ATPases are present in all basal fungal taxa. Additionally, P-Type IIE ATPases should no longer be considered as exclusive to the Ascomycota and the Basidiomycota, since we also demonstrate their presence in the Zygomycota. Finally, a comparison of homologous sequences encoding P-type IID ATPases showed unexpectedly that indel mutations among coding regions, as well as specific gene duplications occur among AMF individuals within the same field. On the basis of these results we suggest that the diversification of P-Type IIC and E ATPases followed the diversification of the extant fungal phyla with independent events of gene gains and losses. Consistent with recent findings on the human genome, but at a much smaller geographic scale, we provided evidence that structural genomic changes, such as exonic indel mutations and gene duplications are less rare than previously thought and that these also occur within fungal populations.

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study.

PubMed

Hanson, Blake; Zhou, Yanjiao; Bautista, Eddy J; Urch, Bruce; Speck, Mary; Silverman, Frances; Muilenberg, Michael; Phipatanakul, Wanda; Weinstock, George; Sodergren, Erica; Gold, Diane R; Sordillo, Joanne E

2016-06-15

Environmental microbes have been associated with both protective and adverse health effects in children and adults. Epidemiological studies often rely on broad biomarkers of microbial exposure (i.e. endotoxin, 1 → 3-beta-d-glucan), but fail to identify the taxonomic composition of the microbial community. Our aim was to characterize the bacterial and fungal microbiome in different types of environmental samples collected in studies of human health effects. We determined the composition of microbial communities present in home, school and outdoor air samples by amplifying and sequencing regions of rRNA genes from bacteria (16S) and fungi (18S and ITS). Samples for this pilot study included indoor settled dust (from both a Boston area birth cohort study on Home Allergens and Asthma (HAA) (n = 12) and a study of school exposures and asthma symptoms (SICAS) (n = 1)), as well as fine and coarse concentrated outdoor ambient particulate (CAP) samples (n = 9). Sequencing of amplified 16S, 18S, and ITS regions was performed on the Roche-454 Life Sciences Titanium pyrosequencing platform. Indoor dust samples were dominated by Gram-positive bacteria (Firmicutes and Actinobacteria); the most abundant bacterial genera were those related to human flora (Streptococcus, Staphylococcus, Corynebacterium and Lactobacillus). Outdoor CAPs were dominated by Gram-negative Proteobacteria from water and soil sources, in particular the genera Acidovorax, and Brevundimonas (which were present at very low levels or entirely absent in indoor dust). Phylum-level fungal distributions identified by 18S or ITS regions showed very similar findings: a predominance of Ascomycota in indoor dust and Basidiomycota in outdoor CAPs. ITS sequencing of fungal genera in indoor dust showed significant proportions of Aureobasidium and Leptosphaerulina along with some contribution from Cryptococcus, Epicoccum, Aspergillus and the human commensal Malassezia. ITS sequencing detected more than 70 fungal genera in indoor dust not observed by culture. Microbiome sequencing is feasible for different types of archived environmental samples (indoor dust, and low biomass air particulate samples), and offers the potential to study how whole communities of microbes (including unculturable taxa) influence human health.

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study†

PubMed Central

Hanson, Blake; Zhou, Yanjiao; Bautista, Eddy J.; Urch, Bruce; Speck, Mary; Silverman, Frances; Muilenberg, Michael; Phipatanakul, Wanda; Weinstock, George; Sodergren, Erica; Gold, Diane R.; Sordillo, Joanne E.

2016-01-01

Environmental microbes have been associated with both protective and adverse health effects in children and adults. Epidemiological studies often rely on broad biomarkers of microbial exposure (i.e. endotoxin, 1→3, Beta-D glucan), but fail to identify the taxonomic composition of the microbial community. Our aim was to characterize the bacterial and fungal microbiome in different types of environmental samples collected in studies of human health effects. We determined the composition of microbial communities present in home, school and outdoor air samples by amplifying and sequencing regions of rRNA genes from bacteria (16S) and fungi (18S and ITS). Samples for this pilot study included indoor settled dust (from both a Boston area birth cohort study on Home Allergens and Asthma (HAA)(n=12) and a study of school exposures and asthma symptoms (SICAS) (n=1)), as well as fine and coarse concentrated outdoor ambient particulate (CAP) samples (n=9). Sequencing of amplified 16S, 18S, and ITS regions was performed on the Roche-454 Life Sciences Titanium pyrosequencing platform. Indoor dust samples were dominated by gram-positive bacteria (Firmicutes and Actinobacteria); the most abundant bacterial genera were those related to human flora (Streptococcus, Staphylococcus, Corynebacterium and Lactobacillus). Outdoor CAPs were dominated by gram-negative Proteobacteria from water and soil sources, in particular the genera Acidovorax, and Brevundimonas (which were present at very low levels or entirely absent in indoor dust). Phylum-level fungal distributions identified by 18S or ITS regions showed very similar findings: a predominance of Ascomycota in indoor dust and Basidiomycota in outdoor CAPs. ITS sequencing of fungal genera in indoor dust showed significant proportions of Aureobasidium and Leptosphaerulina along with some contribution from Cryptococcus, Epicoccum, Aspergillus and the human commensal Malassezia. ITS sequencing detected an additional 70 fungal genera in indoor dust not observed by culture. Microbiome sequencing is feasible for different types of archived environmental samples (indoor dust, and low biomass air particulate samples), and offers the potential to study how whole communities of microbes (including unculturable taxa) influence human health. PMID:27213188

The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared Counterparts

PubMed Central

Siriyappagouder, Prabhugouda; Kiron, Viswanath; Lokesh, Jep; Rajeish, Moger; Kopp, Martina; Fernandes, Jorge

2018-01-01

As an integral part of the resident microbial community of fish intestinal tract, the mycobiota is expected to play important roles in health and disease resistance of the host. The composition of the diverse fungal communities, which colonize the intestine, is greatly influenced by the host, their diet and geographic origin. Studies of fungal communities are rare and the majority of previous studies have relied on culture-based methods. In particular, fungal communities in fish are also poorly characterized. The aim of this study was to provide an in-depth overview of the intestinal mycobiota in a model fish species (zebrafish, Danio rerio) and to determine differences in fungal composition between wild and captive specimens. We have profiled the intestinal mycobiota of wild-caught (Sharavati River, India), laboratory-reared (Bodø, Norway) and wild-caught-laboratory-kept (Uttara, India) zebrafish by sequencing the fungal internal transcribed spacer 2 region on the Illumina MiSeq platform. Wild fish were exposed to variable environmental factors, whereas both laboratory groups were kept in controlled conditions. There were also differences in husbandry practices at Bodø and Uttara, particularly diet. Zebrafish from Bodø were reared in the laboratory for over 10 generations, while wild-caught-laboratory-kept fish from Uttara were housed in the laboratory for only 2 months before sample collection. The intestine of zebrafish contained members of more than 15 fungal classes belonging to the phyla Ascomycota, Basidiomycota, and Zygomycota. Fungal species richness and diversity distinguished the wild-caught and laboratory-reared zebrafish communities. Wild-caught zebrafish-associated mycobiota comprised mainly Dothideomycetes in contrast to their Saccharomycetes-dominated laboratory-reared counterparts. The predominant Saccharomycetes in laboratory-reared fish belonged to the saprotrophic guild. Another characteristic feature of laboratory-reared fish was the significantly higher abundance of Cryptococcus (Tremellomycetes) compared to wild fish. This pioneer study has shed light into the differences in the intestinal fungal communities of wild-caught and laboratory-reared zebrafish and the baseline data generated will enrich our knowledge on fish mycobiota. PMID:29559965

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir

PubMed Central

Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

2018-01-01

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology. PMID:29463021

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada

PubMed Central

Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Sterflinger, Katja; Piñar, Guadalupe

2015-01-01

Background Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain). While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability. Methodology/Principal Findings Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring), employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%), which decreased in the community (44.2%) after 5 months, and Gamma-proteobacteria (30.24%) and Chloroflexi (25.56%) appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1%) appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2%) and Cyanobacteria (57.8%) only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%), while, after five months, Basidiomycota (6.38%) appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33%) once again. Members of green algae (Chlorophyta, Viridiplantae) appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively. Conclusions The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time. The molecular strategy employed here is suggested as an efficient monitoring tool to assess the impact on the stone-autochthonous microbiota of the application of biomineralization processes as a restoration/conservation procedure. PMID:26222040

Energy balance associated with the degradation of lignocellulosic material by white-rot and brown-rot fungi.

NASA Astrophysics Data System (ADS)

Derrien, Delphine; Bédu, Hélène; Buée, Marc; Kohler, Annegret; Goodell, Barry; Gelhaye, Eric

2017-04-01

Forest soils cover about 30% of terrestrial area and comprise between 50 and 80% of the global stock of soil organic carbon (SOC). The major precursor for this forest SOC is lignocellulosic material, which is made of polysaccharides and lignin. Lignin has traditionally been considered as a recalcitrant polymer that hinders access to the much more labile structural polysaccharides. This view appears to be partly incorrect from a microbiology perspective yet, as substrate alteration depends on the metabolic potential of decomposers. In forest ecosystems the wood-rotting Basidiomycota fungi have developed two different strategies to attack the structure of lignin and gain access to structural polysaccharides. White-rot fungi degrade all components of plant cell walls, including lignin, using enzymatic systems. Brown-rot fungi do not remove lignin. They generate oxygen-derived free radicals, such as the hydroxyl radical produced by the Fenton reaction, that disrupt the lignin polymer and depolymerize polysaccharides which then diffuse out to where the enzymes are located The objective of this study was to develop a model to investigate whether the lignin relative persistence could be related to the energetic advantage of brown-rot degradative pathway in comparison to white-rot degradative pathway. The model simulates the changes in substrate composition over time, and determines the energy gained from the conversion of the lost substrate into CO2. The energy cost for the production of enzymes involved in substrate alteration is assessed using information derived from genome and secretome analysis. For brown-rot fungus specifically, the energy cost related to the production of OH radicals is also included. The model was run, using data from the literature on populous wood degradation by Trametes versicolor, a white-rot fungus, and Gloeophyllum trabeum, a brown-rot fungus. It demonstrates that the brown-rot fungus (Gloeophyllum trabeum) was more efficient than the white-rot fungus (Trametes versicolor). The energy advantage could explain the emergence of the brown-rot degradative pathway from a white-rot degradative pathway and subsequently, the relative persistence of lignin in soil.

The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared Counterparts.

PubMed

Siriyappagouder, Prabhugouda; Kiron, Viswanath; Lokesh, Jep; Rajeish, Moger; Kopp, Martina; Fernandes, Jorge

2018-01-01

As an integral part of the resident microbial community of fish intestinal tract, the mycobiota is expected to play important roles in health and disease resistance of the host. The composition of the diverse fungal communities, which colonize the intestine, is greatly influenced by the host, their diet and geographic origin. Studies of fungal communities are rare and the majority of previous studies have relied on culture-based methods. In particular, fungal communities in fish are also poorly characterized. The aim of this study was to provide an in-depth overview of the intestinal mycobiota in a model fish species (zebrafish, Danio rerio ) and to determine differences in fungal composition between wild and captive specimens. We have profiled the intestinal mycobiota of wild-caught (Sharavati River, India), laboratory-reared (Bodø, Norway) and wild-caught-laboratory-kept (Uttara, India) zebrafish by sequencing the fungal internal transcribed spacer 2 region on the Illumina MiSeq platform. Wild fish were exposed to variable environmental factors, whereas both laboratory groups were kept in controlled conditions. There were also differences in husbandry practices at Bodø and Uttara, particularly diet. Zebrafish from Bodø were reared in the laboratory for over 10 generations, while wild-caught-laboratory-kept fish from Uttara were housed in the laboratory for only 2 months before sample collection. The intestine of zebrafish contained members of more than 15 fungal classes belonging to the phyla Ascomycota, Basidiomycota, and Zygomycota. Fungal species richness and diversity distinguished the wild-caught and laboratory-reared zebrafish communities. Wild-caught zebrafish-associated mycobiota comprised mainly Dothideomycetes in contrast to their Saccharomycetes-dominated laboratory-reared counterparts. The predominant Saccharomycetes in laboratory-reared fish belonged to the saprotrophic guild. Another characteristic feature of laboratory-reared fish was the significantly higher abundance of Cryptococcus (Tremellomycetes) compared to wild fish. This pioneer study has shed light into the differences in the intestinal fungal communities of wild-caught and laboratory-reared zebrafish and the baseline data generated will enrich our knowledge on fish mycobiota.

Mycobiome of Cysts of the Soybean Cyst Nematode Under Long Term Crop Rotation.

PubMed

Hu, Weiming; Strom, Noah; Haarith, Deepak; Chen, Senyu; Bushley, Kathryn E

2018-01-01

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe (Phylum Nematoda), is a major pathogen of soybean. It causes substantial yield losses worldwide and is difficult to control because the cyst protects the eggs which can remain viable for nearly a decade. Crop rotation with non-host crops and use of biocontrol organisms such as fungi and bacteria offer promising approaches, but remain hampered by lack of knowledge of the biology of nematode parasitic organisms. We used a high-throughput metabarcoding approach to characterize fungal communities associated with the SCN cyst, a microenvironment in soil that may harbor both nematode parasites and plant pathogens. SCN cysts were collected from a long-term crop rotation experiment in Southeastern Minnesota at three time points over two growing seasons to characterize diversity of fungi inhabiting cysts and to examine how crop rotation and seasonal variation affects fungal communities. A majority of fungi in cysts belonged to Ascomycota and Basidiomycota, but the presence of several early diverging fungal subphyla thought to be primarily plant and litter associated, including Mortierellomycotina and Glomeromycotina (e.g., arbuscular mycorrhizal fungi), suggests a possible role as nematode egg parasites. Species richness varied by both crop rotation and season and was higher in early years of crop rotation and in fall at the end of the growing season. Crop rotation and season also impacted fungal community composition and identified several classes of fungi, including Eurotiomycetes, Sordariomycetes, and Orbiliomycetes (e.g., nematode trapping fungi), with higher relative abundance in early soybean rotations. The relative abundance of several genera was correlated with increasing years of soybean. Fungal communities also varied by season and were most divergent at midseason. The percentage of OTUs assigned to Mortierellomycotina_cls_Incertae_sedis and Sordariomycetes increased at midseason, while Orbiliomycetes decreased at midseason, and Glomeromycetes increased in fall. Ecological guilds of fungi containing an animal-pathogen lifestyle, as well as potential egg-parasitic taxa previously isolated from parasitized SCN eggs, increased at midseason. The animal pathogen guilds included known (e.g., Pochonia chlamydosporia ) and new candidate biocontrol organisms. This research advances knowledge of the ecology of nematophagous fungi in agroecosystems and their use as biocontrol agents of the SCN.

Correlating bioaerosol load with PM2.5 and PM10cf concentrations: a comparison between natural desert and urban-fringe aerosols

NASA Astrophysics Data System (ADS)

Boreson, Justin; Dillner, Ann M.; Peccia, Jordan

2004-11-01

Seasonal allergies and microbial mediated respiratory diseases, can coincide with elevated particulate matter concentrations, often when dry desert soils are disturbed. In addition to effects from the allergens, allergic and asthmatic responses may be enhanced when chemical and biological constituents of particulate matter (PM) are combined together. Because of these associations and also the recent regulatory and health-related interests of monitoring PM2.5, separately from total PM10, the biological loading between the fine (dp<2.5 μm) and coarse (2.5 μm

Mycogenic Mn(II) oxidation promotes remediation of acid mine drainage and other anthropogenically impacted environments

NASA Astrophysics Data System (ADS)

Santelli, C. M.; Chaput, D.; Hansel, C. M.; Burgos, W. D.

2014-12-01

Manganese is a pollutant in worldwide environments contaminated with metals and organics, such as acid mine drainage (AMD), freshwater ponds, and agricultural waste storage sites. Microorganisms contribute to the removal of dissolved Mn compounds in the environment by promoting Mn(II) oxidation reactions. The oxidation of Mn(II) results in the precipitation of sparingly soluble Mn(IV) oxide minerals, effectively removing the metal from the aqueous milieu (e.g., groundwater or wastewater streams). In recent years, our research has identified a diversity of Mn(II)-oxidizing fungi inhabiting these polluted environments, however their overall contribution to the remediation process in situ remains poorly understood. Here we present results of culture-based and Next Generation Sequencing (NGS) studies in AMD treatment systems actively remediating Mn and other metals where we profile the bacterial, fungal, algal and archaeal communities to determine the overall community diversity and to establish the relative abundance of known Mn(II) oxidizers. A variety of treatment systems with varying Mn-removal efficiencies were sampled to understand the relationship between remediation efficiency and microbial community composition and activity. Targeted-amplicon sequencing of DNA and RNA of the 16S rRNA genes (bacteria and archaea), 23S rRNA genes (algae) and ITS region (fungi) was performed using both 454 pyrosequencing and Illumina platforms. Results showed that only the fungal taxonomic profiles significantly differed between sites that removed the majority of influent Mn and those that did not. Specifically, Ascomycota (which include known Mn(II) oxidizers isolated from these treatment systems) dominated greater efficiency systems whereas less efficient systems were dominated by Basidiomycota. Furthermore, known Mn(II) oxidizers accounted for only a minor proportion of bacterial sequences but a far greater proportion of fungal sequences. These culture-independent studies lend further evidence to numerous culture-based studies (of AMD remediation systems here, as well as a variety of other metal-rich systems) that establish Mn(II)-oxidizing fungi as important contributors to the remediation of Mn, and likely other metals, in metal polluted environments.

Study of Holtermanniella wattica, Leucosporidium creatinivorum, Naganishia adeliensis, Solicoccozyma aeria, and Solicoccozyma terricola for their lipogenic aptitude from different carbon sources.

PubMed

Filippucci, Sara; Tasselli, Giorgia; Scardua, Alessandro; Di Mauro, Simone; Cramarossa, Maria Rita; Perini, Davide; Turchetti, Benedetta; Onofri, Andrea; Forti, Luca; Buzzini, Pietro

2016-01-01

The ability of some microorganisms to accumulate lipids is well known; however, only recently the number of studies on microbial lipid biosynthesis for obtaining oleochemical products, namely biofuels and some building blocks for chemistry, is rapidly and spectacularly increased. Since 1990s, some oleaginous yeasts were studied for their ability to accumulate lipids up to 60-70% of their dry weight. Due to the vast array of engineering techniques currently available, the recombinant DNA technology was the main approach followed so far for obtaining lipid-overproducing yeasts, mainly belonging to the Yarrowia lipolytica . However, an alternative approach can be offered by worldwide diversity as source of novel oleaginous yeasts. Lipogenic aptitude of a number of yeast strains has been reviewed, but many of these studies utilized a limited number of species and/or different culture conditions that make impossible the comparison of different results. Accordingly, the lipogenic aptitude inside the yeast world is still far from being fully explored, and finding new oleaginous yeast species can acquire a strategic importance. Holtermanniella wattica , Leucosporidium creatinivorum , Naganishia adeliensis , Solicoccozyma aeria, and Solicoccozyma terricola strains were selected as a result of a large-scale screening on 706 yeasts (both Ascomycota and Basidiomycota). Lipid yields and fatty acid profiles of selected strains were evaluated at 20 and 25 °C on glucose, and on glycerol, xylose, galactose, sucrose, maltose, and cellobiose. A variable fatty acid profile was observed in dependence of both temperature and different carbon sources. On the whole, L. creatinivorum exhibited the highest performances: total lipid yield (Y L ) >7 g/l on glucose and glycerol, % of intracellular lipids on cell biomass (Y L /DW) >70% at 20 °C on glucose, lipid coefficient (Y L /Glu) around 20% on glucose, and daily productivity (Y L /d) on glucose and sucrose >1.6 g/(l*d). This study provides some meaningful information about the lipogenic ability of some yeast species. Variable lipid yields and fatty acid profiles were observed in dependence of both temperature and different carbon sources. L. creatinivorum exhibited the highest lipogenic performances.

Serum immunoglobulin E and immunoglobulin G reactivity to Agaricus bisporus proteins in mushroom cultivation workers.

PubMed

Khakzad, Z; Hedayati, M T; Mahdian, S; Mayahi, S

2015-06-01

Although molds are regarded as the main fungal allergen sources, evidence indicates that spores of Basidiomycota including Agaricus bisporus ( A. bisporus ) can be also found at high concentrations in the environment and may cause as many respiratory allergies as molds. The aim of the present study was to evaluate specific immunoglobulin E (IgE) and immunoglobulin G (IgG) antibodies against A. bisporus via immunoblotting technique in individuals working at mushroom cultivation centers. In this study, 72 workers involved in the cultivation and harvest of button mushrooms were enrolled. For the analysis of serum IgE and IgG, A. bisporus grown in Sabouraud dextrose broth was harvested and ruptured by liquid nitrogen and glass beads. The obtained sample was centrifuged and the supernatant was collected as "crude extract" (CE). CE was separated via Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). The separated proteins were transferred to a nitrocellulose filter and the bands responsive to IgE and IgG were identified by anti-human conjugated antibodies. All participants were screened in terms of total IgE level. Among 72 workers, 18 (25%) had a total IgE level higher than 188 IU/mL. In SDS-PAGE, the CE of A. bisporus showed 23 different protein bands with a molecular weight range of 13-80 kDa. The sera of 23.6% and 55.5% of participants showed positive response, with specific IgE and IgG antibodies against A. bisporus in the blot, respectively. The bands with molecular weights of 62 and 68 kDa were the most reactive protein components of A. bisporus to specific IgE antibodies. Moreover, bands with molecular weights of 57 and 62 kDa showed the highest reactivity to IgG, respectively. Also, 62 and 68 kDa components were the most reactive bands with both specific IgG and IgE antibodies. The obtained findings revealed that A. bisporus has different allergens and antigens, which contribute to its potential as an aeroallergen in hypersensitivity-related reactions of the lungs.

An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi

PubMed Central

Wallen, R. M.; Perlin, Michael H.

2018-01-01

Sexual reproduction likely evolved as protection from environmental stresses, specifically, to repair DNA damage, often via homologous recombination. In higher eukaryotes, meiosis and the production of gametes with allelic combinations different from parental type provides the side effect of increased genetic variation. In fungi it appears that while the maintenance of meiosis is paramount for success, outcrossing is not a driving force. In the subkingdom Dikarya, fungal members are characterized by existence of a dikaryon for extended stages within the life cycle. Such fungi possess functional or, in some cases, relictual, loci that govern sexual reproduction between members of their own species. All mating systems identified so far in the Dikarya employ a pheromone/receptor system for haploid organisms to recognize a compatible mating partner, although the paradigm in the Ascomycota, e.g., Saccharomyces cerevisiae, is that genes for the pheromone precursor and receptor are not found in the mating-type locus but rather are regulated by its products. Similarly, the mating systems in the Ascomycota are bipolar, with two non-allelic idiomorphs expressed in cells of opposite mating type. In contrast, for the Basidiomycota, both bipolar and tetrapolar mating systems have been well characterized; further, at least one locus directly encodes the pheromone precursor and the receptor for the pheromone of a different mating type, while a separate locus encodes proteins that may regulate the first locus and/or additional genes required for downstream events. Heterozygosity at both of two unlinked loci is required for cells to productively mate in tetrapolar systems, whereas in bipolar systems the two loci are tightly linked. Finally, a trade-off exists in wild fungal populations between sexual reproduction and the associated costs, with adverse conditions leading to mating. For fungal mammal pathogens, the products of sexual reproduction can be targets for the host immune system. The opposite appears true for phytopathogenic fungi, where mating and pathogenicity are inextricably linked. Here, we explore, compare, and contrast different strategies used among the Dikarya, both saprophytic and pathogenic fungi, and highlight differences between pathogens of mammals and pathogens of plants, providing context for selective pressures acting on this interesting group of fungi. PMID:29619017

Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.

PubMed

Chen, Wen; Hambleton, Sarah; Seifert, Keith A; Carisse, Odile; Diarra, Moussa S; Peters, Rick D; Lowe, Christine; Chapados, Julie T; Lévesque, C André

2018-05-01

Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris ) and weather conditions (e.g., Mycocentrospora and Leptosphaeria ), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis ). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada. IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers. © Crown copyright 2018.

Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

PubMed Central

Parrent, Jeri Lynn; James, Timothy Y; Vasaitis, Rimvydas; Taylor, Andrew FS

2009-01-01

Background Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi. Results We detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota. Conclusion We found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis. PMID:19566942

Natural succession on abandoned cropland effectively decreases the soil erodibility and improves the fungal diversity.

PubMed

Zhang, Chao; Liu, Guobin; Song, Zilin; Qu, Dong; Fang, Linchuan; Deng, Lei

2017-10-01

Changes in plants and soils during natural succession have been evaluated, but little is known about the effects of succession on the activities of soil microbes and their interactions with soil erodibility. We conducted a field study on the Chinese Loess Plateau, typical of this semiarid area, to determine the effect of secondary succession on the stability of soil structure against erosion and on the composition of soil fungal communities. Characteristics of plant, soil, and fungal communities were assessed across a 30-yr chronosequence of grassland developed from abandoned cropland. The diversity and composition of the fungal communities were determined using high-throughput sequencing of the internal transcribed spacer. Six grasslands were selected to represent different successional age classes: 0 (cropland), 5, 10, 15, 20, and 30 yr. Short-term decreases (initial 5 yr) in the amounts of soil organic carbon, total nitrogen, available phosphorus, and fungal biomass and in fungal diversity had returned to original levels (i.e., cropland) within 15 yr and were much higher after continued succession. Abandoning cropland for succession caused the soil erodibility (K) decrease and the aboveground coverage, soil nutrient levels, content of larger (>5 mm) water-stable aggregate, mean aggregate weight diameter, and diversity of the fungal communities improvement including arbuscular mycorrhizas (AMF), ectomycorrhizas (EMF), and saprotrophs. The fungal communities were dominated by Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota during the succession. The successional patterns of the plant and fungal communities were similar, although distinct fungal communities were not observed in the two initial stages, suggesting that fungal succession may develop more slowly than plant succession. Plant root biomass, EMF, and soil organic carbon content accounted for most of the variation of soil erodibility (28.6%, 19.5%, and 11.8%, respectively), indicating their importance in shaping soil structure to prevent erosion. Our results demonstrated that abandoning cropland for natural succession could decrease soil erodibility and increase fungal diversity. EMF plays an important role in soil stability against erosion in the Loess Plateau. Abandoning cropland for natural succession should be recommended for alleviating soil erosion and improving the degraded soils in this area. © 2017 by the Ecological Society of America.

Mycobiome of Cysts of the Soybean Cyst Nematode Under Long Term Crop Rotation

PubMed Central

Hu, Weiming; Strom, Noah; Haarith, Deepak; Chen, Senyu; Bushley, Kathryn E.

2018-01-01

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe (Phylum Nematoda), is a major pathogen of soybean. It causes substantial yield losses worldwide and is difficult to control because the cyst protects the eggs which can remain viable for nearly a decade. Crop rotation with non-host crops and use of biocontrol organisms such as fungi and bacteria offer promising approaches, but remain hampered by lack of knowledge of the biology of nematode parasitic organisms. We used a high-throughput metabarcoding approach to characterize fungal communities associated with the SCN cyst, a microenvironment in soil that may harbor both nematode parasites and plant pathogens. SCN cysts were collected from a long-term crop rotation experiment in Southeastern Minnesota at three time points over two growing seasons to characterize diversity of fungi inhabiting cysts and to examine how crop rotation and seasonal variation affects fungal communities. A majority of fungi in cysts belonged to Ascomycota and Basidiomycota, but the presence of several early diverging fungal subphyla thought to be primarily plant and litter associated, including Mortierellomycotina and Glomeromycotina (e.g., arbuscular mycorrhizal fungi), suggests a possible role as nematode egg parasites. Species richness varied by both crop rotation and season and was higher in early years of crop rotation and in fall at the end of the growing season. Crop rotation and season also impacted fungal community composition and identified several classes of fungi, including Eurotiomycetes, Sordariomycetes, and Orbiliomycetes (e.g., nematode trapping fungi), with higher relative abundance in early soybean rotations. The relative abundance of several genera was correlated with increasing years of soybean. Fungal communities also varied by season and were most divergent at midseason. The percentage of OTUs assigned to Mortierellomycotina_cls_Incertae_sedis and Sordariomycetes increased at midseason, while Orbiliomycetes decreased at midseason, and Glomeromycetes increased in fall. Ecological guilds of fungi containing an animal-pathogen lifestyle, as well as potential egg-parasitic taxa previously isolated from parasitized SCN eggs, increased at midseason. The animal pathogen guilds included known (e.g., Pochonia chlamydosporia) and new candidate biocontrol organisms. This research advances knowledge of the ecology of nematophagous fungi in agroecosystems and their use as biocontrol agents of the SCN. PMID:29615984

Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences

PubMed Central

Garnica, Sigisfredo; Weiß, Michael; Oertel, Bernhard; Ammirati, Joseph; Oberwinkler, Franz

2009-01-01

Background Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeographic relationships within this lineage at a global scale have been largely unknown. In this study, we obtained DNA sequences from a nearly complete taxon sampling of known species from Europe, Central America and North America. We inferred intra- and interspecific phylogenetic relationships as well as major morphological evolutionary trends within section Calochroi based on 576 ITS sequences, 230 ITS + 5.8S + D1/D2 sequences, and a combined dataset of ITS + 5.8S + D1/D2 and RPB1 sequences of a representative subsampling of 58 species. Results More than 100 species were identified by integrating DNA sequences with morphological, macrochemical and ecological data. Cortinarius section Calochroi was consistently resolved with high branch support into at least seven major lineages: Calochroi, Caroviolacei, Dibaphi, Elegantiores, Napi, Pseudoglaucopodes and Splendentes; whereas Rufoolivacei and Sulfurini appeared polyphyletic. A close relationship between Dibaphi, Elegantiores, Napi and Splendentes was consistently supported. Combinations of specific morphological, pigmentation and molecular characters appear useful in circumscribing clades. Conclusion Our analyses demonstrate that Calochroi is an exclusively northern hemispheric lineage, where species follow their host trees throughout their natural ranges within and across continents. Results of this study contribute substantially to defining European species in this group and will help to either identify or to name new species occurring across the northern hemisphere. Major groupings are in partial agreement with earlier morphology-based and molecular phylogenetic hypotheses, but some relationships were unexpected, based on external morphology. In such cases, their true affinities appear to have been obscured by the repeated appearance of similar features among distantly related species. Therefore, further taxonomic studies are needed to evaluate the consistency of species concepts and interpretations of morphological features in a more global context. Reconstruction of ancestral states yielded two major evolutionary trends within section Calochroi: (1) the development of bright pigments evolved independently multiple times, and (2) the evolution of abruptly marginate to flattened stipe bulbs represents an autapomorphy of the Calochroi clade. PMID:19121213

Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico

PubMed Central

Gasca-Pineda, Jaime; Rosique-Gil, Edmundo; Eguiarte, Luis E.; Espinosa-Asuar, Laura

2016-01-01

The Cuatro Ciénegas Basin (CCB) comprises several oligotrophic aquatic ecosystems limited by phosphorus. These aquatic systems are dominated by a high prokaryotic diversity, shaped by the stress of low nutrient supplies and interspecific competition. Although fungi constitute a diverse and important component of microbial diversity, the microfungal diversity in the CCB remains to be unveiled. With the aim to explore microfungal diversity and ecological patterns in this area, we present the first investigation analyzing cultivable taxa from sediment and water, as well as lignocellulolytic taxa obtained from incubated submerged plant debris, and wood panels in three contrasting freshwater systems in the CCB: Churince, Becerra and Pozas Rojas. We chose a culture-based approach to analyze sediment and water samples in order to obtain fungal cultures, providing opportunities for a posteriori studies, and the possibility of ex situ preservation of the diversity. We evaluated sequence data from the nuclear ribosomal internal transcribed spacer including the 5.8 rDNA region for 126 isolates, revealing 37 OTUs. These OTUs were phylogenetically affiliated to several genera in the fungal phyla: Zygomycota, Basidiomycota, and Ascomycota. We recorded two OTUs with saline affinity, agreeing with previous findings on the prokaryotic communities with ancestral marine resemblances. All the studied systems showed moderate diversity levels, however discrepancies among the diversity indexes were observed, due to the occurrence of abundant taxa in the samples. Our results indicated that lignocellulolytic microfungal communities are dominated by transient fungal taxa, as resident species were not recorded perhaps as a result of the long-term strong competition with the highly adapted prokaryotic community. Moreover, the obtained microfungal taxa occurred mostly on the resident plant debris, rather than submerged wood panels, perhaps as a result of the high adaptation to specific environmental conditions. In conclusion, the CCB possess a moderate taxonomical diversity compared to other arid environments, probably as a result of high selective pressures. Nonetheless, due to high spatial and temporal heterogeneity, the functional fungal diversity was considerable as predicted by the intermediate disturbance hypothesis. Decisively, the assessment of microfungal diversity freshwater systems is relevant, since this ecological group of microorganisms represents an important indicator of trophic complexity and biotic interactions among microbial communities, having important implications for understanding eukaryotic survival at the oligotrophic limit for life. PMID:27280070

Arbuscular and Ectomycorrhizal Fungi Associated with the Invasive Brazilian Pepper Tree (Schinus terebinthifolius) and Two Native Plants in South Florida

PubMed Central

Dawkins, Karim; Esiobu, Nwadiuto

2017-01-01

The potential role of soil fungi in the invasion of the Brazilian pepper tree (Schinus terebinthifolius—BP) in Florida is not known; although the low biotic resistance of Florida soils is often invoked to explain the prevalence of many invasive species. To gain an initial insight into BP's mycorrhizal associations, this study examined the rhizobiome of BP and two native plants (Hamelia patens and Bidens alba) across six locations. Arbuscular mycorrhizal fungi (AMF) associated with the roots of the target plants and bulk soil was characterized by spore morphotyping. Sequence analysis of metagenomic DNA from lateral roots/rhizosphere of BP (n = 52) and a native shrub H. patens (n = 37) on the same parcel yielded other fungal associates. Overall, the total population of AMF associated with BP was about two folds greater than that of the two native plants (p = 0.0001) growing on the same site. The dominant AMF under Schinus were members of the common Glomus and Rhizophagus spp. By contrast, the most prevalent AMF in the bulk soil and rhizosphere of the two Florida native plants, Acaulospora spp (29%) was sharply diminished (9%) under BP rhizosphere. Analysis of the ITS2 sequences also showed that Schinus rhizosphere had a high relative abundance of ectomycorrhizal fungi (76.5%) compared to the native H. patens (2.6%), with the species Lactifluus hygrophoroides (Basidiomycota) being the most prevalent at 61.5% (p < 0.05). Unlike the native plants where pathogenic fungi like Phyllosticta sp., Phoma sp., and Neofusicoccum andium were present (8.1% for H. patens), only one potentially pathogenic fungal taxon was detected (3.9%) under BP. The striking disparity in the relative abundance of AMF and other fungal types between BP and the native species is quite significant. Fungal symbionts could aide plant invasion via resource-use efficiency and other poorly defined mechanisms of protection from pathogens in their invaded range. This report exposes a potentially significant but previously unappreciated fungal dimension of a complex invasion system and underscores the need to characterize these fungal symbionts, their role and mode of action during invasion; with the goal of devising measures for invasion control and ecological restoration. PMID:28473811

A Family of Secretory Proteins Is Associated with Different Morphotypes in Cryptococcus neoformans.

PubMed

Gyawali, Rachana; Upadhyay, Srijana; Way, Joshua; Lin, Xiaorong

2017-03-01

Cryptococcus neoformans , an opportunistic human fungal pathogen, can undergo a yeast-to-hypha transition in response to environmental cues. This morphological transition is associated with changes in the expression of cell surface proteins. The Cryptococcus cell surface and secreted protein Cfl1 was the first identified adhesin in the Basidiomycota. Cfl1 has been shown to regulate morphology, biofilm formation, and intercellular communication. Four additional homologs of CFL1 are harbored by the Cryptococcus genome: DHA1 , DHA2 , CPL1 , and CFL105 The common features of this gene family are the conserved C-terminal SIGC domain and the presence of an N-terminal signal peptide. We found that all these Cfl1 homolog proteins are indeed secreted extracellularly. Interestingly, some of these secretory proteins display cell type-specific expression patterns: Cfl1 is hypha specific, Dha2 is yeast specific, and Dha1 (delayed hypersensitivity antigen 1) is expressed in all cell types but is particularly enriched at basidia. Interestingly, Dha1 is induced by copper limitation and suppressed by excessive copper in the medium. This study further attests to the physiological heterogeneity of the Cryptococcus mating colony, which is composed of cells with heterogeneous morphotypes. The differential expression of these secretory proteins contributes to heterogeneity, which is beneficial for the fungus to adapt to changing environments. IMPORTANCE Heterogeneity in physiology and morphology is an important bet-hedging strategy for nonmobile microbes such as fungi to adapt to unpredictable environmental changes. Cryptococcus neoformans , a ubiquitous basidiomycetous fungus, is known to switch from the yeast form to the hypha form during sexual development. However, in a mating colony, only a subset of yeast cells switch to hyphae, and only a fraction of the hyphal subpopulation will develop into fruiting bodies, where meiosis and sporulation occur. Here, we investigated a basidiomycete-specific secretory protein family. We found that some of these proteins are cell type specific, thus contributing to the heterogeneity of a mating colony. Our study also demonstrates the importance of examining the protein expression pattern at the individual-cell level in addition to population gene expression profiling for the investigation of a heterogeneous community. Copyright © 2017 American Society for Microbiology.

Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target

PubMed Central

Hubbard, Breeana; Kvam, Alexander J.; Gates-Hollingsworth, Marcellene; Green, Heather R.; Soukup, Eric; Limper, Andrew H.; Kozel, Thomas R.

2018-01-01

ABSTRACT Ascomycetes and zygomycetes account for the majority of (i) fungi responsible for cutaneous, subcutaneous, and invasive human fungal infections, (ii) plant fungal pathogens, (iii) fungi that threaten global biodiversity, (iv) fungal agents of agricultural spoilage, and (v) fungi in water-damaged buildings. Rapid recognition of fungal infection (or contamination) enables early treatment (or remediation). A bioinformatics search found homologues of Saccharomyces cerevisiae Mnn9p present in members of the Zygomycota and Ascomycota phyla and absent in members of the Chytridiomycota and Basidiomycota. Mnn9p is a component of the yeast mannan polymerization complex and is necessary for α-1,6 mannan production. A monoclonal antibody (2DA6) was produced that was reactive with purified mannans of Mucor, Rhizopus, Aspergillus, Fusarium, and Candida species. Experimentation using a 2DA6 antigen capture enzyme-linked immunosorbent assay (ELISA) and extracts of fungi from the four phyla found agreement between the presence or absence of Mnn9p homologues and production or lack of production of mannan reactive with 2DA6. Studies of cell extracts from yeast mannan mutants identified α-1,6 mannan as the epitope recognized by 2DA6. To translate this finding into a point-of-use diagnostic, a 2DA6 lateral flow immunoassay was constructed that detected mannan in (i) extracts of dermatophytes and fungi that produce trauma-related infection and (ii) tissue from plants infected with Grosmannia clavigera or Sclerotium cepivorum. These studies (i) revealed that the conservation of α-1,6-linked mannan in fungi of the Zygomycota and Ascomycota can be exploited as a broad diagnostic target and (ii) have provided a means to detect that target in an immunoassay platform that is well suited for clinic or field use. IMPORTANCE A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the problem can lead to remediation or treatment. Zygomycetes and ascomycetes account for the vast majority of fungal causes of human, animal, and plant disease, large-scale biodiversity loss, agricultural spoilage, and contamination of water-damaged buildings. These studies revealed the conservation of a common cell wall structural component of zygomycetes and ascomycetes to be a diagnostic target applicable to multiple pathogenic fungi and have leveraged that insight for practical use. Monoclonal antibodies reactive with this pan-fungal structure were produced and used to construct immunoassays (including ELISA and lateral flow assay) for detection of a broad range of pathogenic fungi. PMID:29720523

Microbial monitoring in treated stone at the Royal Chapel of Granada

NASA Astrophysics Data System (ADS)

Jroundi, Fadwa; Pinar, Guadalupe; González-Muñoz, Maria Theresa; Sterflinger, Katja

2014-05-01

Biomineralization processes have been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain). In few years, this conservation treatment has gained worth attention as environmentally friendly methodology for protection and consolidation of limestone because of the compatibilities shown between the new calcium carbonate cement and the original stone substrate. Moreover, the success of this approach may be related to the diversity of the microbiota inhabiting the stone and activated upon the biotreatment application and throughout the time. González-Muñoz et al. (2008) proposed a nutritional solution that activate among the bacteria inhabiting the stone those with carbonatogenic activity. In this study, a long-term (one, two and three years) monitoring of the microbiota present on the treated and untreated stones was done using a molecular strategy, including total DNA extraction, PCR amplification of 16S rRNA sequences, construction of clone libraries and fingerprinting by DGGE (Denaturing Gradient Gel Electrophoresis) analysis. Sequencing of the 16S rDNA revealed the dominant occurrence of members of Actinobacteria (44.20%), Gamma-proteobacteria (30.24%) and Chloroflexi (25.56%) after one year of the biotreatment. Whereas after two years, members of Cyanobacteria (22.10%) appeared and three years after, the microbiota consisted of only Actinobacteria and Cyanobacteria with approximately the same percentage in comparison with the untreated stones, dominated exclusively by Actinobacteria (100%). Fungal diversity followed the same dynamic as bacterial diversity being Ascomicota the predominant order before treatment. After one year, members of Basidiomycota and Viridiplantae appeared on the stone while two years after, the Viridiplantae dominated with a percentage of 84.77%. Finally, three years after the treatment, fungi population started to stabilize again and Ascomicota predominated next to 16.67% of Viridiplantae. The molecular strategy used here is proposed as an effective monitoring system to evaluate the impact of the application of bacterially induced calcium carbonate mineralization as restoration/conservation procedure for decayed ornamental stone. Moreover, these results confirm that the biotreatment, proposed by González Muñoz et al (2008), is friendly for the microbiota inhabiting the stone, which reaches stability after relatively few years. References: González-Muñoz et al. (2008) Spanish Patent no. 2008/009771 Acknowledgements: Supported by the Junta de Andalucia (grants RNM-3493) and by "José Castillejo" program from the "Ministerio de Educación, Cultura y Deporte" (I-D+i 2008-2011).

Sequence and Secondary Structure of the Mitochondrial Small-Subunit rRNA V4, V6, and V9 Domains Reveal Highly Species-Specific Variations within the Genus Agrocybe

PubMed Central

Gonzalez, Patrice; Labarère, Jacques

1998-01-01

A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The conservation of the sequences of the V4, V6, and V9 domains of the mitochondrial SSU rRNA within species and the high degree of interspecific variation found in the Agrocybe species studied open the way for these sequences to be used as specific molecular markers of the Basidiomycota. PMID:9797259

Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6, and V9 domains reveal highly species-specific variations within the genus Agrocybe.

PubMed

Gonzalez, P; Labarère, J

1998-11-01

A comparative study of variable domains V4, V6, and V9 of the mitochondrial small-subunit (SSU) rRNA was carried out with the genus Agrocybe by PCR amplification of 42 wild isolates belonging to 10 species, Agrocybe aegerita, Agrocybe dura, Agrocybe chaxingu, Agrocybe erebia, Agrocybe firma, Agrocybe praecox, Agrocybe paludosa, Agrocybe pediades, Agrocybe alnetorum, and Agrocybe vervacti. Sequencing of the PCR products showed that the three domains in the isolates belonging to the same species were the same length and had the same sequence, while variations were found among the 10 species. Alignment of the sequences showed that nucleotide motifs encountered in the smallest sequence of each variable domain were also found in the largest sequence, indicating that the sequences evolved by insertion-deletion events. Determination of the secondary structure of each domain revealed that the insertion-deletion events commonly occurred in regions not directly involved in the secondary structure (i.e., the loops). Moreover, conserved sequences ranging from 4 to 25 nucleotides long were found at the beginning and end of each domain and could constitute genus-specific sequences. Comparisons of the V4, V6, and V9 secondary structures resulted in identification of the following four groups: (i) group I, which was characterized by the presence of additional P23-1 and P23-3 helices in the V4 domain and the lack of the P49-1 helix in V9 and included A. aegerita, A. chaxingu, and A. erebia; (ii) group II, which had the P23-3 helix in V4 and the P49-1 helix in V9 and included A. pediades; (iii) group III, which did not have additional helices in V4, had the P49-1 helix in V9 and included A. paludosa, A. firma, A. alnetorum, and A. praecox; and (iv) group IV, which lacked both the V4 additional helices and the P49-1 helix in V9 and included A. vervacti and A. dura. This grouping of species was supported by the structure of a consensus tree based on the variable domain sequences. The conservation of the sequences of the V4, V6, and V9 domains of the mitochondrial SSU rRNA within species and the high degree of interspecific variation found in the Agrocybe species studied open the way for these sequences to be used as specific molecular markers of the Basidiomycota.

Tobacco leaf spot and root rot caused by Rhizoctonia solani Kühn.

PubMed

Gonzalez, Marleny; Pujol, Merardo; Metraux, Jean-Pierre; Gonzalez-Garcia, Vicente; Bolton, Melvin D; Borrás-Hidalgo, Orlando

2011-04-01

Rhizoctonia solani Kühn is a soil-borne fungal pathogen that causes disease in a wide range of plants worldwide. Strains of the fungus are traditionally grouped into genetically isolated anastomosis groups (AGs) based on hyphal anastomosis reactions. This article summarizes aspects related to the infection process, colonization of the host and molecular mechanisms employed by tobacco plants in resistance against R. solani diseases. Teleomorph: Thanatephorus cucumeris (Frank) Donk; anamorph: Rhizoctonia solani Kühn; Kingdom Fungi; Phylum Basidiomycota; Class Agaricomycetes; Order Cantharellales; Family Ceratobasidiaceae; genus Thanatephorus. Somatic hyphae in culture and hyphae colonizing a substrate or host are first hyaline, then buff to dark brown in colour when aging. Hyphae tend to form at right angles at branching points that are usually constricted. Cells lack clamp connections, but possess a complex dolipore septum with continuous parenthesomes and are multinucleate. Hyphae are variable in size, ranging from 3 to 17 µm in diameter. Although the fungus does not produce any conidial structure, ellipsoid to globose, barrel-shaped cells, named monilioid cells, 10-20 µm wide, can be produced in chains and can give rise to sclerotia. Sclerotia are irregularly shaped, up to 8-10 mm in diameter and light to dark brown in colour. Symptoms in tobacco depend on AG as well as on the tissue being colonized. Rhizoctonia solani AG-2-2 and AG-3 infect tobacco seedlings and cause damping off and stem rot. Rhizoctonia solani AG-3 causes 'sore shin' and 'target spot' in mature tobacco plants. In general, water-soaked lesions start on leaves and extend up the stem. Stem lesions vary in colour from brown to black. During late stages, diseased leaves are easily separated from the plant because of severe wilting. In seed beds, disease areas are typically in the form of circular to irregular patches of poorly growing, yellowish and/or stunted seedlings. Knowledge is scarce regarding the mechanisms associated with resistance to R. solani in tobacco. However, recent evidence suggests a complex response that involves several constitutive factors, as well as induced barriers controlled by multiple defence pathways. This fungus can survive for many years in soil as mycelium, and also by producing sclerotia, which makes the management of the disease using conventional means very difficult. Integrated pest management has been most successful; it includes timely fungicide applications, crop rotation and attention to soil moisture levels. Recent developments in biocontrol may provide other tools to control R. solani in tobacco. © 2010 CIGB. MOLECULAR PLANT PATHOLOGY © 2010 BSPP AND BLACKWELL PUBLISHING LTD.

Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

PubMed Central

Arnold, A. Elizabeth

2016-01-01

Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Discussion Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum. PMID:27994976

Identification and quantification of ice nucleation active microorganisms by digital droplet PCR (ddPCR)

NASA Astrophysics Data System (ADS)

Linden, Martin; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

2015-04-01

Several bioaerosol types, including bacteria, fungi, pollen and lichen, have been identified as sources of biological ice nucleators (IN) which induce ice formation already at temperatures as high as -10 °C or above. Accordingly, they potentially contribute widely to environmental ice nucleation in the atmosphere and are of great interest in the study of natural heterogenous ice nucleation processes. Ice nucleation active microorganisms have been found and studied among bacteria (Proteobacteria) and fungi (phyla Basidiomycota and Ascomycota). The mechanisms enabling the microorganisms to ice nucleation are subject to ongoing research. While it has been demonstrated that whole cells can act as ice nucleators in the case of bacteria due to the presence of specific membrane proteins, cell-free ice nucleation active particles seem to be responsible for this phenomenon in fungi and lichen. The identification and quantification of these ice nucleation active microorganisms and their IN in atmospheric samples is crucial to understand their contribution to the pool of atmospheric IN. This is not a trivial task since the respective microorganisms are often prevalent in lowest concentrations and a variety of states, be it viable cells, spores or cell debris from dead cells. Molecular biology provides tools to identify and quantify ice nucleation active microorganisms independent of their state by detecting genetic markers specific for the organism of interest. Those methods are not without their drawbacks in terms of sample material concentration required or reliable standardization. Digital Droplet Polymerase Chain Reaction (ddPCR) was chosen for our demands as a more elegant, quick and specific method in the investigation of ice nucleation active microorganisms in atmospheric samples. The advantages of ddPCR lie in the simultaneous detection and quantification of genetic markers and their original copy numbers in a sample. This is facilitated by the fractionation of the PCR reaction volumes containing template DNA of ice nucleation active microorganisms from atmospheric samples in thousands of identical droplets. Each droplet encapsulates the reagents necessary for DNA amplification. With template DNA concentrations low enough, the droplets will statistically contain either no template molecules or one molecule. A molecule of template DNA corresponds to exactly one cell of an ice nucleation active microorganism in the original sample provided the genetic marker on the template is present in a single copy. Successful amplification in the presence of template DNA is coupled to a measurable fluorescence signal. The original template DNA concentration is automatically derived from the fraction of fluorescence positive droplets to total droplet number. This far, molecular probes against single-copy genetic markers for ice nucleation active fungi Mortierella alpina, Acremonium implicatum, Isaria farinosa and the ice nucleation active bacterium Pseudomonas syringae have been successfully designed and tested by our group.

Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America.

PubMed

U'Ren, Jana M; Arnold, A Elizabeth

2016-01-01

Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth's most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte-saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3-4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro . Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.

Symbiotic fungal associations in 'lower' land plants.

PubMed Central

Read, D J; Ducket, J G; Francis, R; Ligron, R; Russell, A

2000-01-01

An analysis of the current state of knowledge of symbiotic fungal associations in 'lower' plants is provided. Three fungal phyla, the Zygomycota, Ascomycota and Basidiomycota, are involved in forming these associations, each producing a distinctive suite of structural features in well-defined groups of 'lower' plants. Among the 'lower' plants only mosses and Equisetum appear to lack one or other of these types of association. The salient features of the symbioses produced by each fungal group are described and the relationships between these associations and those formed by the same or related fungi in 'higher' plants are discussed. Particular consideration is given to the question of the extent to which root fungus associations in 'lower' plants are analogous to 'mycorrhizas' of 'higher' plants and the need for analysis of the functional attributes of these symbioses is stressed. Zygomycetous fungi colonize a wide range of extant lower land plants (hornworts, many hepatics, lycopods, Ophioglossales, Psilotales and Gleicheniaceae), where they often produce structures analogous to those seen in the vesicular-arbuscular (VA) mycorrhizas of higher plants, which are formed by members of the order Glomales. A preponderance of associations of this kind is in accordance with palaeohbotanical and molecular evidence indicating that glomalean fungi produced the archetypal symbioses with the first plants to emerge on to land. It is shown, probably for the first time, that glomalean fungi forming typical VA mycorrhiza with a higher plant (Plantago lanceolata) can colonize a thalloid liverwort (Pellia epiphylla), producing arbuscules and vesicles in the hepatic. The extent to which these associations, which are structurally analogous to mycorrhizas, have similar functions remains to be evaluated. Ascomycetous associations are found in a relatively small number of families of leafy liverworts. The structural features of the fungal colonization of rhizoids and underground axes of these plants are similar to those seen in mycorrhizal associations of ericaceous plants like Vaccinium. Cross inoculation experiments have confirmed that a typical mycorrhizal endophyte of ericaceous plants, Hymenoscyphus ericae, will form associations in liverworts which are structurally identical to those seen in nature. Again, the functional significance of these associations remains to be examined. Some members of the Jungermanniales and Metzgeriales form associations with basidiomycetous fungi. These produce intracellular coils of hyphae, which are similar to the pelotons seen in orchid mycorrhizas, which also involve basidiomycetes. The fungal associates of the autotrophic Aneura and of its heterotrophic relative Cryptothallus mirabilis have been isolated. In the latter case it has been shown that the fungal symbiont is an ectomycorrhizal associate of Betula, suggesting that the apparently obligate nature of the association between the hepatic and Betula in nature is based upon requirement for this particular heterotroph. PMID:10905611

Puccinia coronata f. sp. avenae: a threat to global oat production.

PubMed

Nazareno, Eric S; Li, Feng; Smith, Madeleine; Park, Robert F; Kianian, Shahryar F; Figueroa, Melania

2018-05-01

Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/. © 2017 BSPP AND JOHN WILEY & SONS LTD.

Symbiotic fungal associations in 'lower' land plants.

PubMed

Read, D J; Ducket, J G; Francis, R; Ligron, R; Russell, A

2000-06-29

An analysis of the current state of knowledge of symbiotic fungal associations in 'lower' plants is provided. Three fungal phyla, the Zygomycota, Ascomycota and Basidiomycota, are involved in forming these associations, each producing a distinctive suite of structural features in well-defined groups of 'lower' plants. Among the 'lower' plants only mosses and Equisetum appear to lack one or other of these types of association. The salient features of the symbioses produced by each fungal group are described and the relationships between these associations and those formed by the same or related fungi in 'higher' plants are discussed. Particular consideration is given to the question of the extent to which root fungus associations in 'lower' plants are analogous to 'mycorrhizas' of 'higher' plants and the need for analysis of the functional attributes of these symbioses is stressed. Zygomycetous fungi colonize a wide range of extant lower land plants (hornworts, many hepatics, lycopods, Ophioglossales, Psilotales and Gleicheniaceae), where they often produce structures analogous to those seen in the vesicular-arbuscular (VA) mycorrhizas of higher plants, which are formed by members of the order Glomales. A preponderance of associations of this kind is in accordance with palaeohbotanical and molecular evidence indicating that glomalean fungi produced the archetypal symbioses with the first plants to emerge on to land. It is shown, probably for the first time, that glomalean fungi forming typical VA mycorrhiza with a higher plant (Plantago lanceolata) can colonize a thalloid liverwort (Pellia epiphylla), producing arbuscules and vesicles in the hepatic. The extent to which these associations, which are structurally analogous to mycorrhizas, have similar functions remains to be evaluated. Ascomycetous associations are found in a relatively small number of families of leafy liverworts. The structural features of the fungal colonization of rhizoids and underground axes of these plants are similar to those seen in mycorrhizal associations of ericaceous plants like Vaccinium. Cross inoculation experiments have confirmed that a typical mycorrhizal endophyte of ericaceous plants, Hymenoscyphus ericae, will form associations in liverworts which are structurally identical to those seen in nature. Again, the functional significance of these associations remains to be examined. Some members of the Jungermanniales and Metzgeriales form associations with basidiomycetous fungi. These produce intracellular coils of hyphae, which are similar to the pelotons seen in orchid mycorrhizas, which also involve basidiomycetes. The fungal associates of the autotrophic Aneura and of its heterotrophic relative Cryptothallus mirabilis have been isolated. In the latter case it has been shown that the fungal symbiont is an ectomycorrhizal associate of Betula, suggesting that the apparently obligate nature of the association between the hepatic and Betula in nature is based upon requirement for this particular heterotroph.

Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target.

PubMed

Burnham-Marusich, Amanda R; Hubbard, Breeana; Kvam, Alexander J; Gates-Hollingsworth, Marcellene; Green, Heather R; Soukup, Eric; Limper, Andrew H; Kozel, Thomas R

2018-01-01

Ascomycetes and zygomycetes account for the majority of (i) fungi responsible for cutaneous, subcutaneous, and invasive human fungal infections, (ii) plant fungal pathogens, (iii) fungi that threaten global biodiversity, (iv) fungal agents of agricultural spoilage, and (v) fungi in water-damaged buildings. Rapid recognition of fungal infection (or contamination) enables early treatment (or remediation). A bioinformatics search found homologues of Saccharomyces cerevisiae Mnn9p present in members of the Zygomycota and Ascomycota phyla and absent in members of the Chytridiomycota and Basidiomycota. Mnn9p is a component of the yeast mannan polymerization complex and is necessary for α-1,6 mannan production. A monoclonal antibody (2DA6) was produced that was reactive with purified mannans of Mucor , Rhizopus , Aspergillus , Fusarium , and Candida species. Experimentation using a 2DA6 antigen capture enzyme-linked immunosorbent assay (ELISA) and extracts of fungi from the four phyla found agreement between the presence or absence of Mnn9p homologues and production or lack of production of mannan reactive with 2DA6. Studies of cell extracts from yeast mannan mutants identified α-1,6 mannan as the epitope recognized by 2DA6. To translate this finding into a point-of-use diagnostic, a 2DA6 lateral flow immunoassay was constructed that detected mannan in (i) extracts of dermatophytes and fungi that produce trauma-related infection and (ii) tissue from plants infected with Grosmannia clavigera or Sclerotium cepivorum These studies (i) revealed that the conservation of α-1,6-linked mannan in fungi of the Zygomycota and Ascomycota can be exploited as a broad diagnostic target and (ii) have provided a means to detect that target in an immunoassay platform that is well suited for clinic or field use. IMPORTANCE A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the problem can lead to remediation or treatment. Zygomycetes and ascomycetes account for the vast majority of fungal causes of human, animal, and plant disease, large-scale biodiversity loss, agricultural spoilage, and contamination of water-damaged buildings. These studies revealed the conservation of a common cell wall structural component of zygomycetes and ascomycetes to be a diagnostic target applicable to multiple pathogenic fungi and have leveraged that insight for practical use. Monoclonal antibodies reactive with this pan-fungal structure were produced and used to construct immunoassays (including ELISA and lateral flow assay) for detection of a broad range of pathogenic fungi. Copyright © 2018 Burnham-Marusich et al.

Biological Particle Emissions From a South-East Asian Tropical Rainforest Using a Real- Time Dual Channel UV Fluorescence Bio-Aerosol Spectrometer

NASA Astrophysics Data System (ADS)

Gabey, A.; Coe, H.; Gallagher, M.; McFiggans, G.; Kaye, P.; Stanley, W.; Foot, V.

2008-12-01

Primary biogenic aerosols (PBA) contribute typically up to half of coarse mode particulate loading in tropical regions (e.g. Elbert et al. 2007). PBA contribute to the spread of genetic material and hence biodiversity within the biosphere either directly by transport of the organisms or their reproductive components. This spread via various vectors contributes to disease both animal and plant. Many studies have suggested PBA might be important for initiation of cloud formation and subsequent precipitation evolution by acting as cloud condensation nuclei (CCN) or possibly as ice nuclei (IN). This link is inferred from laboratory studies demonstrating the high activation efficiency of PBA at warm temperatures, coupled with observations that biological particles are ubiquitous in the atmosphere. Despite more than two hundred years of research, e.g. Ehrenberg (1830), information on the abundance, composition and more importantly the sources and heterogeneity of PBA on global scales are still poorly understood. The first realistic estimates of global average emission rates of PBA based on observations (mainly in Amazonia) and budget calculations, were provided by Elbert et al. (2007). They demonstrate that fungi, which have evolved many passive and active spore dispersal mechanisms, contribute a major fraction of the observed PBA and coarse particulate mass (particles with diameters between 1-10 μ m) in many, but in particular, tropical regions. Two major classes of fungal spores are commonly identified, these being AAM and ABM, Acomycota and Basidiomycota respectively (we will adopt the nomenclature used by Elbert et al. 2007, in this study). These species discharge their spores via wet spore active discharge mechanisms. Elbert et al. (2007) estimate a global average spore emission rate for ABM of ~17-50 Tg yr-1. This is consistent with observed typical concentrations of ABS which range from ~103 to 104 m- 3; and ~0.1-1 μ g m-3 by mass. The global average abundance and net emission for all fungal spores is ~1 μ g m-3 and ~50 Tg yr-1. These calculations demonstrate the potential importance of PBA, and in particular fungal spores, for global budgets of organic aerosols, particularly in tropical regions, however uncertainties are extremely large, ranging from 50 - 1000 Tg yr- 1. In this study we use the WIBS-3: a low-cost portable single-particle dual-channel UV fluorescence spectrometer (Kaye et al., 2008) to investigate the dynamics of PBA in real-time within and above a tropical forest of 50 m height in Borneo, Malaysia, to estimate net PBA emissions. Different circadian cycles were observed for bio and non-bio aerosol sources and the factors controlling bioaerosol emissions will be discussed in detail.

Possible role of Rhodotorula sp. in the formation of jarosite in the AMD environment of Muskau Arch, Poland

NASA Astrophysics Data System (ADS)

Jakus, Natalia; Chlebicki, Andrzej; Bożęcki, Piotr; Manecki, Maciej

2016-04-01

The Muskau Arch is situated in the west of Poland and in the east of Germany. This region is a belt formed by push and frontal moraines during the Middle-Polish (Riss) glaciation, especially during the Wartanian glaciation. The occurrence of glacier caused folding and forming the glacitectonic type of lignit deposits which were mined for over 150 years. Both open pit and underground mining methods has exposed metal sulfides (mainly pyrite) to air and water causing bio-oxidation. Due to this process the acidity of many reservoirs have increased significantly (pH values between 2 and 4). As a consequence of changes in the environment, new mineral phases precipitated from highly acid waters rich in, among others, various forms of Fe and S. Precipitation of ochreous minerals such as schwertmannite, goethite and jarosite was partly catalyzed by many various acidophilic and acid-tolerant microorganisms: bacteria, archaea and probably yeasts. Jarosite KFe33+(OH)6(SO4)2 can be precipitated both in abiotic conditions and as a by-product of the activity of living organisms. The example of biomineralization induced by fungi Purpureocillium lilacinum in similar AMD environment of Rio Tinto is reported (Oggerin et al, 2014). Recently, jarosite is also considered as a possible biosignature of life on Mars. The assessment of microbial participation in formation of jarosite is an elementary step in geomicrobiological and astrobiological research. Isolated by us Rhodotorula sp. is an unicellular pigmented yeast. Fungi from the genus Rhodotorula F.C. Harrison belong to Sporidiobolalas part of phylum Basidiomycota. They are common environmental inhabitants. Some species, known from Rio Tinto, can live in extreme acidic soils at pH of about 2 (Lopez-Archila et al, 2004). For the first time, authors isolated strain Rhodotorula sp. from surface precipitates in Ł ęknica region (Muskau Arch). This ochreous precipitate contains jarosite. The yeast might be an important factor in indirect enzymatic catalysis of the oxidation of pyrite. Jarosite precipitates from solution containing sulphate, possibly product of active enzymatic oxidation of sulphur compounds by Rhodotorula. As a result of this investigation a model of sulphur transformation mediated by Rhodotorula in AMD environment and its role in precipitation of jarosite was proposed. This work is partially funded by AGH research grant no 11.11.140.319. López-Archilla, A., González, A., Terrón, M., Amils, R. 2004. Ecological study of the fungal populations of the acidic Tinto River in southwestern Spain. Canadian Journal of Microbiology, 50 (11), 923-934. Oggerin, M., Rodriguez, N., del Moral, C., Amils, R. 2014. Fungal jarosite biomineralization in Rio Tinto. Research in Microbiology. 165, 719-725.

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

PubMed Central

2014-01-01

Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity. PMID:24422981

Bacterial and fungal community composition and functioning of two different peatlands in China

NASA Astrophysics Data System (ADS)

Wang, Meng; Tian, Jianqing; Bu, Zhaojun; Chen, Huai; Zhu, Qiuan; Peng, Changhui

2017-04-01

Peatlands are important carbon sinks which store one third of the global soil carbon ( 550 Gt) with only 3% of the land surface. The slow rate of organic matter decomposition associated with low microbial diversity and limited functioning under cold, acidic and anoxic condition is of critical importance in controlling biogeochemical cycles in northern peatlands. To evaluate the variation in microbial community composition and functionality can advance our understanding of the underlying mechanisms of the biogeochemical processes and interactions. However, there is still a lack of information for Chinese peatlands. Here, we sampled peat profiles at three different depths (10-20, 30-40 and 60-70 cm) from two typical peatlands in China: a rich fen in Qinghai-Tibet Plateau (QTP) and a poor fen in the Changbai Mountains (CBM). We investigated the bacterial (16S rRNA) and fungal (ITS2) community composition and diversity with high-throughput sequencing and predicted the metagenome functioning with PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States). The results showed that Proteobacteria, Acidobacteria and Actinobacteria were the most abundant bacterial phyla in the upper peat layer (10-20 cm) for both sites, with increasing abundance of Chloroflexi and Bacteroidetes down to the saturated zone (60-70 cm in CMB; 30-40 and 60-70 cm in QTP). For fungi, Ascomycota, Ciliophora and Basidiomycota were the most abundant phyla in both sites, with decreasing Ciliophora abundance down to the saturated zone. The α-diversity of both bacterial and fungal showed a decreasing trend with depth in QTP, with the largest diversity occurring at the depth of 30-40 cm in CMB. Regardless of sampling sites, the bacterial communities at the depth of 60-70 cm were more similar than the other depths. The fungal community was clustered into two groups, corresponding to two sampling sites. The variation in fungal community with depth was larger in QTP than in CBM. The predicted abundances of KEGG orthologs (KOs) assigned to the metabolism of amino acid, lipid and xenobiotics, as well as environmental adaptation, were decreased with depth in CBM, with energy metabolism showing the opposite trend. In contrast, the KO abundances of amino acid and lipid metabolism and environmental adaptation were the highest in the middle layer (30-40 cm) in QTP, where the KO abundance of energy metabolism was the lowest. In general, the difference in predicted metagenome functioning between sites was less obvious than between depths. These results highlight the important role of hydrology in shaping the microbial community in minerotrophic peatlands. The effect of environmental drivers on microbial diversity and functioning may be mediated by shifting in hydrological dynamics (e.g. land use change and desiccation) which should be considered under future global change condition.

Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom

PubMed Central

Kuramae, Eiko E; Robert, Vincent; Echavarri-Erasun, Carlos; Boekhout, Teun

2007-01-01

Background The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL) and barcoding projects by comparing the cophenetic correlation coefficients (CCC) among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40–45 concatenated proteins seem needed to resolve fungal TOL. Results In total 4852 orthologous proteins (KOGs) were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before [14] were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular processes and signaling KOG category seem more informative than those belonging to the other three categories: information storage and processing; metabolism; and the poorly characterized category. After concatenation of 40 proteins the topology of the phylogenetic tree remained stable, but after concatenation of 60 or more proteins the bootstrap support values of some branches decreased, most likely due to the inclusion of proteins with lowers CCC values. The selection of protein sequences to be used in various TOL projects remains a critical and important process. The method described in this paper will contribute to a more objective selection of phylogenetically informative protein sequences. Conclusion This study provides candidate protein sequences to be considered as phylogenetic markers in different branches of fungal TOL. The selection procedure described here will be useful to select informative protein sequences to resolve branches of TOL that contain few or no species with completely sequenced genomes. The robust phylogenetic trees resulting from this method may contribute to our understanding of organismal diversification processes. The method proposed can be extended easily to other branches of TOL. PMID:17688684

Safeguarding saproxylic fungal biodiversity in Apennine beech forest priority habitats

NASA Astrophysics Data System (ADS)

Maggi, Oriana; Lunghini, Dario; Pecoraro, Lorenzo; Sabatini, Francesco Maria; Persiani, Anna Maria

2015-04-01

The FAGUS LIFE Project (LIFE11/NAT/IT/135) targets two European priority habitats, i.e. Habitat 9210* Apennine beech forests with Taxus and Ilex, and Habitat 9220* Apennine beech forests with Abies alba, within two National Parks: Cilento, Vallo di Diano and Alburni; Gran Sasso and Monti della Laga. The current limited distribution of the target habitats is also due to the impact of human activities on forest systems, such as harvesting and grazing. The FAGUS project aims at developing and testing management strategies able to integrate the conservation of priority forest habitats (9210* and 9220*) and the sustainable use of forest resources. In order to assess the responses to different management treatments the BACI monitoring design (Before-After, Control-Intervention) has been applied on forest structure and diversity of focus taxa before and after experimental harvesting treatments. Conventional management of Apennine beech forests impacts a wealth of taxonomic groups, such as saproxylic beetles and fungi, which are threatened throughout Europe by the lack of deadwood and of senescing trees, and by the homogeneous structure of managed forests. Deadwood has been denoted as the most important manageable habitat for biodiversity in forests not only for supporting a wide diversity of organisms, but also for playing a prominent role in several ecological processes, creating the basis for the cycling of photosynthetic energy, carbon, and nutrients stored in woody material. Especially fungi can be regarded as key group for understanding and managing biodiversity associated with decaying wood. The before-intervention field sampling was carried out in Autumn 2013 in 33 monitoring plots across the two national Parks. The occurrence at plot level of both Ascomycota and Basidiomycota sporocarps was surveyed. All standing and downed deadwood with a minimum diameter of 10 cm was sampled for sporocarps larger than 1 mm, and information on decay class and fungal morphogroups was recorded. Our results confirm Apennine beech forests as important repositories of saproxylic fungal diversity. We identified species of high scientific concern, in both National Parks. The most represented genus is Mycena with six and five species in the sampling units of "Gran Sasso and Monti della Laga" and "Cilento,Vallo di Diano and Alburni" national Parks respectively. Within the "Gran Sasso and Monti della Laga National Park" the area of Incodara is of special interest due to the occurrence of the species Ossicaulis lignatilis, which is among the 21 identified indicator species for assessing conservation value of beech forests in Europe. A consistent group of Ascomycota species, including Biscogniauxia nummularia, Bisporella citrina, Diatrype disciformis, Kretzschmaria deusta, Nemania serpens, and Xylaria hypoxylon, was tightly associated with coarse woody debris in "Gran Sasso and Monti della Laga National Park" plots. The decay stage seemed to exert a major influence on both species richness and their spatial patterns, with coarse woody debris in the intermediate to late stages of decay being the richest in species. (471 words)

Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe?

PubMed

Meinhardt, Lyndel W; Rincones, Johana; Bailey, Bryan A; Aime, M Catherine; Griffith, Gareth W; Zhang, Dapeng; Pereira, Gonçalo A G

2008-09-01

Moniliophthora perniciosa (=Crinipellis perniciosa) causes one of the three main fungal diseases of Theobroma cacao (cacao), the source of chocolate. This pathogen causes Witches' broom disease (WBD) and has brought about severe economic losses in all of the cacao-growing regions to which it has spread with yield reductions that range from 50 to 90%. Cacao production in South America reflects the severity of this pathogen, as the yields in most of the infected regions have not returned to pre-outbreak levels, even with the introduction of resistant varieties. In this review we give a brief historical account and summarize the current state of knowledge focusing on developments in the areas of systematics, fungal physiology, biochemistry, genomics and gene expression in an attempt to highlight this disease. Moniliophthora perniciosa is a hemibiotrophic fungus with two distinct growth phases. The ability to culture a biotrophic-like phase in vitro along with new findings derived from the nearly complete genome and expression studies clearly show that these different fungal growth phases function under distinct metabolic parameters. These new findings have greatly improved our understanding of this fungal/host interaction and we may be at the crossroads of understanding how hemibiotrophic fungal plant pathogens cause disease in other crops. The first WDB symptoms appear to have been described in the diaries of Alexandre Rodrigues Ferreira (described as lagartão; meaning big lizard) from his observations of cacao trees in 1785 and 1787 in Amazonia, which is consistent with the generally accepted idea that M. perniciosa, like its main host T. cacao, evolved in this region. The disease subsequently arrived in Surinam in 1895. WBD moved rapidly, spreading to Guyana in 1906, Ecuador in 1918, Trinidad in 1928, Colombia in 1929 and Grenada in 1948. In each case, cacao production was catastrophically affected with yield reductions of 50-90%. After the arrival of M. perniciosa in Bahia in 1989, Brazil went from being the world's 3rd largest producer of cacao (347 000 tonnes in 1988-1990; c. 15% of the total world production at that time) to a net importer (141 000 tonnes in 1998-2000). Fortunately for chocolate lovers, other regions of the world such as West Africa and South East Asia have not yet been affected by this disease and have expanded production to meet growing world demand (predicted to reach 3 700 000 tonnes by 2010). Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora: super-kingdom Eukaryota; kingdom Fungi; phylum Basidiomycota; subphylum Agaricomycotina; class Agaricomycetes; subclass Agaricomycetidae; order Agaricales; family Marasmiaceae; genus Moniliophthora. http://www.lge.ibi.unicamp.br/vassoura/, http://nt.ars-grin.gov/taxadescriptions/keys/TrichodermaIndex.cfm, http://www.worldcocoafoundation.org/info-center/research-updates.asp, http://www.ars.usda.gov/ba/psi/spcl.

Contribution of fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions

NASA Astrophysics Data System (ADS)

Elbert, W.; Taylor, P. E.; Andreae, M. O.; Pöschl, U.

2007-09-01

Biogenic aerosols play important roles in atmospheric chemistry physics, the biosphere, climate, and public health. Here, we show that fungi which actively discharge their spores with liquids into the air, in particular actively wet spore discharging Ascomycota (AAM) and actively wet spore discharging Basidiomycota (ABM), are a major source of primary biogenic aerosol particles and components. We present the first estimates for the global average emission rates of fungal spores. Measurement results and budget calculations based on investigations in Amazonia (Balbina, Brazil, July 2001) indicate that the spores of AAM and ABM may account for a large proportion of coarse particulate matter in tropical rainforest regions during the wet season (0.7-2.3 μg m-3). For the particle diameter range of 1-10 μm, the estimated proportions are ~25% during day-time, ~45% at night, and ~35% on average. For the sugar alcohol mannitol, the budget calculations indicate that it is suitable for use as a molecular tracer for actively wet discharged basidiospores (ABS). ABM emissions seem to account for most of the atmospheric abundance of mannitol (10-68 ng m-3), and can explain the observed diurnal cycle (higher abundance at night). ABM emissions of hexose carbohydrates might also account for a significant proportion of glucose and fructose in air particulate matter (7-49 ng m-3), but the literature-derived ratios are not consistent with the observed diurnal cycle (lower abundance at night). AAM emissions appear to account for a large proportion of potassium in air particulate matter over tropical rainforest regions during the wet season (17-43 ng m-3), and they can also explain the observed diurnal cycle (higher abundance at night). The results of our investigations and budget calculations for tropical rainforest aerosols are consistent with measurements performed at other locations. Based on the average abundance of mannitol reported for extratropical continental boundary layer air (~25 ng m-3), we have also calculated a value of ~17 Tg yr-1 as a first estimate for the global average emission rate of ABS over land surfaces, which is consistent with the typically observed concentrations of ABS (~10³-104 m-3; ~0.1-1 μg m-3). The global average atmospheric abundance and emission rate of total fungal spores, including wet and dry discharged species, are estimated to be higher by a factor of about three, i.e. 1 μg m-3 and ~50 Tg yr-1. Comparisons with estimated rates of emission and formation of other major types of organic aerosol (~47 Tg yr-1 of anthropogenic primary organic aerosol; 12-70 Tg yr-1 of secondary organic aerosol) indicate that emissions from fungi should be taken into account as a significant global source of organic aerosol. The effects of fungal spores and related chemical components might be particularly important in tropical regions, where both physicochemical processes in the atmosphere and biological activity at the Earth's surface are particularly intense, and where the abundance of fungal spores and related chemical compounds are typically higher than in extratropical regions.

Biodiversity of Soil Microbial Communities Following Woody Plant Invasion of Grassland: An Assessment Using Molecular Methods

NASA Astrophysics Data System (ADS)

Kantola, I. B.; Gentry, T. J.; Filley, T. R.; Boutton, T. W.

2012-12-01

Woody plants have encroached into grasslands, savannas, and other grass-dominated ecosystems throughout the world during the last century. This dramatic vegetation change is likely driven by livestock grazing, altered fire frequencies, elevated atmospheric CO2 concentrations, and/or changes in atmospheric deposition patterns. Woody invasion often results in significant changes in ecosystem function, including alterations in above- and belowground primary productivity, soil C, N, and P storage and turnover, and the size and activity of the soil microbial biomass pool. The purpose of this study was to examine the relationships and interactions between plant communities and soil microbial communities in the Rio Grande Plains region of southern Texas where grasslands have been largely replaced by woodlands. Research was conducted along a successional chronosequence representing the stages of woody plant encroachment from open grassland to closed-canopy woodland. To characterize soil microbial community composition, soil samples (0-7.5 cm) were collected in remnant grasslands (representing time 0) and near the centers of woody plant clusters, groves, and drainage woodlands ranging in age from 10 to 130 yrs. Ages of woody plant stands were determined by dendrochronology. Community DNA was extracted from each soil sample with a MoBio PowerMax Soil DNA isolation kit. The DNA concentrations were quantified on a NanoDrop ND-1000 spectrophotometer and diluted to a standard concentration. Pyrosequencing was performed by the Research and Testing Laboratory (Lubbock, TX) according to Roche 454 Titanium chemistry protocols. Samples were amplified with primers 27F and 519R for bacteria, and primers ITS1F and ITS4 for fungi. Sequences were aligned using BioEdit and the RDP Pipeline and analyzed in MOTHUR. Non-metric multidimensional scaling of the operational taxonomic units identified by pyrosequencing revealed that both bacterial and fungal community composition were significantly different between remnant grasslands and all woody plant community types. Phylum-level classification of the 16S bacterial sequences showed that five phyla (Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, and Gemmatiomonadetes) represented 85-91% of classifiable sequences in all landscape elements. The relative abundances of Acidobacteria were significantly higher (p<0.05) in grassland samples (29.5%) than in all wooded landscape elements (17.1-25.6%), while the relative abundances of Actinobacteria was lower in grasslands (8.8%) than wooded areas (16.1-19.7%). Phylum-level classification of fungal sequences showed that four phyla accounted for 61.8 to 86.3% of identified sequences. Ascomycota was the most common phylum in all samples (55.8-62.1%), with significant contributions from Basidiomycota, Chytridiomycota, and Blastocladiomycota. The largest change in fungal community composition at the phylum level was observed in the Chytridiomycota, which declined from 4.0% in the grasslands to 0.8-1.4% in the wooded landscape elements. These significant changes in microbial community composition that occur following grassland to woodland conversion may have important implications for key biogeochemical processes that influence ecosystem structure and function in this region.

Soil Communities of Central Park, New York City: A Biodiversity Melting Pot

NASA Astrophysics Data System (ADS)

Ramirez, K. S.; Leff, J. W.; Wall, D. H.; Fierer, N.

2013-12-01

The majority of earth's biodiversity lives in and makes up the soil, but the majority of soil biodiversity has yet to be characterized or even quantified. This may be especially true of urban soil systems. The last decade of advances in molecular, technical and bioinformatic techniques have contributed greatly to our understanding of belowground biodiversity, from global distribution to species counts. Yet, much of this work has been done in ';natural' systems and it is not known if established patterns of distribution, especially in relation to soil factors hold up in urban soils. Urban soils are intensively managed and disturbed, often by effects unique to urban settings. It remains unclear how urban pressures influence soil biodiversity, or if there is a defined or typical ';urban soil community'. Here we describe a study to examine the total soil biodiversity - Bacteria, Archaea and Eukarya- of Central Park, New York City and test for patterns of distribution and relationships to soil characteristics. We then compare the biodiversity of Central Park to 57 global soils, spanning a number of biomes from Alaska to Antarctica. In this way we can identify similarities and differences in soil communities of Central Park to soils from ';natural' systems. To generate a broad-scale survey of total soil biodiversity, 596 soil samples were collected from across Central Park (3.41 km2). Soils varied greatly in vegetation cover and soil characteristics (pH, moisture, soil C and soil N). Using high-throughput Illumina sequencing technology we characterized the complete soil community from 16S rRNA (Bacteria and Archaea) and 18S rRNA gene sequences (Eukarya). Samples were rarified to 40,000 sequences per sample. To compare Central Park to the 57 global soils the complete soil community of the global soils was also characterized using Illumina sequencing technology. All samples were rarified to 40,000 sequences per sample. The total measured biodiversity in Central Park was high: >540,000 bacterial and archaeal species; and >97,000 eukaryotic species (as determined using a 97% sequence similarity cutoff). The most dominant bacterial phyla include Proteobacteria, Acidobacteria, Bacteroidetes, Verrucomicrobia and Actinobacteria, and Archaea represent 1-8% of the sequences. Additionally, the distribution patterns of Acidobacteria and consequently beta-diversity, was strongly related to soil pH. The most dominant eukaryotic taxa include many Protists (Rhizara, Gregarinia), Fungi (Basidiomycota, Ascomycota), and Metazoa (Nematodes, Rotifers, Arthropods and Annelids). No single soil factor could predict eukaryotic distribution. Central Park soil diversity was strikingly similar to the diversity of the 57 global soils. Central Park and the global soils had similarities in alpha diversity, taxon abundances. Interestingly, there was significant overlap in a number of dominant species between Central Park and the global soils. Together these results represent the most comprehensive analysis of soil biodiversity conducted to date. Our data suggest that even well-studied locations like Central Park harbor very high levels of unexplored biodiversity, and that Central Park biodiversity is comparable to soil biodiversity found globally.

Characterising coarse PBA dynamics in real-time above and below a tropical rainforest canopy using a dual channel UV fluorescence aerosol spectrometer.

NASA Astrophysics Data System (ADS)

Gabey, A.; Gallagher, M. W.; Burgess, R.; Coe, H.; McFiggans, G.,; Kaye, P. H.; Stanley, W. R.; Davies, F.; Foot, V. E.

2009-04-01

Primary biogenic aerosols (PBA) are used by organisms as a means to propagate their genetic material, either by transport of the organisms themselves, such as bacterial clusters and viruses, or of their reproductive components in the case of fungi and plants that release spores and pollen. Many studies have suggested PBA might be important for initiation of cloud formation and subsequent precipitation evolution by acting as cloud condensation nuclei (CCN) or possibly as ice nuclei (IN). This link is inferred from laboratory studies demonstrating the high activation efficiency of PBA at warm temperatures, coupled with observations that biological particles are ubiquitous in the atmosphere. Despite more than two hundred years of research (e.g. Ehrenberg, 1830) information on the abundance, composition and more importantly the sources and heterogeneity of PBA on global scales is still lacking. The first estimates of global average PBA emission rates based on observations and budget calculations were provided by Elbert et al. (2007). They demonstrate that fungi contribute a major fraction of the observed coarse PBA PM10 mass (particles with diameters between 1-10 m), particularly Acomycota (AAM) and Basidiomycota (ABM) commonly seen in tropical regions. These species discharge their spores via so-called "active wet" mechanisms that eject spores inside liquid droplets. Elbert et al. (2007) estimate a global average spore emission rate for ABM of ~17-50 Tg yr-1, corresponding to a global average abundance of ~1 g m-3 and a net emission rate for all fungal spores of 50 Tg yr-1. Uncertainty in the latter estimate is significant compared to the result, placed at 50-1000 Tg yr-1. Nonetheless, these calculations demonstrate the potential importance of PBA and particularly fungal spores in the tropics, where up to half of the coarse mode particulate loading is PBA, and potentially in the global organic aerosol budget. Data was collected using the WIBS-3: a low-cost, portable single-particle dual channel UV fluorescence spectrometer (Kaye et al., 2008) capable of detecting PBA by inducing fluorescence in two so-called biofluorophores - one present during metabolism and the other an amino acid - in the particle size range 1 m < Dp < 20 m. Real-time PBA measurements were performed above and below the canopy of a tropical rainforest in Borneo, Malaysia as part of the Oxidant and Particle Photochemical Processes (OP3) and the Aerosol Coupling in the Earth System (ACES) projects. PBA were found to dominate the coarse loading at Dp > 2 m. In qualitative agreement with measurements of culturable airborne material in a tropical forest's understory (Gilbert, 2005) a diurnal cycle of PBA number concentration is present, reaching a maximum of ~4000 l-1 at local midnight and falling to ~100 l-1 around midday. The role of the planetary boundary layer's collapse and re-establishment in dictating this variation in is also investigated using LIDAR data. Transient PBA concentration spikes lasting several minutes are superposed on the smooth underlying diurnal variation and occur at similar times each day. Nucleopore filter samples were also taken in-situ and analysed under an Environmental scanning electron microscope (ESEM) in Manchester. The images obtained showed the PBA fraction to be dominated by fungal spores of diameter 2-5 m, from various species including ABM. Since such species tend to release spores in bursts at regular times this appears to account for the PBA concentration spikes.

Field Observations of Bioaerosols: What We've Learned from Fluorescence, Genetic, and Microscopic Techniques (Invited)

NASA Astrophysics Data System (ADS)

Huffman, J. A.; Fröhlich-Nowoisky, J.; Després, V. R.; Elbert, W.; Sinha, B.; Andreae, M. O.; Pöschl, U.

2009-12-01

Biogenic aerosols are ubiquitous in the Earth’s atmosphere, influencing atmospheric chemistry and physics, the biosphere, climate, and public health. They play an important role in the spread of biological organisms, and they can cause or enhance human, animal, and plant diseases. Moreover, they can initiate the formation of clouds and precipitation as cloud condensation and ice nuclei (CCN, IN). Primary biogenic aerosol particles (PBAP) such as pollen, fungal spores, and bacteria are emitted directly from the biosphere to the atmosphere. Microscopic investigations have shown that PBAP account for up to ~30% of fine and up to ~70% of coarse particulate matter in rural and rain forest air, and the estimates of PBA emissions range from ~60 Tg a-1 of fine particles up to ~1000 Tg a-1 of total particulate matter. Fungal spores account for a large proportion of PBA with typical number and mass concentrations of ~104 m-3 and ~1 μg m-3 in continental boundary layer air and estimated global emissions of the order of ~50 Tg a-1 and 200 m-2 s-1, respectively [1]. The actual abundance, variability and diversity of PBAP are still poorly understood and quantified, however. By measuring fluorescence at excitation and emission wavelengths specific to viable cells, online techniques with time resolution of minutes are able to detect fluorescent biological aerosol particles (FBAP), which represent a lower limit for the actual abundance of coarse (> 1 μm) PBAP [2]. Continuous sampling (1 - 4 months) was performed at various locations including pristine rain forest, rural and polluted urban sites. Each study exhibited a similar average particle number distribution dominated by a peak at ~3 μm, with coarse FBAP concentrations of the order of ~5x104 m-3 and ~1 μg m-3. Recent advances in the DNA analysis and molecular genetic characterization of aerosol filter samples yield new information about the sources and composition of PBA and provide new insight into regional and global biodiversity [3,4]. Filters collected at a semi-urban site in Germany for approximately one year determined that ~34% of the airborne fungal species were Ascomycota (sac fungi), 64% were Basidiomycota (club fungi), and that their relative proportions changed seasonally. Numerical simulations with state-of-the-art atmospheric chemistry and climate models are helping to unravel the regional and global distribution and transport of PBA [5]. The atmospheric abundance and environmental effects of PBA are particularly pronounced in tropical regions, where both the biological activity at the Earth’s surface and the physicochemical processes in the atmosphere are particularly intense and important for the Earth system and global climate. If climate change and human activities lead to changes in the abundance and properties of PBA, this might influence the hydrological cycle and provide a feedback to climate change [1]. [1] Elbert et al. (2007) Atmos. Chem. Phys., 7, 4569 - 4588. [2] Huffman et al. (2009) Atmos. Chem. Phys. Discuss., 9, 17705 - 17751. [3] Després et al. (2007) Biogeosciences, 4, 1127-1141. [4] Fröhlich-Nowoisky et al. (2009) Proc. Nat. Acad. Sci., 106, 12814 - 12819. [5] Burrows et al. (2009) Atmos. Chem. Phys. Discuss., 9, 10829 - 10881.