Response of fungal and actinobacterial communities to water-level drawdown in boreal peatland sites

"We used PCR-DGGE fingerprinting and direct sequencing to analyse the response of fungal and actinobacterial communities to changing hydrological conditions at 3 different sites in a boreal peatland complex in Finland. The experimental design involved a short-term (3 years; STD) and a long-term (43 years; LTD) water-level drawdown. Correspondence analyses of DGGE bands revealed differences in the communities between natural sites representing the nutrient-rich mesotrophic fen, the nutrient-poorer oligotrophic fen, and the nutrient-poor ombrotrophic bog. Still, most fungi and actinobacteria found in the pristine peatland seemed robust to the environmental variables. Both fungal and actinobacterial diversity was higher in the fens than in the bog. Fungal diversity increased significantly after STD whereas actinobacterial diversity did not respond to hydrology. Both fungal and actinobacterial communities became more similar between peatland types after LTD, which was not apparent after STD. Most sequences clustered equally between the two main fungal phyla Ascomycota and Basidiomycota. Sequencing revealed that basidiomycetes may respond more (either positively or negatively) to hydrological changes than ascomycetes. Overall, our results suggest that fungal responses to water-level drawdown depend on peatland type. Actinobacteria seem to be less sensitive to hydrological changes, although the response of some may similarly depend on peatland type. (C) 2009 Elsevier Ltd. All rights reserved."

华中地区多孔菌物种多样性和资源研究

多孔菌是指具有孔状子实层的木材腐朽菌，该类群隶属于担子菌门(Basidiomycota)，担子菌纲 (Basidiomycetes)，是一类数量较多、组成较为复杂的真菌。 多孔菌具有重要的生态功能和经济价值。该类群真菌能够降解木质素和纤维素，在森林生态系统中起着关键的降解还原作用。同时，多孔菌还是重要的生物资源。部分种类能够造成林木病害是林木病原菌；部分多孔菌具有药用、食用价值；有些种类的多孔菌还具有重要的工业应用价值。 华中地区是我国生物多样性最丰富的地区之一，该地区多孔菌资源丰富。然而华中地区的多孔菌研究非常薄弱，该地区的多孔菌资源的种类和分布仍不明确。本文对华中地区不同森林生态类型中的多孔菌进行了广泛调查和标本采集。通过形态学、分子生物学和遗传交配实验，对华中地区的多孔菌多样性与资源进行了系统的研究，并初步分析了华中地区多孔菌的区系特点。 通过本论文的研究，明确了华中地区多孔菌的种类与多孔菌资源的分布，丰富了我国木生真菌的种类，为控制林木病原菌、开发利用有益真菌资源提供了基础数据和科学依据。本论文的主要研究结论如下： 1.华中地区采集的近2000号标本，按照现代分类系统共鉴定出257种多孔 菌，包括5个新种：庄氏地花孔菌Albatrellus zhuangii Y.C. Dai & Juan Li，宽孢全缘孔菌Haploporus latisporus Juan Li & Y.C. Dai，河南纤孔菌Inonotus henanensis Juan Li & Y.C. Dai，覆瓦拟硬孔菌Rigidoporopsis tegularis Juan Li & Y.C. Dai，菌索干皮孔菌Skeletocutis fimbriata Juan Li & Y.C. Dai；4个中国新记录种：假斑点嗜蓝孢孔菌Fomitiporia pseudopunctata (A. David, Dequatre & Fiasson) Fiasson，仲氏针层孔菌Phellinus johnsonianus (Murrill) Ryvarden，合生坛担菌Sistotrema confluens Pers.，姬氏芮氏孔菌Wrightoporia gillesii A. David & Rajchenb.。 2.利用分子系统学方法，确定了两种通过形态学研究难鉴定的种类的分类学地位，并探讨了针层孔菌属和地花孔菌属的系统发育关系。 3.华中地区的异担子菌有岛生异担子菌和小孔异担子菌两种，不存在多年异担子菌这一严重的森林病原菌。该地区的岛生异担子菌为该复合种中的T生物种，为腐生菌，不对针叶树造成严重病害。 4.华中地区的257种多孔菌隶属于担子菌门、担子菌纲，共有8目、17科、75属。优势科依次为多孔菌科，锈革孔菌科和拟层孔菌科。这三科的种类构成了华中地区多孔菌区系的主体。针层孔菌属为华中地区多孔菌的优势属，其他依次为多孔菌属，波氏孔菌属，多年卧孔菌属，干皮孔菌属，栓孔菌属和薄孔菌属。 5.华中地区多孔菌的75个属共划分为6种地理成分：世界广布属，北温带分布属，热带–亚热带分布属，东亚–北美分布属，大洋洲–北美洲分布属和东亚分布属。除世界广布属外，北温带分布属和热带–亚热带分布属是华中地区多孔菌的主体。 6.华中地区的257种多孔菌划分为8种地理成分：世界广布成分，北温带分布成分，泛热带分布成分，亚–欧共有成分，东亚–北美共有成分，东亚–澳大利亚共有成分，东亚成分，中国特有种。除世界广布成分外，以北温带分布成分和泛热带成分为主。华中地区多孔菌区系基本上属温带性质，同时具有一定比例的泛热带成分，说明华中地区多孔菌区系具有明显的从温带到热带的过渡性质。 7.华中地区的多孔菌资源丰富，野生的食、药用多孔菌48种；工业用多孔菌有21种；林木病原菌有37种，其中新报道病原菌1种。 8.华中地区稀有多孔菌有22种，濒危多孔菌10种。

中国产丝齿菌属Hyphodontia分类学研究

革菌是指平伏的具有光滑、齿状或瘤状子实层体表面的木材腐朽菌，该类群属于担子菌门（Basidiomycota），担子菌纲（Basidiomycetes），是一类数量较多、组成较为复杂的高等真菌。 革菌具有重要的生态学功能和经济价值。该类群真菌能够降解木质素和纤维素，在森林生态系统中起着关键的降解还原作用；同时，革菌还是重要的生物资源，部分种类能够造成林木病害是林木病原菌；部分革菌具有药用、食用价值；有些种类的革菌还具有重要的工业应用价值。 对采集自我国不同地区、不同森林生态类型中的，以及现保存于中国科学院沈阳应用生态研究所东北生物标本馆（IFP），中国科学院微生物研究所真菌标本馆（HMAS）等国内主要标本馆的非褶菌目木材腐朽菌 — 产丝齿菌属（Hyphodontia J. Erikss.）的真菌标本进行了全面系统的研究，其中自采标本约800余号，馆藏标本600余号。按照Donk，Eriksson和Parmasto提出的传统分类方法对该属的种类进行详细的描述和显微结构绘图，记载了每个种类的寄主、国内外分布及研究标本，并对每种与相似种的联系和区别进行了讨论。我国范围内共记录及描述产丝齿菌属（Hyphodontia）39种，其中共发现新种3个，分别是：头状囊产丝齿菌Hyphodontia capitatocystidiata H.X. Xiong, Y.C. Dai & Sheng H. Wu，异囊产丝齿菌H. heterocystidiata H.X. Xiong, Y.C. Dai & Sheng H. Wu 和 似土黄产丝齿菌H. subpallidula H.X. Xiong, Y.C. Dai & Sheng H. Wu；发现中国新记录种2个：冷杉产丝齿菌Hyphodontia abieticola (Bourdot & Galzin) J. Erikss.和弯孢产丝齿菌H. curvispora J. Erikss. & Hjortstam；大陆新记录种7个，分别是：台湾产丝齿菌Hyphodontia formosana Sheng H. Wu & Burds.，羊毛状产丝齿菌Hyphodontia lanata Burds. & Nakasone，膜质产丝齿菌Hyphodontia pelliculae (H. Furuk.) N. Maek.，无锁产丝齿菌Hyphodontia poroideoefibulata Sheng H. Wu，近球孢产丝齿菌Hyphodontia subglobasa Sheng H. Wu，热带产丝齿菌Hyphodontia tropica Sheng H. Wu和管形产丝齿菌Hyphodontia tubuliformis Sheng H. Wu。

产于海南的中国大陆多孔菌目一新记录属——伪壶担菌属(Pseudolagarobasidium)(英文)

文中报道了采自海南省乐东县尖峰岭自然保护区阔叶树倒枝上的中国大陆多孔菌目一新记录属——伪壶担菌属(Pseudolagarobasidium)。该属隶属于担子菌门(Basidiomycota)、伞菌纲(Agaricomycetes)、多孔菌目(Polyporales)、原毛平革菌科(Phanerochaetaceae)。其中的白色伪壶担菌(Pseudolagarobasidium calcareum)是中国大陆新记录种。根据采集到的标本对该种进行了详细描述和显微结构绘图。

Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex.

The fungal species Cryptococcus neoformans and Cryptococcus gattii cause respiratory and neurological disease in animals and humans following inhalation of basidiospores or desiccated yeast cells from the environment. Sexual reproduction in C. neoformans and C. gattii is controlled by a bipolar system in which a single mating type locus (MAT) specifies compatibility. These two species are dimorphic, growing as yeast in the asexual stage, and producing hyphae, basidia, and basidiospores during the sexual stage. In contrast, Filobasidiella depauperata, one of the closest related species, grows exclusively as hyphae and it is found in association with decaying insects. Examination of two available strains of F. depauperata showed that the life cycle of this fungal species shares features associated with the unisexual or same-sex mating cycle in C. neoformans. Therefore, F. depauperata may represent a homothallic and possibly an obligately sexual fungal species. RAPD genotyping of 39 randomly isolated progeny from isolate CBS7855 revealed a new genotype pattern in one of the isolated basidiospores progeny, therefore suggesting that the homothallic cycle in F. depauperata could lead to the emergence of new genotypes. Phylogenetic analyses of genes linked to MAT in C. neoformans indicated that two of these genes in F. depauperata, MYO2 and STE20, appear to form a monophyletic clade with the MATa alleles of C. neoformans and C. gattii, and thus these genes may have been recruited to the MAT locus before F. depauperata diverged. Furthermore, the ancestral MATa locus may have undergone accelerated evolution prior to the divergence of the pathogenic Cryptococcus species since several of the genes linked to the MATa locus appear to have a higher number of changes and substitutions than their MATalpha counterparts. Synteny analyses between C. neoformans and F. depauperata showed that genomic regions on other chromosomes displayed conserved gene order. In contrast, the genes linked to the MAT locus of C. neoformans showed a higher number of chromosomal translocations in the genome of F. depauperata. We therefore propose that chromosomal rearrangements appear to be a major force driving speciation and sexual divergence in these closely related pathogenic and saprobic species.

Determinants of root-associated fungal communities within Asteraceae in a semi-arid grassland

Summary

1.While plant–fungal interactions are important determinants of plant community assembly and ecosystem functioning, the processes underlying fungal community composition are poorly understood.
2.Here, we studied for the first time the root-associated eumycotan communities in a set of co-occurring plant species of varying relatedness in a species-rich, semi-arid grassland in Germany. The study system provides an opportunity to evaluate the importance of host plants and gradients in soil type and landscape structure as drivers of fungal community structure on a relevant spatial scale. We used 454 pyrosequencing of the fungal internal transcribed spacer region to analyse root-associated eumycotan communities of 25 species within the Asteraceae, which were sampled at different locations within a soil type gradient. We partitioned the variance accounted for by three predictors (host plant phylogeny, spatial distribution and soil type) to quantify their relative roles in determining fungal community composition and used null model analyses to determine whether community composition was influenced by biotic interactions among the fungi.
3.We found a high fungal diversity (156 816 sequences clustered in 1100 operational taxonomic units (OTUs)). Most OTUs belonged to the phylum Ascomycota (35.8%); the most abundant phylotype best-matched Phialophora mustea. Basidiomycota were represented by 18.3%, with Sebacina as most abundant genus. The three predictors explained 30% of variation in the community structure of root-associated fungi, with host plant phylogeny being the most important variance component. Null model analysis suggested that many fungal taxa co-occurred less often than expected by chance, which demonstrates spatial segregation and indicates that negative interactions may prevail in the assembly of fungal communities.
4.Synthesis. The results show that the phylogenetic relationship of host plants is the most important predictor of root-associated fungal community assembly, indicating that fungal colonization of host plants might be facilitated by certain plant traits that may be shared among closely related plant species.

The fungal microbiota of de-novo paediatric inflammatory bowel disease

Inflammatory bowel disease (IBD) is characterised by an inappropriate chronic immune response against resident gut microbes. This may be on account of distinct changes in the gut microbiota termed as dysbiosis. The role of fungi in this altered luminal environment has been scarcely reported. We studied the fungal microbiome in de-novo paediatric IBD patients utilising next generation sequencing and compared with adult disease and normal controls. We report a distinct difference in fungal species with Ascomycota predominating in control subjects compared to Basidiomycota dominance in children with IBD, which could be as a result of altered tolerance in these patients. 

Contrasting effects of necrotrophic and biotrophic plant pathogens on the aphid Aphis fabae

Phytophagous insects have to contend with a wide variation in food quality brought about by a variety of factors intrinsic and extrinsic to the plant. One of the most important factors is infection by plant pathogenic fungi. Necrotrophic and biotrophic plant pathogenic fungi may have contrasting effects on insect herbivores due to their different infection mechanisms and induction of different resistance pathways, although this has been little studied and there has been no study of their combined effect. We studied the effect of the biotrophic rust fungus Uromyces viciae-fabae (Pers.) Schroet (Basidiomycota: Uredinales: Pucciniaceae) and the necrotrophic fungus Botrytis cinerea Pers. (Ascomycota: Helotiales: Sclerotiniaceae) singly and together on the performance of the aphid Aphis fabae Scop. (Hemiptera: Aphididae) on Vicia faba (L.) (Fabaceae). Alone, botrytis had an inhibitory effect on individual A. fabae development, survival and fecundity, while rust infection consistently enhanced individual aphids’ performance. These effects varied in linear relation to lesion or pustule density. However, whole-plant infection by either pathogen resulted in a smaller aphid population of smaller aphids than on uninfected plants, indicating a lowering of aphid carrying capacity with infection. When both fungi were applied simultaneously to a leaf they generally cancelled the effect of each other out, resulting in most performance parameters being similar to the controls, although fecundity was reduced. However, sequential plant infection (pathogens applied five days apart) led to a 70% decrease in fecundity and 50% reduction in intrinsic rate of increase. The application of rust before botrytis had a greater inhibitory effect on aphids than applying botrytis before rust. Rust infection increased leaf total nitrogen concentration by 30% while infection by botrytis with or without rust led to a 38% decrease. The aphids’ responses to the two plant pathogens individually is consistent with the alteration in plant nutrient content by infection and also the induction of different plant defence pathways and the possible cross-talk between them. This is the first demonstration of the complex effects of the dual infection of a plant by contrasting pathogens on insect herbivores. Key words: Vicia faba, Botrytis cinerea, Uromyces viciae-fabae, tripartite interactions, induced resistance

Microbial diversity associated with algae, ascidians and sponges from the north coast of Sao Paulo state, Brazil

Little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. The aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. Data derived from ARDRA and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. Microbial strains identified up to the genus level revealed 144 distinct ribotypes out of 256 fungal strains and 158 distinct ribotypes out of 181 bacterial strains. Filamentous fungi were distributed among 24 different genera belonging to Ascomycota, Zygomycota and Basidiomycota, some of which had never been reported in the literature as marine invertebrate-inhabiting fungi (Pestalotiopsis, Xylaria, Botrysphaeria and Cunnninghamella). Bacterial isolates were affiliated to 41 different genera, being Bacillus, Ruegeria, Micrococcus, Pseudovibrio and Staphylococcus the most abundant ones. Results revealed an unexpected high microbial diversity associated to the macroorganisms which have been collected and suggested the selection of certain microbial taxonomic groups according to the host. The combined data gathered from this investigation contribute to broaden the knowledge of microbial diversity associated to marine macroorganisms, including as a promising source for the discovery of new natural products. (C) 2009 Elsevier GmbH. All rights reserved.

Contribution of fungi to primary biogenic aerosols in the atmosphere: wet and dry discharged spores, carbohydrates, and inorganic ions

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.

Espécies de Hypholoma (Fr.) P. Kumm. e Stropharia (Fr.) Quél. (Strophariaceae,Agaricales) no Rio Grande do Sul, Brasil

Espécimes de Hypholoma (Fr.) P. Kumm. e Stropharia (Fr.) Quél., ambos pertencentes à família Strophariaceae Singer & A.H. Sm., de ocorrência no estado do Rio Grande do Sul foram estudados. O estudo baseou-se em coletas realizadas pelo autor no período entre março de 2004 e setembro de 2005, e também na revisão do material depositado em herbários do estado, Brasil e exterior. As análises macro e microscópica dos basidiomas foram realizadas segundo metodologia usual para estudo de fungos agaricóides, e todo o material coletado encontra-se preservado no Herbário do Departamento de Botânica da Universidade Federal do Rio Grande do Sul (ICN). Neste estudo, concluiu-se que o gênero Hypholoma está representado no Rio Grande do Sul pelas seguintes espécies: H. aurantiacum (Cooke) Faus, H. ericaeum (Pers.: Fr.) Kühner, e H. subviride (Berk. & M.A. Curtis) Dennis. Da mesma forma, o gênero Stropharia encontra-se representado no estado por: S. acanthocystis Cortez & R.M. Silveira, S. aeruginosa (Curtis: Fr.) Quél., S. alcis var. austrobrasiliensis Cortez & R.M. Silveira, S. apiahyna (Speg.) Cortez & R.M. Silveira, S. araucariae Cortez & R.M. Silveira, S. coronilla (Bull.: Fr.) Quél., S. dorsipora Esteve-Rav. & Barrasa, S. earlei Norvell & Redhead, S. rugosoannulata Farl. ex Murrill e S. semiglobata (Batsch: Fr.) Quél. Dentre estas, Stropharia acanthocystis, S. alcis var. austrobrasiliensis e S. araucariae, são descritos como novos táxons para a ciência; S. apiahyna é proposta como uma nova combinação; S. dorsipora, S. aeruginosa e S. earlei são citadas, respectivamente, pela primeira vez para a América do Sul, Brasil e Rio Grande do Sul. São apresentadas chaves de identificação, descrições e ilustrações macro e microscópicas de todas as espécies estudadas.

Filogenia molecular de fungos gasteroides das ordens Phallales e Geastrales (Phallomycetidae)

Gasteroids fungi are characterized by the basidiospores maturation inside the basidioma, from which spores liberation occurs in a passive manner. These fungi were once seen as a well definite class of Basidiomycota, but nowadays they are considered an artificial assemblage, because the organisms have independent evolutionary histories forming a polyphyletic group with a vast morphological variety. Despite their diversity, studies with this group in the tropics are incipient, and the phylogenetic relationships of the species from temperate climate remain unknown. Thus, this work aimed to elucidate the phylogenetic relationships of gasteroids fungi from the Geastrales and Phallales orders, with the inclusion of tropical and temperate species, and with these analyses suggest a systematic position of species like Aseroë floriformis and Phallus roseus, as well as to verify if the lignicolous habit can indicate parental relationship in the Geastrum genus. For this, basidiomata were collected at Atlantic rain forest areas, during the rainy season, and the specimen identification followed specific literature for gasteroid fungi. The phylogenetic analyses were performed with Maximum Parsimony and Bayesian Analysis, making use of RPB2 and 28S nuclear genes and atp6 mitochondrial gene. It could be observed on the Phallales dendogram, that Aseroë floriformis did not cluster with A. rubra, and that it has an anterior divergence from all others species of the family Clathraceae used in this analysis, assuming a basal position in the clade. Phallus roseus, which once was recognized as Itajahya, has previous divergence from the group formed by Phallus species. At the Geastrales dendogram, in the group corresponding to Geastrum genus, it could be observed that species with lignicolous habitat clustered in a clade with high support values. So, the results suggest the creation of a new genus to accommodate A. floriformis, and the revalidation of Itajahya, as well as it can be affirmed that the lignicolous habitat on the Geastrum genus in fact indicates parental relationships, and that it has arised only once at the evolutionary history of the genus

Plant or fungal sequences? An alternative optimized PCR protocol to avoid ITS (nrDNA) misamplification

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Yeasts isolated from a fungus-growing ant nest, including the description of Trichosporon chiarellii sp nov., an anamorphic basidiomycetous yeast

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)