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Sample records for fungal community composition

  1. Fungicide effects on fungal community composition in the wheat phyllosphere.

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    Karlsson, Ida; Friberg, Hanna; Steinberg, Christian; Persson, Paula

    2014-01-01

    The fungicides used to control diseases in cereal production can have adverse effects on non-target fungi, with possible consequences for plant health and productivity. This study examined fungicide effects on fungal communities on winter wheat leaves in two areas of Sweden. High-throughput 454 sequencing of the fungal ITS2 region yielded 235 operational taxonomic units (OTUs) at the species level from the 18 fields studied. It was found that commonly used fungicides had moderate but significant effect on fungal community composition in the wheat phyllosphere. The relative abundance of several saprotrophs was altered by fungicide use, while the effect on common wheat pathogens was mixed. The fungal community on wheat leaves consisted mainly of basidiomycete yeasts, saprotrophic ascomycetes and plant pathogens. A core set of six fungal OTUs representing saprotrophic species was identified. These were present across all fields, although overall the difference in OTU richness was large between the two areas studied.

  2. Arctic root-associated fungal community composition reflects environmental filtering.

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    Blaalid, Rakel; Davey, Marie L; Kauserud, Håvard; Carlsen, Tor; Halvorsen, Rune; Høiland, Klaus; Eidesen, Pernille B

    2014-02-01

    There is growing evidence that root-associated fungi have important roles in Arctic ecosystems. Here, we assess the diversity of fungal communities associated with roots of the ectomycorrhizal perennial herb Bistorta vivipara on the Arctic archipelago of Svalbard and investigate whether spatial separation and bioclimatic variation are important structuring factors of fungal community composition. We sampled 160 plants of B. vivipara from 32 localities across Svalbard. DNA was extracted from entire root systems, and 454 pyrosequencing of ITS1 amplicons was used to profile the fungal communities. The fungal communities were predominantly composed of Basidiomycota (55% of reads) and Ascomycota (35%), with the orders Thelephorales (24%), Agaricales (13.8%), Pezizales (12.6%) and Sebacinales (11.3%) accounting for most of the reads. Plants from the same site or region had more similar fungal communities to one another than plants from other sites or regions, and sites clustered together along a weak latitudinal gradient. Furthermore, a decrease in per-plant OTU richness with increasing latitude was observed. However, no statistically significant spatial autocorrelation between sites was detected, suggesting that environmental filtering, not dispersal limitation, causes the observed patterns. Our analyses suggest that while latitudinal patterns in community composition and richness might reflect bioclimatic influences at global spatial scales, at the smaller spatial scale of the Svalbard archipelago, these changes more likely reflect varied bedrock composition and associated edaphic factors. The need for further studies focusing on identifying those specific bioclimatic and edaphic factors structuring root-associated fungal community composition at both global and local scales is emphasized.

  3. Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

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    Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

    2014-12-01

    Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status.

  4. Changes in fungal community composition in response to experimental soil warming at the alpine treeline

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    Solly, Emily; Lindahl, Bjorn; Dawes, Melissa; Peter, Martina; Souza, Romulo; Rixen, Christian; Hagedorn, Frank

    2017-04-01

    Increased CO2 emissions and global warming may alter the composition of fungal communities through the reduction of low temperature limitation in the plant-soil system, faster nitrogen cycling and changes in the carbon allocation of host plants to the rhizosphere. Shifts in fungal community composition due to global changes are likely to affect the routes of carbon and nitrogen flows in the plant-soil system and alter the rates at which organic matter is decomposed. The main aim of our study was to estimate the effects of multiple years of free air CO2 enrichment (ambient concentration +200 ppm) and soil warming (+ 4°C) on the fungal community structure and composition. At an alpine treeline in Switzerland featuring two key high-elevation tree species, Larix decidua and Pinus uncinata, fungal communities within different organic horizons were analysed by high-throughput 454-pyrosequencing of ITS2 amplicons. In addition, we assessed the ectomycorrhizal community composition on root tips and monitored changes in sporocarp productivity of fungal species during the course of the experiment. Three years of experimental warming at the alpine treeline altered the composition of the fungal community in the organic horizons, whereas nine years of CO2 enrichment had only weak effects. Tree species influenced the composition of the fungal community and the magnitude of the responses of fungal functional groups to soil warming differed between plots with Larix and those with Pinus. The abundance of ectomycorrhizal fungi was positively correlated with nitrogen availability, and ectomycorrhizal taxa specialized for conditions of high nitrogen availability proliferated with warming, corresponding to considerable increases in extractable inorganic nitrogen in warmed soils. Changes in productivity of specific fungal fruiting bodies in response to soil warming (e.g. more Lactarius rufus sporocarps and less Hygrophorus speciousus sporocarps) were consistent with the 454-sequencing

  5. Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient.

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    Yao, Fang; Vik, Unni; Brysting, Anne K; Carlsen, Tor; Halvorsen, Rune; Kauserud, Håvard

    2013-10-01

    The main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind-exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag-encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.

  6. Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

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    McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

    2012-05-01

    Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

  7. Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities.

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    Morgado, Luis N; Semenova, Tatiana A; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József

    2016-09-01

    Many arctic ecological processes are regulated by soil temperature that is tightly interconnected with snow cover distribution and persistence. Recently, various climate-induced changes have been observed in arctic tundra ecosystems, e.g. shrub expansion, resulting in reduction in albedo and greater C fixation in aboveground vegetation as well as increased rates of soil C mobilization by microbes. Importantly, the net effects of these shifts are unknown, in part because our understanding of belowground processes is limited. Here, we focus on the effects of increased snow depth, and as a consequence, increased winter soil temperature on ectomycorrhizal (ECM) fungal communities in dry and moist tundra. We analyzed deep DNA sequence data from soil samples taken at a long-term snow fence experiment in Northern Alaska. Our results indicate that, in contrast with previously observed responses of plants to increased snow depth at the same experimental site, the ECM fungal community of the dry tundra was more affected by deeper snow than the moist tundra community. In the dry tundra, both community richness and composition were significantly altered while in the moist tundra, only community composition changed significantly while richness did not. We observed a decrease in richness of Tomentella, Inocybe and other taxa adapted to scavenge the soil for labile N forms. On the other hand, richness of Cortinarius, and species with the ability to scavenge the soil for recalcitrant N forms, did not change. We further link ECM fungal traits with C soil pools. If future warmer atmospheric conditions lead to greater winter snow fall, changes in the ECM fungal community will likely influence C emissions and C fixation through altering N plant availability, fungal biomass and soil-plant C-N dynamics, ultimately determining important future interactions between the tundra biosphere and atmosphere.

  8. Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

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    Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

    2015-12-01

    Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of

  9. Arbuscular mycorrhizal fungal community composition associated with Juniperus brevifolia in native Azorean forest

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    Melo, Catarina Drumonde; Luna, Sara; Krüger, Claudia; Walker, Christopher; Mendonça, Duarte; Fonseca, Henrique M. A. C.; Jaizme-Vega, Maria; da Câmara Machado, Artur

    2017-02-01

    The communities of glomeromycotan fungi (arbuscular mycorrhizal fungi, AMF) under native Juniperus brevifolia forest from two Azorean islands, Terceira and São Miguel, were compared, mainly by spore morphology, and when possible, by molecular analysis. Thirty-nine morphotypes were detected from 12 genera. Glomeromycotan fungal richness was similar in Terceira and São Miguel, but significantly different among the four fragments of native forest. Spore diversity and community composition differed significantly between the two islands. The less degraded island, Terceira, showed 10 exclusive morphotypes including more rare types, whereas the more disturbed forest on São Miguel showed 13 morphs, mostly of common types. Forests from Terceira were dominated by Acaulosporaceae and Glomeraceae. Whereas members of Acaulosporaceae, Glomeraceae and Ambisporaceae were most frequent and abundant in those from São Miguel. Spore abundance was greatest on Terceira, and correlated with soil chemical properties (pH), average monthly temperature and relative humidity.

  10. Soil-inhabiting fungal community composition as qualitative indicator of C metabolism processes

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    Manici, L.; Ciavatta, C.; Caputo, F.

    2009-04-01

    growth may depend on readily available energy sources, such as soluble carbohydrates (Hudson, 1968). The high ratio of Ascomycetes in the top layer where crop residues of the recurrent had represented the main substrate for saprophytic fungi could explain these results. On the contrary, Basidiomycetes are the most important synthesizing biomass organisms in forest soils as well as the most effective organisms in lignin decomposition with an important role in humic substances processes (Hurst et al., 1963; Cook and Rayner, 1986). Preliminary results of this study suggest that the composition of soil-inhabiting fungal communities, which are the organisms most involved in C metabolism processes, could represents an useful indicator in programs aimed to increase the quality of organic matter in arable soils. Bailey V., Smith L., Bolton Jr K. 2002. Fungal-to-bacteria ratio investigated for enhanced C sequestration. Soil Biol. Biochem. 34, 997-1007. Cook R., Rayner A.D.M. 1984. Ecology of Saprotrophic Fungi. Longman, London, New York, 415 pp. Gardes M., Bruns T.D. 1993. ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts. Molec. Ecol. 2, 113-118. Hudson H.J. 1968. The ecology of fungi on plant remains above the soil. New Phytol. 67, 837-874. Hurst H.M., A. Burges, P. Latter. 1963. Some aspects of the biochemistry of humic acid decomposition by fungi. Phytochem. 1, 227-231. Larena I., Salazar O., González V, Julián M.C., Rubio V. 1999. Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for Ascomycetes. J. Biotech. 75, 187-194. Osolko T., Fukasawa Y., Takeda H. 2003. Roles of diverse fungi in Larch neerle-litter decomposition. Mycologia 95, 820-826.

  11. Bacterial and fungal community composition and functioning of two different peatlands in China

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    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

  12. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

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    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.

  13. Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

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    Nicolas Chemidlin Prévost-Bouré

    Full Text Available Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2: i to examine their spatial structuring; ii to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at

  14. Composition of fungal communities in soil and endophytic in raspberry production systems

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    Fungi play important roles as decomposers, plant symbionts and pathogens in soil. While endophytes are microorganisms that dwell within plant tissues and have a symbiotic association with the host. The structures of fungal communities in the soil and in endophytic association are dependent up comple...

  15. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

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    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.

  16. Diversity and composition of airborne fungal community associated with particulate matters in Beijing during haze and non-haze days

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    Dong eYan

    2016-04-01

    Full Text Available Abstract: To assess the diversity and composition of airborne fungi associated with particulate matter in Beijing, China, a total of 81 PM samples were collected, which 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 1,633 operational taxonomic units were observed. Of these, 1,102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Capnodiales (27.95%, Pleosporales (26.8%, Eurotiales (10.64%, and Hypocreales (9.09%. 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 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.

  17. Simulated atmospheric N deposition alters fungal community composition and suppresses ligninolytic gene expression in a northern hardwood forest.

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    Ivan P Edwards

    Full Text Available High levels of atmospheric nitrogen (N deposition may result in greater terrestrial carbon (C storage. In a northern hardwood ecosystem, exposure to over a decade of simulated N deposition increased C storage in soil by slowing litter decay rates, rather than increasing detrital inputs. To understand the mechanisms underlying this response, we focused on the saprotrophic fungal community residing in the forest floor and employed molecular genetic approaches to determine if the slower decomposition rates resulted from down-regulation of the transcription of key lignocellulolytic genes, by a change in fungal community composition, or by a combination of the two mechanisms. Our results indicate that across four Acer-dominated forest stands spanning a 500-km transect, community-scale expression of the cellulolytic gene cbhI under elevated N deposition did not differ significantly from that under ambient levels of N deposition. In contrast, expression of the ligninolytic gene lcc was significantly down-regulated by a factor of 2-4 fold relative to its expression under ambient N deposition. Fungal community composition was examined at the most southerly of the four sites, in which consistently lower levels of cbhI and lcc gene expression were observed over a two-year period. We recovered 19 basidiomycete and 28 ascomycete rDNA 28S operational taxonomic units; Athelia, Sistotrema, Ceratobasidium and Ceratosebacina taxa dominated the basidiomycete assemblage, and Leotiomycetes dominated the ascomycetes. Simulated N deposition increased the proportion of basidiomycete sequences recovered from forest floor, whereas the proportion of ascomycetes in the community was significantly lower under elevated N deposition. Our results suggest that chronic atmospheric N deposition may lower decomposition rates through a combination of reduced expression of ligninolytic genes such as lcc, and compositional changes in the fungal community.

  18. Changes in fungal community composition in response to elevated atmospheric CO2 and nitrogen fertilization varies with soil horizon

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    Carolyn F Weber

    2013-04-01

    Full Text Available Increasing levels of atmospheric carbon dioxide (CO2 and rates of nitrogen (N-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2 and N-fertilization in spatially separated field samples, in the forest floor, 0-2 cm, 2-5 cm and 5-10 cm depth intervals in a loblolly pine Free-Air-Carbon Dioxide Enrichment (FACE experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0-2 cm and forest floor intervals. Composition shifted in forest floor, 0-2 cm and 2-5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0-2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e phosphorus, organic matter, calcium, pH was also observed. In the 0-2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes.

  19. Soil fungal community responses to global changes

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    Haugwitz, Merian Skouw

    Global change will affect the functioning and structure of terrestrial ecosystems and since soil fungi are key players in organic matter decomposition and nutrient turnover, shifts in fungal community composition might have a strong impact on soil functioning. The main focus of this thesis...... and nutrient availability and storage. By combining molecular methods such as 454 pyrosequencing and quantitative PCR of fungal ITS amplicons with analyses of soil enzymes, nutrient pools of carbon, nitrogen and phosphorus we were able to characterize soil fungal communities as well as their impact on nutrient...... was therefore to investigate the impact of global environmental changes on soil fungal communities in a temperate and subartic heath ecosystem. The objective was further to determine global change effects on major functional groups of fungi and analyze the influence of fungal community changes on soil carbon...

  20. Structure and species composition of ectomycorrhizal fungal communities colonizing seedlings and adult trees of Pinus montezumae in Mexican neotropical forests.

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    Reverchon, Frédérique; Ortega-Larrocea, María del Pilar; Bonilla-Rosso, Germán; Pérez-Moreno, Jesús

    2012-05-01

    Mexico is a center of diversity for pines, but few studies have examined the ectomycorrhizal (ECM) fungal communities associated with pines in this country. We investigated the ECM communities associated with Pinus montezumae seedlings and mature trees in neotropical forests of central Mexico and compared their structure and species composition. Root tips were sampled on both planted seedlings and naturally occurring adult trees. A total of 42 ECM operational taxonomic units (OTUs) was found on P. montezumae. Diversity and similarity indices showed that community structure was similar for both plant growth stages, but phylogenetic diversity and Chao-estimated richness were higher for seedlings. Species composition differed between communities. The dominant OTUs belonged to the families Atheliaceae, Cortinariaceae, and Sebacinaceae, although different taxa appeared to colonize seedlings and adults. Only 12 OTUs were shared between seedlings and adults, which suggests that ECM fungi which colonize seedlings are still not fully incorporated into mycelial networks and that ECM taxa colonizing young individuals of P. montezumae are likely to come from fungal propagules. Intra-generic diversity could be an insurance mechanism to maintain forest productivity under stressed conditions. This is the first report describing the abundance of Atheliaceae in tree roots in neotropical ecosystems. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  1. Soil fungal community responses to global changes

    DEFF Research Database (Denmark)

    Haugwitz, Merian Skouw

    Global change will affect the functioning and structure of terrestrial ecosystems and since soil fungi are key players in organic matter decomposition and nutrient turnover, shifts in fungal community composition might have a strong impact on soil functioning. The main focus of this thesis...... composition of fungi, but the effects were generally limited to the litter layer and the uppermost humus layer (0-5 cm), which was unexpected considering the ecosystem had been manipulated for 18 years. Taken together the global change experiments altered the soil fungal communities and thereby highlight...... was therefore to investigate the impact of global environmental changes on soil fungal communities in a temperate and subartic heath ecosystem. The objective was further to determine global change effects on major functional groups of fungi and analyze the influence of fungal community changes on soil carbon...

  2. Could biological invasion by Cryptostegia madagascariensis alter the composition of the arbuscular mycorrhizal fungal community in semi-arid Brazil?

    Directory of Open Access Journals (Sweden)

    Tancredo Augusto Feitosa de Souza

    2016-03-01

    Full Text Available Biological invasions pose a serious threat to native semi-arid areas of Brazil, especially in areas of the state of Ceará that are typically invaded byCryptostegia madagascariensis, an exotic plant species from Madagascar. However, how this biological invasion influences the composition of the arbuscular mycorrhizal fungal (AMF community and how this affects further invasion by C. madagascariensis is not well known. Here we tested how inoculation with species of AMF affects the development of this invasive plant. We analyzed and compared the AMF community composition of four different stages of biological invasion by C. madagascariensis, and examined the effects of inoculation with these four AMF communities, plus a dominant AMF species (Rhizoglomus intraradices on plant dry biomass, root colonization, plant phosphorous concentration, and plant responsiveness to mycorrhizas of plants of C. madagascariensis. We found that all studied treatments (except the inoculum from the native plant root zone promoted the growth of C. madagascariensis and lead to a higher P concentration. Our results demonstrate that the invader might be altering the composition of the AMF community in field conditions, because inoculation with this community enhanced invader growth, root colonization, and P uptake.

  3. Diversity and composition of dead wood inhabiting fungal and bryophyte communities

    NARCIS (Netherlands)

    Ódor, P.; Heilmann-Clausen, J.; Christensen, M.; Aude, E.; Dort, van K.W.; Piltaver, A.; Veerkamp, M.T.; Walleyn, R.; Standovár, T.; Hees, van A.F.M.; Kosec, J.; Matocec, N.; Kraigher, H.; Grebenc, T.

    2004-01-01

    Species composition and diversity of fungi and bryophyte communities occurring on dead beech trees were analysed in five European countries (Slovenia, Hungary, The Netherlands, Belgium and Denmark). Altogether 1009 trees were inventoried in 19 beech dominated forest reserves. The realized species po

  4. Fungal community assembly in the Amazonian Dark Earth

    NARCIS (Netherlands)

    Reis Lucheta, Adriano; Souza Cannavan, F.S.; Roesch, L.; Tsai, S.M.; Kuramae, E.E.

    2016-01-01

    Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in

  5. Fungal community assembly in the Amazonian Dark Earth

    NARCIS (Netherlands)

    Lucheta, A.R.; Souza Cannavan, F.S.; Roesch, L.; Tsai, S.M.; Kuramae, E.E.

    2016-01-01

    Here, we compare the fungal community composition and diversity in Amazonian Dark Earth (ADE) and the respective non-anthropogenic origin adjacent (ADJ) soils from four different sites in Brazilian Central Amazon using pyrosequencing of 18S ribosomal RNA (rRNA) gene. Fungal community composition in

  6. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    Science.gov (United States)

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture.

  7. Arbuscular mycorrhizal fungal community composition affected by original elevation rather than translocation along an altitudinal gradient on the Qinghai-Tibet Plateau

    Science.gov (United States)

    Yang, Wei; Zheng, Yong; Gao, Cheng; Duan, Ji-Chuang; Wang, Shi-Ping; Guo, Liang-Dong

    2016-11-01

    Elucidating arbuscular mycorrhizal (AM) fungal responses to elevation changes is critical to improve understanding of microbial function in ecosystems under global asymmetrical climate change scenarios. Here we examined AM fungal community in a two-year reciprocal translocation of vegetation-intact soil blocks along an altitudinal gradient (3,200 m to 3,800 m) in an alpine meadow on the Qinghai-Tibet Plateau. AM fungal spore density was significantly higher at lower elevation than at higher elevation regardless of translocation, except that this parameter was significantly increased by upward translocation from original 3,200 m to 3,400 m and 3,600 m. Seventy-three operational taxonomic units (OTUs) of AM fungi were recovered using 454-pyrosequencing of 18S rDNA sequences at a 97% sequence similarity. Original elevation, downward translocation and upward translocation did not significantly affect AM fungal OTU richness. However, with increasing altitude the OTU richness of Acaulosporaceae and Ambisporaceae increased, but the OTU richness of Gigasporaceae and Glomeraceae decreased generally. The AM fungal community composition was significantly structured by original elevation but not by downward translocation and upward translocation. Our findings highlight that compared with the short-term reciprocal translocation, original elevation is a stronger determinant in shaping AM fungal community in the Qinghai-Tibet alpine meadow.

  8. Patterns of fungal diversity and composition along a salinity gradient

    Science.gov (United States)

    Mohamed, Devon J; Martiny, Jennifer BH

    2011-01-01

    Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution. PMID:20882058

  9. Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic).

    Science.gov (United States)

    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 (SiO4 (2-)-Si), nitrite nitrogen (NO2 (-)-N), phosphate phosphorus (PO4 (3-)-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.

  10. Soil pH is a key determinant of soil fungal community composition in the Ny-Ålesund Region, Svalbard (High Arctic

    Directory of Open Access Journals (Sweden)

    Tao eZhang

    2016-02-01

    Full Text Available 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 (>8 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 soil samples 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.

  11. Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest.

    Science.gov (United States)

    Sheldrake, Merlin; Rosenstock, Nicholas P; Revillini, Daniel; Olsson, Pål Axel; Mangan, Scott; Sayer, Emma J; Wallander, Håkan; Turner, Benjamin L; Tanner, Edmund V J

    2017-04-01

    Tropical forest productivity is sustained by the cycling of nutrients through decomposing organic matter. Arbuscular mycorrhizal (AM) fungi play a key role in the nutrition of tropical trees, yet there has been little experimental investigation into the role of AM fungi in nutrient cycling via decomposing organic material in tropical forests. We evaluated the responses of AM fungi in a long-term leaf litter addition and removal experiment in a tropical forest in Panama. We described AM fungal communities using 454-pyrosequencing, quantified the proportion of root length colonised by AM fungi using microscopy, and estimated AM fungal biomass using a lipid biomarker. AM fungal community composition was altered by litter removal but not litter addition. Root colonisation was substantially greater in the superficial organic layer compared with the mineral soil. Overall colonisation was lower in the litter removal treatment, which lacked an organic layer. There was no effect of litter manipulation on the concentration of the AM fungal lipid biomarker in the mineral soil. We hypothesise that reductions in organic matter brought about by litter removal may lead to AM fungi obtaining nutrients from recalcitrant organic or mineral sources in the soil, besides increasing fungal competition for progressively limited resources.

  12. The effect of sulfur on the composition of arbuscular mycorrhizal fungal communities during the pod-setting stage of different soybean cultivars.

    Science.gov (United States)

    Jie, Weiguang; Cai, Baiyan; Zhang, Yong; Li, Jin; Ge, Jingping

    2012-11-01

    This study sought to investigate the effect of sulfur levels on changes in the fungal community composition of arbuscular mycorrhizae (AM) at the pod-setting stage and the relationship between the amount of applied sulfur and AM fungal diversity in different soybean cultivars. The objective of the research was to determine the optimal sulfur application level for different soybean cultivars and to improve soybean yield and quality from the perspective of AM fungal diversity. Three soybean cultivars, Heinong 44, Heinong 48, and Heinong 37, were selected as study materials. In addition to 0.033 g each of N, P(2)O(5) and K(2)O per kg of soil, 0, 0.02, 0.04, or 0.06 g of elemental sulfur was applied to each kg of soil for the four treatment groups, S1, S2, S3, and S4, respectively. The AM fungal community structure was analyzed in the soil and root of different soybean cultivars using the PCR-DGGE technology. The results indicated a significant effect of sulfur on the AM fungal community structure in the roots and rhizospheric soil of different soybean cultivars. The three soybean cultivars in group S2 exhibited the highest diversity in AM fungus. Significant changes in the dominant fungal species were observed in the DGGE fingerprints of each sample, and Glomus, Funneliformis, Rhizophagus, and Claroideoglomus fungi were the dominant species of AM fungus in the roots and soil of soybean. The application of an appropriate amount of sulfur improved the diversity of AM fungi in roots and rhizospheric soil of different soybean cultivars.

  13. Adaptations in bacterial and fungal communities to termite fungiculture

    DEFF Research Database (Denmark)

    Otani, Saria

    . We therefore propose that division of labour extends beyond the termites to their gut bacterial communities. We also show that Termitomyces-fed cockroaches undergo compositional changes in their gut microbiotas. A step-wise gradient pattern in gut bacterial community that correlated with an increase...... in the proportion of fungal material provided to the cockroaches. However, gut microbiotas remained distinct from those of termites after Termitomyces-feeding, indicating that a fungal diet can play a role in structuring gut community composition, but at the same time exemplifies how original community compositions...

  14. Structure and composition of bacterial and fungal community in soil under soybean monoculture in the Brazilian Cerrado

    Directory of Open Access Journals (Sweden)

    J.D Bresolin

    2010-06-01

    Full Text Available Soybean is the most important oilseed cultivated in the world and Brazil is the second major producer. Expansion of soybean cultivation has direct and indirect impacts on natural habitats of high conservation value, such as the Brazilian savannas (Cerrado. In addition to deforestation, land conversion includes the use of fertilizers and pesticides and can lead to changes in the soil microbial communities. This study evaluated the soil bacterial and fungal communities and the microbial biomass C in a native Cerrado and in a similar no-tillage soybean monoculture area using PCR-DGGE and sequencing of bands. Compared to the native area, microbial biomass C was lower in the soybean area and cluster analysis indicated that the structure of soil microbial communities differed. 16S and 18S rDNA dendrograms analysis did not show differences between row and inter-row samples, but microbial biomass C values were higher in inter-rows during soybean fructification and harvest. The study pointed to different responses and alterations in bacterial and fungal communities due to soil cover changes (fallow x growth period and crop development. These changes might be related to differences in the pattern of root exudates affecting the soil microbial community. Among the bands chosen for sequencing there was a predominance of actinobacteria, y-proteobacteria and ascomycetous divisions. Even under no-tillage management methods, the soil microbial community was affected due to changes in the soil cover and crop development, hence warning of the impacts caused by changes in land use.

  15. Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

    Science.gov (United States)

    McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

    2017-01-01

    Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

  16. The composition of arbuscular mycorrhizal fungal communities in the roots of a ruderal forb is not related to the forest fragmentation process.

    Science.gov (United States)

    Grilli, Gabriel; Urcelay, Carlos; Galetto, Leonardo; Davison, John; Vasar, Martti; Saks, Ülle; Jairus, Teele; Öpik, Maarja

    2015-08-01

    Land-use changes and forest fragmentation have strong impact on biodiversity. However, little is known about the influence of new landscape configurations on arbuscular mycorrhizal fungal (AMF) community composition. We used 454 pyrosequencing to assess AMF diversity in plant roots from a fragmented forest. We detected 59 virtual taxa (VT; phylogenetically defined operational taxonomic units) of AMF - including 10 new VT - in the roots of Euphorbia acerensis. AMF communities were mainly composed of members of family Glomeraceae and were similar throughout the fragmented landscape, despite variation in forest fragment size (i.e. small, medium and large) and isolation (i.e. varying pairwise distances). AMF communities in forest fragments were phylogenetically clustered compared with the global, but not regional and local AMF taxon pools. This indicates that non-random community assembly processes possibly related to dispersal limitation at a large scale, rather than habitat filtering or biotic interactions, may be important in structuring the AMF communities. In this system, forest fragmentation did not appear to influence AMF community composition in the roots of the ruderal plant. Whether this is true for AMF communities in soil and the roots of other ecological groups of host plants or in other habitats deserves further study.

  17. Seasonal dynamics of fungal communities in a temperate oak forest soil

    National Research Council Canada - National Science Library

    Voříšková, Jana; Brabcová, Vendula; Cajthaml, Tomáš; Baldrian, Petr

    2014-01-01

    .... Vertical stratification of and seasonal changes in fungal abundance, activity and community composition were investigated in the litter, organic and upper mineral soils of a temperate Quercus petraea...

  18. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America

    Science.gov (United States)

    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

  19. Diverse honeydew-consuming fungal communities associated with scale insects.

    Science.gov (United States)

    Dhami, Manpreet K; Weir, Bevan S; Taylor, Michael W; Beggs, Jacqueline R

    2013-01-01

    Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated

  20. Diverse honeydew-consuming fungal communities associated with scale insects.

    Directory of Open Access Journals (Sweden)

    Manpreet K Dhami

    Full Text Available Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks. Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community

  1. Impacts of Asian dust events on atmospheric fungal communities

    Science.gov (United States)

    Jeon, Eun Mi; Kim, Yong Pyo; Jeong, Kweon; Kim, Ik Soo; Eom, Suk Won; Choi, Young Zoo; Ka, Jong-Ok

    2013-12-01

    The composition of atmospheric fungi in Seoul during Asian dust events were assessed by culturing and by molecular methods such as mold specific quantitative PCR (MSQPCR) and internal transcribed spacer cloning (ITS cloning). Culturable fungal concentrations in the air were monitored from May 2008 to July 2011 and 3 pairs of ITS clone libraries, one during Asian dust (AD) day and the other during the adjacent non Asian dust (NAD) day for each pair, were constructed after direct DNA extraction from total suspended particles (TSP) samples. In addition, six aeroallergenic fungi in the atmosphere were also assessed by MSQPCR from October, 2009 to November, 2011. The levels of the airborne culturable fungal concentrations during AD days was significantly higher than that of NAD days (P libraries. Thus, it was concluded that AD impacts not only airborne fungal concentrations but also fungal communities.

  2. TEMPORALLY VARIABLE GEOGRAPHICAL DISTANCE EFFECTS CONTRIBUTE TO THE ASSEMBLY OF ROOT-ASSOCIATED FUNGAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Christopher James Barnes

    2016-02-01

    Full Text Available Root-associated fungi are key contributors to ecosystem functioning, however the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance between fungal communities on composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal biogeography.

  3. Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities.

    Science.gov (United States)

    Barnes, Christopher J; van der Gast, Christopher J; Burns, Caitlin A; McNamara, Niall P; Bending, Gary D

    2016-01-01

    Root-associated fungi are key contributors to ecosystem functioning, however, the factors which determine community assembly are still relatively poorly understood. This study simultaneously quantified the roles of geographical distance, environmental heterogeneity and time in determining root-associated fungal community composition at the local scale within a short rotation coppice (SRC) willow plantation. Culture independent molecular analyses of the root-associated fungal community suggested a strong but temporally variable effect of geographical distance among fungal communities in terms of composition at the local geographical level. Whilst these distance effects were most prevalent on October communities, soil pH had an effect on structuring of the communities throughout the sampling period. Given the temporal variation in the effects of geographical distance and the environment for shaping root-associated fungal communities, there is clearly need for a temporal component to sampling strategies in future investigations of fungal ecology.

  4. Fungal communities associated with degradation of polyester polyurethane in soil.

    Science.gov (United States)

    Cosgrove, Lee; McGeechan, Paula L; Robson, Geoff D; Handley, Pauline S

    2007-09-01

    Soil fungal communities involved in the biodegradation of polyester polyurethane (PU) were investigated. PU coupons were buried in two sandy loam soils with different levels of organic carbon: one was acidic (pH 5.5), and the other was more neutral (pH 6.7). After 5 months of burial, the fungal communities on the surface of the PU were compared with the native soil communities using culture-based and molecular techniques. Putative PU-degrading fungi were common in both soils, as soil, and only a few species in the PU communities were detectable in the soil, indicating that only a small subset of the soil fungal communities colonized the PU. Soil type influenced the composition of the PU fungal communities. Geomyces pannorum and a Phoma sp. were the dominant species recovered by culturing from the PU buried in the acidic and neutral soils, respectively. Both fungi degraded Impranil and represented >80% of cultivable colonies from each plastic. However, PU was highly susceptible to degradation in both soils, losing up to 95% of its tensile strength. Therefore, different fungi are associated with PU degradation in different soils but the physical process is independent of soil type.

  5. Impacts of fertilization regimes on arbuscular mycorrhizal fungal (AMF community composition were correlated with organic matter composition in maize rhizosphere soil

    Directory of Open Access Journals (Sweden)

    Chen Zhu

    2016-11-01

    Full Text Available The understanding of the response of arbuscular mycorrhizal fungi (AMF community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well established yet. A field experiment located in northeast China in typical black soil (Chernozem was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC-MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2% of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analysed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three OTUs belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community

  6. Habitat filters in fungal endophyte community assembly

    Science.gov (United States)

    Fungal endophytes can influence host health, and more broadly, can instigate trophic cascades with effects scaling to the ecosystem level. Despite this, biotic mechanisms of endophyte community assembly are largely unknown. We used maize to investigate three potential habitat filters in endophyte co...

  7. Abundance, richness and structure of soil fungal communities across an European transect

    OpenAIRE

    Buee, Marc; Tisserant, Emilie; Hannula, S. E.; Fauchery, Laure; Plassart, Pierre; Stone, D; R. Creamer; W. Boer; van Veen, J.A.; Martin, Francis; and al, ..

    2014-01-01

    In contrast with plants and animals, biogeographical patterns of fungal assemblages have been little explored. Consequently, the factors driving the diversity and the composition of these communities are poorly understood. The EcoFINDERS project aimed at (i) characterizing the soil fungal diversity according to soil types, land uses and climate, and (ii) determining environmental variables explaining the fungal richness and community structure. Highthroughput sequencing of the ITS2 region was...

  8. Girdling affects ectomycorrhizal fungal (EMF) diversity and reveals functional differences in EMF community composition in a beech forest.

    Science.gov (United States)

    Pena, Rodica; Offermann, Christine; Simon, Judy; Naumann, Pascale Sarah; Gessler, Arthur; Holst, Jutta; Dannenmann, Michael; Mayer, Helmut; Kögel-Knabner, Ingrid; Rennenberg, Heinz; Polle, Andrea

    2010-03-01

    The relationships between plant carbon resources, soil carbon and nitrogen content, and ectomycorrhizal fungal (EMF) diversity in a monospecific, old-growth beech (Fagus sylvatica) forest were investigated by manipulating carbon flux by girdling. We hypothesized that disruption of the carbon supply would not affect diversity and EMF species numbers if EM fungi can be supplied by plant internal carbohydrate resources or would result in selective disappearance of EMF taxa because of differences in carbon demand of different fungi. Tree carbohydrate status, root demography, EMF colonization, and EMF taxon abundance were measured repeatedly during 1 year after girdling. Girdling did not affect root colonization but decreased EMF species richness of an estimated 79 to 90 taxa to about 40 taxa. Cenococcum geophilum, Lactarius blennius, and Tomentella lapida were dominant, colonizing about 70% of the root tips, and remained unaffected by girdling. Mainly cryptic EMF species disappeared. Therefore, the Shannon-Wiener index (H') decreased but evenness was unaffected. H' was positively correlated with glucose, fructose, and starch concentrations of fine roots and also with the ratio of dissolved organic carbon to dissolved organic nitrogen (DOC/DON), suggesting that both H' and DOC/DON were governed by changes in belowground carbon allocation. Our results suggest that beech maintains numerous rare EMF species by recent photosynthate. These EM fungi may constitute biological insurance for adaptation to changing environmental conditions. The preservation of taxa previously not known to colonize beech may, thus, form an important reservoir for future forest development.

  9. Experimental soil warming at the treeline shifts fungal communities species

    Science.gov (United States)

    Solly, Emily; Lindahl, Björn; Dawes, Melissa; Peter, Martina; Rixen, Christian; Hagedorn, Frank

    2016-04-01

    In terrestrial ecosystems, fungi play a major role in decomposition processes, plant nutrient uptake and nutrient cycling. In high elevation ecosystems in Alpine and Arctic regions, the fungal community may be particularly sensitive to climate warming due to the removal of temperature limitation in the plant and soil system, faster nutrient cycling and changes in plant carbon allocation to maintain roots systems and sustain the rhizosphere. In our study, we estimated the effects of 9 years CO2 enrichment and three years of experimental soil warming on the community structure of fungal microorganisms in an alpine treeline ecosystem. In the Swiss Alps, we worked on a total of 40 plots, with c. 40-year-old Larix decidua and Pinus mugo ssp. uncinata trees (20 plots for each tree species). Half of the plots with each tree species were randomly assigned to an elevated CO2 treatment (ambient concentration +200 ppm), whereas the remaining plots received no supplementary CO2. Five individual plots for each combination of CO2 concentration and tree species were heated by an average of 4°C during the growing season with heating cables at the soil surface. At the treeline, the fungal diversity analyzed by high-throughput 454-sequencing of genetic markers, was generally low as compared to low altitude systems and mycorrhizal species made a particularly small contribution to the total fungal DNA. Soil warming led to a shift in the structure and composition of the fungal microbial community, with an increase of litter degraders and ectomycorrhizal fungi. We further observed changes in the productivity of specific fungal fruiting bodies (i.e. more Lactarius rufus sporocarps and less Hygrophorus lucorum sporocarps) during the course of the experiment, that were consistent with the 454-sequencing data. The warming effect was more pronounced in the Larix plots. These shifts were accompanied by an increased soil CO2 efflux (+40%), evidence of increased N availability and a

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    A. M. Womack

    2015-05-01

    Full Text Available 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-throughout 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, suggesting that inputs of fungi to the atmosphere are from local, rather than distant, sources. 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.

  12. Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities

    Science.gov (United States)

    Zhou, Xingang; Zhang, Jianhui; Gao, Danmei; Gao, Huan; Guo, Meiyu; Li, Li; Zhao, Mengliang; Wu, Fengzhi

    2017-01-01

    Understanding soil microbial communities in agroecosystems has the potential to contribute to the improvement of agricultural productivity and sustainability. Effects of conversion from long-term wheat plantation to Jerusalem artichoke (JA) plantation on soil fungal communities were determined by amplicon sequencing of total fungal ITS regions. Quantitative PCR and PCR-denaturing gradient gel electrophoresis were also used to analyze total fungal and Trichoderma spp. ITS regions and Fusarium spp. Ef1α genes. Results showed that soil organic carbon was higher in the first cropping of JA and Olsen P was lower in the third cropping of JA. Plantation conversion changed soil total fungal and Fusarium but not Trichoderma spp. community structures and compositions. The third cropping of JA had the lowest total fungal community diversity and Fusarium spp. community abundance, but had the highest total fungal and Trichoderma spp. community abundances. The relative abundances of potential fungal pathogens of wheat were higher in the wheat field. Fungal taxa with plant growth promoting, plant pathogen or insect antagonistic potentials were enriched in the first and second cropping of JA. Overall, short-term conversion from wheat to JA plantation changed soil fungal communities, which is related to changes in soil organic carbon and Olsen P contents.

  13. Foliar fungal communities strongly differ between habitat patches in a landscape mosaic

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    Thomas Fort

    2016-11-01

    Full Text Available Background Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. Methods We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2 region. Results In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. Discussion These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.

  14. Primer sets developed for fungal functional genes reveal shifts in functionality of fungal community in soils

    Directory of Open Access Journals (Sweden)

    Emilia Silja Hannula

    2016-11-01

    Full Text Available Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

  15. Concentration of Petroleum-Hydrocarbon Contamination Shapes Fungal Endophytic Community Structure in Plant Roots.

    Science.gov (United States)

    Bourdel, Guillaume; Roy-Bolduc, Alice; St-Arnaud, Marc; Hijri, Mohamed

    2016-01-01

    Plant-root inhabiting fungi are a universal phenomenon found in all ecosystems where plants are able to grow, even in harsh environments. Interactions between fungi and plant roots can vary widely from mutualism to parasitism depending on many parameters. The role of fungal endophytes in phytoremediation of polluted sites, and characterization of the endophytic diversity and community assemblages in contaminated areas remain largely unexplored. In this study, we investigated the composition of endophytic fungal communities in the roots of two plant species growing spontaneously in petroleum-contaminated sedimentation basins of a former petro-chemical plant. The three adjacent basins showed a highly heterogeneous pattern of pollutant concentrations. We combined a culture-based isolation approach with the pyrosequencing of fungal ITS ribosomal DNA. We selected two species, Eleocharis erythropoda Steud. and Populus balsamifera L., and sampled three individuals of each species from each of three adjacent basins, each with a different concentration of petroleum hydrocarbons. We found that contamination level significantly shaped endophytic fungal diversity and community composition in E. erythropoda, with only 9.9% of these fungal Operational Taxonomic Units (OTUs) retrieved in all three basins. However, fungal community structure associated with P. balsamifera remained unaffected by the contamination level with 28.2% of fungal OTUs shared among all three basins. This could be explained by the smaller differences of pollutant concentrations in the soil around our set of P. balsamifera sampless compared to that around our set of E. erythropoda samples. Our culture-based approach allowed isolation of 11 and 30 fungal endophytic species from surface-sterilized roots of E. erythropoda and P. balsamifera, respectively. These isolates were ribotyped using ITS, and all were found in pyrosequensing datasets. Our results demonstrate that extreme levels of pollution reduce fungal

  16. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.

    Science.gov (United States)

    Mueller, Rebecca C; Paula, Fabiana S; Mirza, Babur S; Rodrigues, Jorge L M; Nüsslein, Klaus; Bohannan, Brendan J M

    2014-07-01

    Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.

  17. Digging the New York City Skyline: soil fungal communities in green roofs and city parks.

    Science.gov (United States)

    McGuire, Krista L; Payne, Sara G; Palmer, Matthew I; Gillikin, Caitlyn M; Keefe, Dominique; Kim, Su Jin; Gedallovich, Seren M; Discenza, Julia; Rangamannar, Ramya; Koshner, Jennifer A; Massmann, Audrey L; Orazi, Giulia; Essene, Adam; Leff, Jonathan W; Fierer, Noah

    2013-01-01

    In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.

  18. Digging the New York City Skyline: soil fungal communities in green roofs and city parks.

    Directory of Open Access Journals (Sweden)

    Krista L McGuire

    Full Text Available In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.

  19. Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Eiko E Kuramae

    Full Text Available We assessed soil fungal diversity and community structure at two sampling times (t1 = 47 days and t2 = 104 days of plant age in pots associated with four maize cultivars, including two genetically modified (GM cultivars by high-throughput pyrosequencing of the 18S rRNA gene using DNA and RNA templates. We detected no significant differences in soil fungal diversity and community structure associated with different plant cultivars. However, DNA-based analyses yielded lower fungal OTU richness as compared to RNA-based analyses. Clear differences in fungal community structure were also observed in relation to sampling time and the nucleic acid pool targeted (DNA versus RNA. The most abundant soil fungi, as recovered by DNA-based methods, did not necessary represent the most "active" fungi (as recovered via RNA. Interestingly, RNA-derived community compositions at t1 were highly similar to DNA-derived communities at t2, based on presence/absence measures of OTUs. We recovered large proportions of fungal sequences belonging to arbuscular mycorrhizal fungi and Basidiomycota, especially at the RNA level, suggesting that these important and potentially beneficial fungi are not affected by the plant cultivars nor by GM traits (Bt toxin production. Our results suggest that even though DNA- and RNA-derived soil fungal communities can be very different at a given time, RNA composition may have a predictive power of fungal community development through time.

  20. Fungal community dynamics and driving factors during agricultural waste composting.

    Science.gov (United States)

    Yu, Man; Zhang, Jiachao; Xu, Yuxin; Xiao, Hua; An, Wenhao; Xi, Hui; Xue, Zhiyong; Huang, Hongli; Chen, Xiaoyang; Shen, Alin

    2015-12-01

    This study was conducted to identify the driving factors behind fungal community dynamics during agricultural waste composting. Fungal community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis combined with DNA sequencing. The effects of physico-chemical parameters on fungal community abundance and structure were evaluated by least significant difference tests and redundancy analysis. The results showed that Cladosporium bruhnei, Hanseniaspora uvarum, Scytalidium thermophilum, Tilletiopsis penniseti, and Coprinopsis altramentaria were prominent during the composting process. The greatest variation in the distribution of fungal community structure was statistically explained by pile temperature and total organic carbon (TOC) (P composting.

  1. Ectomycorrhizal fungal community structure of pinyon pines growing in two environmental extremes

    Energy Technology Data Exchange (ETDEWEB)

    Gehring, C.A.; Theimer, T.C.; Whitham, T.G.; Keim, P. [Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences

    1998-07-01

    The authors used molecular techniques to examine the ectomycorrhizal fungal community associated with pinyon pine (Pinus edulis) growing in two soil types in a semiarid region of northern Arizona. Pinyon performance (e.g., growth, reproduction, water stress) has been shown to be markedly lower in cinder than in sandy-loam environments. Fungal community composition and richness were determined using RFLP (restriction fragment length polymorphism) analysis of ectomycorrhizal root tips collected from three sites within each soil type. Several patterns emerged from these analyses. First, communities in both cinder and sandy-loam soils were dominated by one or a few abundant ectomytcorrhizal types, a species abundance pattern common to many plant and animal communities. Second, unlike the pattern for many other organisms, ectomycorrhizal fungal type richness was not correlated with measures of ecosystem productivity such as soil nutrient and moisture levels; cinder and sandy-loam soils had similar numbers of ectomycorrhizal fungal types. Third, soil type and fungal community composition were linked, as cluster analysis demonstrated greater similarity of fungal communities from sites within soil types than between them. Fourth, a preliminary survey of 14--45 ectomycorrhizal root tips from each of 20 trees at one cinder site indicated that trees were dominated by one or a few ectomycorrhizal RFLP types. Fifth, the RFLP patterns of some fungal sporocarps matched those of ectomycorrhizal root tips, but many did not, indicating that many of the ectomycorrhizal fungi at these sites fruit infrequently, whereas other fungi with more abundant sporocarps may not form ectomycorrhiza.

  2. Divergent habitat filtering of root and soil fungal communities in temperate beech forests

    Science.gov (United States)

    Goldmann, Kezia; Schröter, Kristina; Pena, Rodica; Schöning, Ingo; Schrumpf, Marion; Buscot, François; Polle, Andrea; Wubet, Tesfaye

    2016-01-01

    Distance decay, the general reduction in similarity of community composition with increasing geographical distance, is known as predictor of spatial variation and distribution patterns of organisms. However, changes in fungal communities along environmental gradients are little known. Here we show that distance decays of soil-inhabiting and root-associated fungal assemblages differ, and identify explanatory environmental variables. High-throughput sequencing analysis of fungal communities of beech-dominated forests at three study sites across Germany shows that root-associated fungi are recruited from the soil fungal community. However, distance decay is substantially weaker in the root-associated than in the soil community. Variance partitioning of factors contributing to the observed distance decay patterns support the hypothesis that host trees stabilize the composition of root-associated fungi communities, relative to soil communities. Thus, they not only have selective impacts on associated communities, but also buffer effects of changes in microclimatic and environmental variables that directly influence fungal community composition. PMID:27511465

  3. Divergent habitat filtering of root and soil fungal communities in temperate beech forests

    Science.gov (United States)

    Goldmann, Kezia; Schröter, Kristina; Pena, Rodica; Schöning, Ingo; Schrumpf, Marion; Buscot, François; Polle, Andrea; Wubet, Tesfaye

    2016-08-01

    Distance decay, the general reduction in similarity of community composition with increasing geographical distance, is known as predictor of spatial variation and distribution patterns of organisms. However, changes in fungal communities along environmental gradients are little known. Here we show that distance decays of soil-inhabiting and root-associated fungal assemblages differ, and identify explanatory environmental variables. High-throughput sequencing analysis of fungal communities of beech-dominated forests at three study sites across Germany shows that root-associated fungi are recruited from the soil fungal community. However, distance decay is substantially weaker in the root-associated than in the soil community. Variance partitioning of factors contributing to the observed distance decay patterns support the hypothesis that host trees stabilize the composition of root-associated fungi communities, relative to soil communities. Thus, they not only have selective impacts on associated communities, but also buffer effects of changes in microclimatic and environmental variables that directly influence fungal community composition.

  4. Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type

    Science.gov (United States)

    Ellis, J. Christopher; Fay, Philip A.; Polley, H. Wayne; Jackson, Robert B.

    2014-01-01

    Soils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2 is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2 experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2 differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2 in the black clay (P 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2 in the sandy loam (P = 0.02, R2 = 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r = 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r = 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2 may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2 in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2. PMID:25239904

  5. Age and gender affect the composition of fungal population of the human gastrointestinal tract

    Directory of Open Access Journals (Sweden)

    Francesco Strati

    2016-08-01

    Full Text Available The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C, to acidic and oxidative stress and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals’ life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics

  6. Diverse ecological roles within fungal communities in decomposing logs of Picea abies.

    Science.gov (United States)

    Ottosson, Elisabet; Kubartová, Ariana; Edman, Mattias; Jönsson, Mari; Lindhe, Anders; Stenlid, Jan; Dahlberg, Anders

    2015-03-01

    Fungal communities in Norway spruce (Picea abies) logs in two forests in Sweden were investigated by 454-sequence analyses and by examining the ecological roles of the detected taxa. We also investigated the relationship between fruit bodies and mycelia in wood and whether community assembly was affected by how the dead wood was formed. Fungal communities were highly variable in terms of phylogenetic composition and ecological roles: 1910 fungal operational taxonomic units (OTUs) were detected; 21% were identified to species level. In total, 58% of the OTUs were ascomycetes and 31% basidiomycetes. Of the 231 337 reads, 38% were ascomycetes and 60% basidiomycetes. Ecological roles were assigned to 35% of the OTUs, accounting for 62% of the reads. Wood-decaying fungi were the most common group; however, other saprotrophic, mycorrhizal, lichenized, parasitic and endophytic fungi were also common. Fungal communities in logs formed by stem breakage were different to those in logs originating from butt breakage or uprooting. DNA of specific species was detected in logs many years after the last recorded fungal fruiting. Combining taxonomic identification with knowledge of ecological roles may provide valuable insights into properties of fungal communities; however, precise ecological information about many fungal species is still lacking. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Phylogenetic structure of ectomycorrhizal fungal communities of western hemlock changes with forest age and stand type.

    Science.gov (United States)

    Lim, SeaRa; Berbee, Mary L

    2013-08-01

    On Vancouver Island, British Columbia, fertilization with nitrogen (N) and phosphorus (P) following clearcutting increases growth of western hemlock. To explore whether fertilization also resulted in ectomycorrhizal fungal communities that were more or less similar to neighboring unlogged stands, we sampled roots from western hemlock from three replicate plots from each of five different, well-characterized, forest stand types that differed in site type, and in logging and fertilization history. We harvested four samples of 100 ectomycorrhizal root tips from each plot, a total of 60 samples per stand type. From each sample, we analyzed fungal ribosomal internal transcribed spacers and 28S DNA, sequencing 15-29 clones per sample and 60-116 clones per plot. We detected 147 fungal operational taxonomic units among a total of 1435 sequences. Craterellus tubaeformis was frequently present and resulted in a pattern of phylogenetic overdispersion in the fungal communities. Fungal species composition was strongly correlated with foliar nitrogen concentration. However, other site quality factors were also important because the fertilized regenerating hemlock and mature hemlock-amabilis fir forests had similar foliar nitrogen content but little overlap in fungal species. Compared with unfertilized regenerating forests, fungal communities in N + P-fertilized regenerating forests had significantly more species overlap with old growth forests. However, the fungal communities of all regenerating forest were similar to one another and all differed significantly from older forests. By correlating fungal clades with habitats, this research improves understanding of how forest management can contribute to maintaining diverse ectomycorrhizal fungal communities across a landscape.

  8. Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil.

    Science.gov (United States)

    Singh, Brajesh K; Nunan, Naoise; Millard, Peter

    2009-10-01

    In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.

  9. Changes in fungal communities along a boreal forest soil fertility gradient.

    Science.gov (United States)

    Sterkenburg, Erica; Bahr, Adam; Brandström Durling, Mikael; Clemmensen, Karina E; Lindahl, Björn D

    2015-09-01

    Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  10. Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest.

    Science.gov (United States)

    Sun, Hui; Terhonen, Eeva; Kovalchuk, Andriy; Tuovila, Hanna; Chen, Hongxin; Oghenekaro, Abbot O; Heinonsalo, Jussi; Kohler, Annegret; Kasanen, Risto; Vasander, Harri; Asiegbu, Fred O

    2016-05-01

    Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (Pstructure (Psoil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

  11. Vertical and seasonal dynamics of fungal communities in boreal Scots pine forest soil.

    Science.gov (United States)

    Santalahti, Minna; Sun, Hui; Jumpponen, Ari; Pennanen, Taina; Heinonsalo, Jussi

    2016-11-01

    Fungal communities are important for carbon (C) transformations in boreal forests that are one of the largest C pools in terrestrial ecosystems, warranting thus further investigation of fungal community dynamics in time and space. We investigated fungal diversity and community composition seasonally and across defined soil horizons in boreal Scots pine forest in Finland using 454 pyrosequencing. We collected a total of 120 samples from five vertical soil horizons monthly from March to October; in March, under snow. Boreal forest soil generally harbored diverse fungal communities across soil horizons. The communities shifted drastically and rapidly over time. In late winter, saprotrophs dominated the community and were replaced by ectomycorrhizal fungi during the growing season. Our studies are among the first to dissect the spatial and temporal dynamics in boreal forest ecosystems and highlights the ecological importance of vertically distinct communities and their rapid seasonal dynamics. As climate change is predicted to result in warmer and longer snow-free winter seasons, as well as increase the rooting depth of trees in boreal forest, the seasonal and vertical distribution of fungal communities may change. These changes are likely to affect the organic matter decomposition by the soil-inhabiting fungi and thus alter organic C pools. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Land-use intensity and host plant simultaneously shape the composition of arbuscular mycorrhizal fungal communities in a Mediterranean drained peatland.

    Science.gov (United States)

    Ciccolini, Valentina; Ercoli, Laura; Davison, John; Vasar, Martti; Öpik, Maarja; Pellegrino, Elisa

    2016-12-01

    Land-use change is known to be a major threat to biodiversity and ecosystem services in Mediterranean areas. However, the potential for different host plants to modulate the effect of land-use intensification on community composition of arbuscular mycorrhizal fungi (AMF) is still poorly understood. To test the hypothesis that low land-use intensity promotes AMF diversity at different taxonomic scales and to determine whether any response is dependent upon host plant species identity, we characterised AMF communities in the roots of 10 plant species across four land use types of differing intensity in a Mediterranean peatland system. AMF were identified using 454 pyrosequencing. This revealed an overall low level of AMF richness in the peaty soils; lowest AMF richness in the intense cropping system at both virtual taxa and family level; strong modulation by the host plant of the impact of land-use intensification on AMF communities at the virtual taxa level; and a significant effect of land-use intensification on AMF communities at the family level. These findings have implications for understanding ecosystem stability and productivity and should be considered when developing soil-improvement strategies in fragile ecosystems, such as Mediterranean peatlands.

  13. Reintroduction of locally extinct vertebrates impacts arid soil fungal communities.

    Science.gov (United States)

    Clarke, Laurence J; Weyrich, Laura S; Cooper, Alan

    2015-06-01

    Introduced species have contributed to extinction of native vertebrates in many parts of the world. Changes to vertebrate assemblages are also likely to alter microbial communities through coextinction of some taxa and the introduction of others. Many attempts to restore degraded habitats involve removal of exotic vertebrates (livestock and feral animals) and reintroduction of locally extinct species, but the impact of such reintroductions on microbial communities is largely unknown. We used high-throughput DNA sequencing of the fungal internal transcribed spacer I (ITS1) region to examine whether replacing exotic vertebrates with reintroduced native vertebrates led to changes in soil fungal communities at a reserve in arid central Australia. Soil fungal diversity was significantly different between dune and swale (interdune) habitats. Fungal communities also differed significantly between sites with exotic or reintroduced native vertebrates after controlling for the effect of habitat. Several fungal operational taxonomic units (OTUs) found exclusively inside the reserve were present in scats from reintroduced native vertebrates, providing a direct link between the vertebrate assemblage and soil microbial communities. Our results show that changes to vertebrate assemblages through local extinctions and the invasion of exotic species can alter soil fungal communities. If local extinction of one or several species results in the coextinction of microbial taxa, the full complement of ecological interactions may never be restored.

  14. Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube

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    Peng Liu

    2015-01-01

    Full Text Available Fungi are important soil components as both decomposers and plant symbionts and play a major role in ecological and biogeochemical processes. However, little is known about the richness and structure of fungal communities. DNA sequencing technologies allow for the direct estimation of microbial community diversity, avoiding culture-based biases. We therefore used 454 pyrosequencing to investigate the fungal communities in the rhizosphere of Xinjiang jujube. We obtained no less than 40,488 internal transcribed spacer (ITS rDNA reads, the number of each sample was 6943, 6647, 6584, 6550, 6860, and 6904, and we used bioinformatics and multivariate statistics to analyze the results. The index of diversity showed greater richness in the rhizosphere fungal community of a 3-year-old jujube than in that of an 8-year-old jujube. Most operational taxonomic units belonged to Ascomycota, and taxonomic analyses identified Hypocreales as the dominant fungal order. Our results demonstrated that the fungal orders are present in different proportions in different sampling areas. Redundancy analysis (RDA revealed a significant correlation between soil properties and the abundance of fungal phyla. Our results indicated lower fungal diversity in the rhizosphere of Xinjiang jujube than that reported in other studies, and we hope our findings provide a reference for future research.

  15. Soil Influences Colonization of Root-Associated Fungal Endophyte Communities of Maize, Wheat, and Their Progenitors

    Directory of Open Access Journals (Sweden)

    Deepak Bokati

    2016-01-01

    Full Text Available Root-associated fungal endophytes are vital component of root microbiome as some mitigate their host’s abiotic and biotic stress. We characterized root-associated fungal endophytes in cereal grains and their progenitors grown on two different soil-types. We aimed at determining how clay and desert soil affects the colonization of root fungal community. Both culture-dependent and culture-independent methods were employed to identify endophytes that successfully colonized greenhouse-grown host plants. The Internal Transcriber Spacer region of fungal ribosomal DNA was utilized for identification purposes. This study revealed soil as a prominent factor influencing the composition of microfungal communities inhabiting the roots of maize (Zea mays subsp. mays and its conspecific progenitor, teosinte (Zea mays subsp. parviglumis. Similar results were found in wheat (Triticum aestivum subsp. aestivum and its progenitor (Triticum monococcum subsp. monococcum. The multidimensional comparisons of Morisita-Horn similarity values of fungal colonists of various host plant taxa indicated that soil plays a primary role in shaping the root fungal community; a secondary effect was plant host identity, even when the plant host is a conspecific. Future studies focused on characterizing root endophytes in other cereal grains, and studying the effect of edaphic factors on fungal colonization, can ultimately contribute to crop productivity.

  16. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees.

    Science.gov (United States)

    Vincent, J B; Weiblen, G D; May, G

    2016-02-01

    Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.

  17. Investigation of the fungal community structures of imported wheat using high-throughput sequencing technology

    Science.gov (United States)

    Wang, Ying; Zhang, Guiming; Gao, Ruifang; Xiang, Caiyu; Feng, Jianjun; Lou, Dingfeng; Liu, Ying

    2017-01-01

    This study introduced the application of high-throughput sequencing techniques to the investigation of microbial diversity in the field of plant quarantine. It examined the microbial diversity of wheat imported into China, and established a bioinformatics database of wheat pathogens based on high-throughput sequencing results. This study analyzed the nuclear ribosomal internal transcribed spacer (ITS) region of fungi through Illumina Miseq sequencing to investigate the fungal communities of both seeds and sieve-through. A total of 758,129 fungal ITS sequences were obtained from ten samples collected from five batches of wheat imported from the USA. These sequences were classified into 2 different phyla, 15 classes, 33 orders, 41 families, or 78 genera, suggesting a high fungal diversity across samples. Apairwise analysis revealed that the diversity of the fungal community in the sieve-through is significantly higher than those in the seeds. Taxonomic analysis showed that at the class level, Dothideomycetes dominated in the seeds and Sordariomycetes dominated in the sieve-through. In all, this study revealed the fungal community composition in the seeds and sieve-through of the wheat, and identified key differences in the fungal community between the seeds and sieve-through. PMID:28241020

  18. Soil bacterial and fungal communities across a pH gradient in an arable soil.

    Science.gov (United States)

    Rousk, Johannes; Bååth, Erland; Brookes, Philip C; Lauber, Christian L; Lozupone, Catherine; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2010-10-01

    Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

  19. Assessment of the effects of genetically modified potatoes on structure and functioning of soil fungal communities

    NARCIS (Netherlands)

    Hannula, Emilia

    2012-01-01

    This thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter composition, and compares the observed differences between the GM- and its parental variety in the context o

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Caio T C C Rachid

    Full Text Available 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.

  2. Variation of soil arbuscular mycorrhizal fungal communities across land use gradient

    Science.gov (United States)

    Moora, M.; Davison, J.; Metsis, M.; Öpik, M.; Vasar, M.; Zobel, M.

    2012-04-01

    Arbuscular mycorrhizal (AM) fungi (phylum Glomeromycota) colonize the roots of most terrestrial plants, facilitating mineral nutrient uptake from soil in exchange for plant-assimilated carbon. While investigating functional aspects of plant-AM fungi interactions has been a major focus of research, there is increasing interest in describing and explaining the distribution of AM fungal diversity. Different management practices has been shown to influence the AM fungal communities while more intense management can bring along the loss of AM fungal diversity. Such a loss may have negative consequences on ecosystem service delivery, primary production and soil sustainability. However, due to cryptic lifestyle of AM fungi, relatively few information is available about variability of diversity and composition of AM fungal communities in the soils from differently managed ecosystems. To study the variation of soil AM fungal communities in response to the land use intensity, replicated soil samples were collected along land use gradient from intensively managed agricultural fields, organic fields, forest plantations and managed natural forest to primeval forest in Estonia. Soil AM fungal communities were described using molecular tools: DNA extraction, amplicon isolation and 454 large scale parallel pyrosequencing. Glomeromycota sequences were amplified using the SSU rDNA primers NS31 and AML2. We shall analyse and describe AM fungal community changes along land use intensity gradient and seek finding indicator taxa characteristic to particular land use types. We shall also address changes in the diversity of AM fungal taxa and check whether the decrease of diversity along land use intensity is a ubiquitous phenomenon.

  3. The composition of arbuscular mycorrhizal fungal communities differs among the roots, spores and extraradical mycelia associated with five Mediterranean plant species.

    Science.gov (United States)

    Varela-Cervero, Sara; Vasar, Martti; Davison, John; Barea, José Miguel; Öpik, Maarja; Azcón-Aguilar, Concepción

    2015-08-01

    Arbuscular mycorrhizal fungi (AMF) are essential constituents of most terrestrial ecosystems. AMF species differ in terms of propagation strategies and the major propagules they form. This study compared the AMF community composition of different propagule fractions - colonized roots, spores and extraradical mycelium (ERM) - associated with five Mediterranean plant species in Sierra de Baza Natural Park (Granada, Spain). AMF were identified using 454 pyrosequencing of the SSU rRNA gene. A total of 96 AMF phylogroups [virtual taxa (VT)] were detected in the study site, including 31 novel VT. After per-sample sequencing depth standardization, 71 VT were recorded from plant roots, and 47 from each of the spore and ERM fractions. AMF communities differed significantly among the propagule fractions, and the root-colonizing fraction differed among host plant species. Indicator VT were detected for the root (13 Glomus VT), spore (Paraglomus VT281, VT336, Pacispora VT284) and ERM (Diversispora VT62) fractions. This study provides detailed evidence from a natural system that AMF taxa are differentially allocated among soil mycelium, soil spores and colonized root propagules. This has important implications for interpreting AMF diversity surveys and designing applications of AMF in vegetation restoration.

  4. Fungal Communities Associated with Degradation of Polyester Polyurethane in Soil▿

    OpenAIRE

    Cosgrove, Lee; McGeechan, Paula L.; Robson, Geoff D.; Handley, Pauline S.

    2007-01-01

    Soil fungal communities involved in the biodegradation of polyester polyurethane (PU) were investigated. PU coupons were buried in two sandy loam soils with different levels of organic carbon: one was acidic (pH 5.5), and the other was more neutral (pH 6.7). After 5 months of burial, the fungal communities on the surface of the PU were compared with the native soil communities using culture-based and molecular techniques. Putative PU-degrading fungi were common in both soils, as 80% of cultiv...

  5. Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

    Science.gov (United States)

    Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

    2017-09-08

    Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

  6. Experimental Climate Change Modifies Degradative Succession in Boreal Peatland Fungal Communities.

    Science.gov (United States)

    Asemaninejad, Asma; Thorn, R Greg; Lindo, Zoë

    2017-04-01

    Peatlands play an important role in global climate change through sequestration of atmospheric CO2. Climate-driven changes in the structure of fungal communities in boreal peatlands that favor saprotrophic fungi can substantially impact carbon dynamics and nutrient cycling in these crucial ecosystems. In a mesocosm study using a full factorial design, 100 intact peat monoliths, complete with living Sphagnum and above-ground vascular vegetation, were subjected to three climate change variables (increased temperature, reduced water table, and elevated CO2 concentrations). Peat litterbags were placed in mesocosms, and fungal communities in litterbags were monitored over 12 months to assess the impacts of climate change variables on peat-inhabiting fungi. Changes in fungal richness, diversity, and community composition were assessed using Illumina MiSeq sequencing of ribosomal DNA (rDNA). While general fungal richness reduced under warming conditions, Ascomycota exhibited higher diversity under increased temperature treatments over the course of the experiment. Both increased temperature and lowered water table position drove shifts in fungal community composition with a strong positive effect on endophytic and mycorrhizal fungi (including one operational taxonomic unit (OTU) tentatively identified as Barrenia panicia) and different groups of saprotrophs identified as Mortierella, Galerina, and Mycena. These shifts were observed during a predicted degradative succession in the decomposer community as different carbon substrates became available. Since fungi play a central role in peatland communities, increased abundances of saprotrophic fungi under warming conditions, at the expense of reduced fungal richness overall, may increase decomposition rates under future climate scenarios and could potentially aggravate the impacts of climate change.

  7. Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains.

    Science.gov (United States)

    Miyamoto, Yumiko; Sakai, Atsushi; Hattori, Masahira; Nara, Kazuhide

    2015-08-01

    Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the regional scale. Soil cores were collected from various forest types along an elevation gradient in southwestern Japan. Fungal species were identified by the internal transcribed spacer regions of the rDNA using direct sequencing. The occurrence of fungal species in this study was compared with a previous study conducted on a mountain separated by ∼550 km. In total, we recorded 454 EM fungi from 330 of 350 soil cores. Forty-seven fungal species (∼20% of the total excluding singletons) were shared between two mountains, mostly between similar forest types on both mountains. Variation partitioning in redundancy analysis revealed that climate explained the largest variance in EM fungal composition. The similarity of forest tree composition, which is usually determined by climatic conditions, was positively correlated with the similarity of the EM fungal composition. However, the lack of large host effects implied that communities of forest trees and EM fungi may be determined independently by climate. Our data provide important insights that host plants and mutualistic fungi may respond to climate change idiosyncratically, potentially altering carbon and nutrient cycles in relation to the plant-fungus associations.

  8. Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

    Science.gov (United States)

    Panzer, Katrin; Yilmaz, Pelin; Weiß, Michael; Reich, Lothar; Richter, Michael; Wiese, Jutta; Schmaljohann, Rolf; Labes, Antje; Imhoff, Johannes F; Glöckner, Frank Oliver; Reich, Marlis

    2015-01-01

    Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of

  9. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests.

    Science.gov (United States)

    Saravesi, Karita; Aikio, Sami; Wäli, Piippa R; Ruotsalainen, Anna Liisa; Kaukonen, Maarit; Huusko, Karoliina; Suokas, Marko; Brown, Shawn P; Jumpponen, Ari; Tuomi, Juha; Markkola, Annamari

    2015-05-01

    Climate change has important implications on the abundance and range of insect pests in forest ecosystems. We studied responses of root-associated fungal communities to defoliation of mountain birch hosts by a massive geometrid moth outbreak through 454 pyrosequencing of tagged amplicons of the ITS2 rDNA region. We compared fungal diversity and community composition at three levels of moth defoliation (intact control, full defoliation in one season, full defoliation in two or more seasons), replicated in three localities. Defoliation caused dramatic shifts in functional and taxonomic community composition of root-associated fungi. Differentially defoliated mountain birch roots harbored distinct fungal communities, which correlated with increasing soil nutrients and decreasing amount of host trees with green foliar mass. Ectomycorrhizal fungi (EMF) abundance and richness declined by 70-80 % with increasing defoliation intensity, while saprotrophic and endophytic fungi seemed to benefit from defoliation. Moth herbivory also reduced dominance of Basidiomycota in the roots due to loss of basidiomycete EMF and increases in functionally unknown Ascomycota. Our results demonstrate the top-down control of belowground fungal communities by aboveground herbivory and suggest a marked reduction in the carbon flow from plants to soil fungi following defoliation. These results are among the first to provide evidence on cascading effects of natural herbivory on tree root-associated fungi at an ecosystem scale.

  10. Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase

    Science.gov (United States)

    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

  11. Strong linkage between plant and soil fungal communities along a successional coastal dune system.

    Science.gov (United States)

    Roy-Bolduc, Alice; Laliberté, Etienne; Boudreau, Stéphane; Hijri, Mohamed

    2016-10-01

    Complex interactions between plants and soil microorganisms drive key ecosystem and community properties such as productivity and diversity. In nutrient-poor systems such as sand dunes, plant traits and fungal symbioses related to nutrient acquisition can strongly influence vegetation dynamics. We investigated plant and fungal communities in a relic foredune plain located on an archipelago in Québec, Canada. We detected distinct communities across the edaphic and successional gradient. Our results showed a clear increase in plant species richness, as well as in the diversity of nutrient-acquisition strategies. We also found a strong correlation between aboveground vegetation and soil fungal communities, and both responded similarly to soil physicochemical properties. Soil pH influenced the composition of plant and fungal communities, and could act as an important environmental filter along this relic foredune plain. The increasing functional diversity in plant nutrient-acquisition strategies across the gradient might favor resource partitioning and facilitation among co-occurring plant species. The coordinated changes in soil microbial and plant communities highlight the importance of aboveground-belowground linkages and positive biotic interactions during ecological succession in nutrient-poor environments.

  12. Genetic and ontogenetic variation in an endangered tree structures dependent arthropod and fungal communities.

    Directory of Open Access Journals (Sweden)

    Benjamin J Gosney

    Full Text Available Plant genetic and ontogenetic variation can significantly impact dependent fungal and arthropod communities. However, little is known of the relative importance of these extended genetic and ontogenetic effects within a species. Using a common garden trial, we compared the dependent arthropod and fungal community on 222 progeny from two highly differentiated populations of the endangered heteroblastic tree species, Eucalyptus morrisbyi. We assessed arthropod and fungal communities on both juvenile and adult foliage. The community variation was related to previous levels of marsupial browsing, as well as the variation in the physicochemical properties of leaves using near-infrared spectroscopy. We found highly significant differences in community composition, abundance and diversity parameters between eucalypt source populations in the common garden, and these were comparable to differences between the distinctive juvenile and adult foliage. The physicochemical properties assessed accounted for a significant percentage of the community variation but did not explain fully the community differences between populations and foliage types. Similarly, while differences in population susceptibility to a major marsupial herbivore may result in diffuse genetic effects on the dependent community, this still did not account for the large genetic-based differences in dependent communities between populations. Our results emphasize the importance of maintaining the populations of this rare species as separate management units, as not only are the populations highly genetically structured, this variation may alter the trajectory of biotic colonization of conservation plantings.

  13. Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs

    Science.gov (United States)

    Metabarcoding, defined as Next Generation Sequencing (NGS) of amplicons of the ITS2 region (DNA barcode), was used to identify the composition of the fungal community on different strawberry organs i.e. leaves, flowers, and immature and mature fruits grown on a farm using disease and insect control ...

  14. Spatial and temporal variation in fungal endophyte communities isolated from cultivated cotton (Gossypium hirsutum.

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    María J Ek-Ramos

    Full Text Available Studies of fungi in upland cotton (Gossypium hirsutum cultivated in the United States have largely focused on monitoring and controlling plant pathogens. Given increasing interest in asymptomatic fungal endophytes as potential biological control agents, surveys are needed to better characterize their diversity, distribution patterns and possible applications in integrated pest management. We sampled multiple varieties of cotton in Texas, USA and tested for temporal and spatial variation in fungal endophyte diversity and community composition, as well as for differences associated with organic and conventional farming practices. Fungal isolates were identified by morphological and DNA identification methods. We found members of the genera Alternaria, Colletotrichum and Phomopsis, previously isolated as endophytes from other plant species. Other recovered species such as Drechslerella dactyloides (formerly Arthrobotrys dactyloides and Exserohilum rostratum have not, to our knowledge, been previously reported as endophytes in cotton. We also isolated many latent pathogens, but some species such as Alternaria tennuissima, Epicoccum nigrum, Acremonium alternatum, Cladosporium cladosporioides, Chaetomium globosum and Paecilomyces sp., are known to be antagonists against plant pathogens, insects and nematode pests. We found no differences in endophyte species richness or diversity among different cotton varieties, but did detect differences over time and in different plant tissues. No consistent patterns of community similarity associated with variety, region, farming practice, time of the season or tissue type were observed regardless of the ecological community similarity measurements used. Results indicated that local fungal endophyte communities may be affected by both time of the year and plant tissue, but the specific community composition varies across sites. In addition to providing insights into fungal endophyte community structure, our survey

  15. Spatial and temporal variation in fungal endophyte communities isolated from cultivated cotton (Gossypium hirsutum).

    Science.gov (United States)

    Ek-Ramos, María J; Zhou, Wenqing; Valencia, César U; Antwi, Josephine B; Kalns, Lauren L; Morgan, Gaylon D; Kerns, David L; Sword, Gregory A

    2013-01-01

    Studies of fungi in upland cotton (Gossypium hirsutum) cultivated in the United States have largely focused on monitoring and controlling plant pathogens. Given increasing interest in asymptomatic fungal endophytes as potential biological control agents, surveys are needed to better characterize their diversity, distribution patterns and possible applications in integrated pest management. We sampled multiple varieties of cotton in Texas, USA and tested for temporal and spatial variation in fungal endophyte diversity and community composition, as well as for differences associated with organic and conventional farming practices. Fungal isolates were identified by morphological and DNA identification methods. We found members of the genera Alternaria, Colletotrichum and Phomopsis, previously isolated as endophytes from other plant species. Other recovered species such as Drechslerella dactyloides (formerly Arthrobotrys dactyloides) and Exserohilum rostratum have not, to our knowledge, been previously reported as endophytes in cotton. We also isolated many latent pathogens, but some species such as Alternaria tennuissima, Epicoccum nigrum, Acremonium alternatum, Cladosporium cladosporioides, Chaetomium globosum and Paecilomyces sp., are known to be antagonists against plant pathogens, insects and nematode pests. We found no differences in endophyte species richness or diversity among different cotton varieties, but did detect differences over time and in different plant tissues. No consistent patterns of community similarity associated with variety, region, farming practice, time of the season or tissue type were observed regardless of the ecological community similarity measurements used. Results indicated that local fungal endophyte communities may be affected by both time of the year and plant tissue, but the specific community composition varies across sites. In addition to providing insights into fungal endophyte community structure, our survey provides

  16. Ascomycete fungal communities associated with early decaying leaves of Spartina spp. from central California estuaries.

    Science.gov (United States)

    Lyons, Justine I; Alber, Merryl; Hollibaugh, James T

    2010-02-01

    Ascomycetous fungi play an important role in the early stages of decomposition of Spartina alterniflora, but their role in the decomposition of other Spartina species has not been investigated. Here we use fingerprint (terminal restriction fragment length polymorphism) and phylogenetic analyses of the 18S to 28S internal transcribed spacer region to compare the composition of the ascomycete fungal communities on early decay blades of Spartina species (Spartina alterniflora, Spartina densiflora, Spartina foliosa, and a hybrid (S. alterniflora x S. foliosa)) collected from three salt marshes in San Francisco Bay and one in Tomales Bay, California, USA. Phaeosphaeria spartinicola was found on all samples collected and was often dominant. Two other ascomycetes, Phaeosphaeria halima and Mycosphaerella sp. strain 2, were also common. These three species are the same ascomycetes previously identified as the dominant fungal decomposers on S. alterniflora on the east coast. Ascomycetes appeared to exhibit varying degrees of host specificity, demonstrated by grouping patterns on phylogenetic trees. Neither the exotic S. alterniflora nor the hybrid supported fungal flora different from that of the native S. foliosa. However, S. densiflora had a significantly different fungal community than the other species, and hosted at least two unique ascomycetes. Significant differences in the fungal decomposer communities were also detected within species (two clones of S. foliosa), but these were minor and may be due to morphological differences among the plants.

  17. Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding

    Science.gov (United States)

    Li, Wei; Wang, Meng Meng; Wang, Xi Guang; Cheng, Xiao Li; Guo, Jia Jia; Bian, Xiao Meng; Cai, Lei

    2016-01-01

    Ribosomal RNA internal transcribed spacer-1 (ITS1) metabarcoding was used to investigate the distribution patterns of fungal communities and the factors influencing these patterns in subtropical Chinese seas, including the southern and northern Yellow Sea and the Bohai Sea. These seas were found to harbor high levels of fungal diversity, with 816 operational taxonomic units (OTUs) that span 130 known genera, 36 orders, 14 classes and 5 phyla. Ascomycota was the most abundant phylum, containing 72.18% and 79.61% of all OTUs and sequences, respectively, followed by Basidiomycota (19.98%, 18.64%), Zygomycota (1.10%, 0.11%), Chytridiomycota (0.25%, 0.04%) and Rozellomycota (0.12%, 0.006%). The compositions of fungal communities across these three sea regions were found to be vary, which may be attributed to sediment source, geographical distance, latitude and some environmental factors such as the temperature and salinity of bottom water, water depth, total nitrogen, and the ratio of total organic carbon to nitrogen. Among these environmental factors, the temperature of bottom water is the most important driver that governs the distribution patterns of fungal communities across the sampled seas. Our data also suggest that the cold-water mass of the Yellow Sea likely balances competitive relationships between fungal taxa rather than increasing species richness levels. PMID:27198490

  18. The interactions between plant life form and fungal traits of arbuscular mycorrhizal fungi determine the symbiotic community.

    Science.gov (United States)

    López-García, Álvaro; Azcón-Aguilar, Concepción; Barea, José M

    2014-12-01

    Arbuscular mycorrhizal (AM) fungi have traditionally been considered generalist symbionts. However, an increasing number of studies are pointing out the selectivity potential of plant hosts. Plant life form, determined by plant life history traits, seems to drive the AM fungal community composition. The AM fungi also exhibit a wide diversity of functional traits known to be responsible for their distribution in natural ecosystems. However, little is known about the role of plant and fungal traits driving the resultant symbiotic assemblages. With the aim of testing the feedback relationship between plant and fungal traits on the resulting AM fungal community, we inoculated three different plant life forms, i.e. annual herbs, perennial herbs and perennial semi-woody plants, with AM fungal communities sampled in different seasons. We hypothesized that the annual climate variation will induce changes in the mean traits of the AM fungal communities present in the soil throughout the year. Furthermore, the association of plants with different life forms with AM fungi with contrasting life history traits will show certain preferences according to reciprocal traits of the plants and fungi. We found changes in the AM fungal community throughout the year, which were differentially disrupted by disturbance and altered by plant growth form and plant biomass. Both plant and fungal traits clearly contributed to the resultant AM fungal communities. The revealed process can have implications for the functioning of ecosystems since changes in dominant plant life forms or climatic variables could influence the traits of AM fungal communities in soil and hence ecosystem processes.

  19. The Selection Exerted by Oil Contamination on Mangrove Fungal Communities

    NARCIS (Netherlands)

    Fasanella, Cristiane Cipola; Franco Dias, Armando Cavalcante; Rigonato, Janaina; Fiore, Marli de Fatima; Soares, Fabio Lino; Melo, Itamar Soares; Pizzirani-Kleiner, Aline Aparecida; van Elsas, Jan Dirk; Andreote, Fernando Dini

    2012-01-01

    Mangrove ecosystems are tropical environments that are characterized by the interaction between the land and the sea. As such, this ecosystem is vulnerable to oil spills. Here, we show a culture-independent survey of fungal communities that are found in the sediments of the following two mangroves t

  20. Spatial Distribution of Fungal Communities in an Arable Soil

    Science.gov (United States)

    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment. PMID:26840453

  1. Spatial Distribution of Fungal Communities in an Arable Soil.

    Directory of Open Access Journals (Sweden)

    Julia Moll

    Full Text Available Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a ploughed soil in 0-10 cm, b rooted soil in 40-50 cm, c root-free soil in 60-70 cm soil depth and d maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit, occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment.

  2. Elucidating biotic factors that influence assembly of fungal endophyte communities

    Science.gov (United States)

    Most plants harbor a diverse assemblage of non-mycorrhizal fungal endophytes. These fungi can directly influence the host plant, and can instigate trophic cascades that affect surrounding communities of herbivores, plants, and animals. Despite this, biotic mechanisms that influence assembly of funga...

  3. Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape.

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    Lucie Zinger

    Full Text Available BACKGROUND: The advent of molecular techniques in microbial ecology has aroused interest in gaining an understanding about the spatial distribution of regional pools of soil microbes and the main drivers responsible of these spatial patterns. Here, we assessed the distribution of crenarcheal, bacterial and fungal communities in an alpine landscape displaying high turnover in plant species over short distances. Our aim is to determine the relative contribution of plant species composition, environmental conditions, and geographic isolation on microbial community distribution. METHODOLOGY/PRINCIPAL FINDINGS: Eleven types of habitats that best represent the landscape heterogeneity were investigated. Crenarchaeal, bacterial and fungal communities were described by means of Single Strand Conformation Polymorphism. Relationships between microbial beta diversity patterns were examined by using Bray-Curtis dissimilarities and Principal Coordinate Analyses. Distance-based redundancy analyses and variation partitioning were used to estimate the relative contributions of different drivers on microbial beta diversity. Microbial communities tended to be habitat-specific and did not display significant spatial autocorrelation. Microbial beta diversity correlated with soil pH. Fungal beta-diversity was mainly related to soil organic matter. Though the effect of plant species composition was significant for all microbial groups, it was much stronger for Fungi. In contrast, geographic distances did not have any effect on microbial beta diversity. CONCLUSIONS/SIGNIFICANCE: Microbial communities exhibit non-random spatial patterns of diversity in alpine landscapes. Crenarcheal, bacterial and fungal community turnover is high and associated with plant species composition through different set of soil variables, but is not caused by geographical isolation.

  4. Mechanical soil disturbance as a determinant of arbuscular mycorrhizal fungal communities in semi-natural grassland

    DEFF Research Database (Denmark)

    Schnoor, Tim Krone; Lekberg, Ylva; Rosendahl, Søren

    2011-01-01

    to Diversisporaceae. Only three phylotypes were closely related to known morphospecies. Soil disturbance significantly reduced phylotype richness and changed the AM fungal community composition. Most phylotypes, even closely related ones, showed little or no overlap in their distribution and occurred in either......While the effect of disturbance on overall abundance and community composition of arbuscular mycorrhizal (AM) fungi has been researched in agricultural fields, less is known about the impact in semi-natural grasslands. We sampled two AM plant species, Festuca brevipila and Plantago lanceolata, from...

  5. Linking fungal communities to wood density loss after 12 years of log decay.

    Science.gov (United States)

    Kubartová, Ariana; Ottosson, Elisabet; Stenlid, Jan

    2015-05-01

    Changes in biodiversity might alter decomposition processes and, consequently, carbon and nutrient cycling. We examined fungal diversity and density loss in experimental Norway spruce logs after 12 years of decay in a hemiboreal forest. Between 28 and 50% of the original wood biomass remained, depending on the fungal community composition in the log, operational taxonomic unit (OTU) richness had only a minor effect on the log biomass. Although the communities were OTU rich (190-340 OTUs per log), the majority of OTUs were infrequent or rare; wood degradation therefore depended mostly on the most abundant OTUs and their decomposing abilities. The least decayed logs were characterized by continuous dominance of an earlier colonizer and by high within-log community diversity, which was significantly related to sample variables (position in log, density and moisture). In the most decayed logs, the earlier colonizers were generally replaced by white-rot species able to exploit the highly decomposed wood. The communities were relatively spatially uniform within whole logs, independent of the sample variables, whereas among-log diversity was high. Importance of fungal community composition in decomposition processes should be taken into account when studying and modeling carbon dynamics in forest ecosystems.

  6. Local adaptation to soil hypoxia determines the structure of an arbuscular mycorrhizal fungal community in roots from natural CO₂ springs.

    Science.gov (United States)

    Maček, Irena; Dumbrell, Alex J; Nelson, Michaela; Fitter, Alastair H; Vodnik, Dominik; Helgason, Thorunn

    2011-07-01

    The processes responsible for producing and maintaining the diversity of natural arbuscular mycorrhizal (AM) fungal communities remain largely unknown. We used natural CO(2) springs (mofettes), which create hypoxic soil environments, to determine whether a long-term, directional, abiotic selection pressure could change AM fungal community structure and drive the selection of particular AM fungal phylotypes. We explored whether those phylotypes that appear exclusively in hypoxic soils are local specialists or widespread generalists able to tolerate a range of soil conditions. AM fungal community composition was characterized by cloning, restriction fragment length polymorphism typing, and the sequencing of small subunit rRNA genes from roots of four plant species growing at high (hypoxic) and low (control) geological CO(2) exposure. We found significant levels of AM fungal community turnover (β diversity) between soil types and the numerical dominance of two AM fungal phylotypes in hypoxic soils. Our results strongly suggest that direct environmental selection acting on AM fungi is a major factor regulating AM fungal communities and their phylogeographic patterns. Consequently, some AM fungi are more strongly associated with local variations in the soil environment than with their host plant's distribution.

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

    Science.gov (United States)

    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.

  8. Fungal communities living in the wood of different cultivars of young Vitis vinifera plants

    Directory of Open Access Journals (Sweden)

    L. Casieri

    2009-05-01

    Full Text Available The fungal communities associated with fi ve Vitis vinifera cultivars grown in Switzerland (‘Humagne’, ‘Chasselas’, ‘Arvine’, ‘Gamaret’ and ‘Gamay’ were examined. Of the 703 fungal isolates obtained in pure culture, 66 operational taxonomic units (OTUs were defi ned. The results show that: the great majority of the fungi isolated in this study were ascomycetes, with a high proportion of Sordariomycetes (mainly Hypocreales, Sordariales and Diaporthales; different fungal OTUs were associated with different cultivars; graft and rootstock contributed equally to the fungal community composition; Esca- or Petri-related species occurred sporadically in the different cultivars, with some of them occupying specifi c tissues or parts of the plant (e.g.: Botryosphaeriaceous species, Phaeomoniella chlamydospora and Phomopsis viticola; almost 25% of OTUs occurred in different plant parts in most cultivars, which suggests an easy spread outwards from the infected material (graft or rootstock, which might be explained by the fungal propagules being transported through the xylem vessels.

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

    Science.gov (United States)

    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

  10. Initial colonization, community assembly and ecosystem function: fungal colonist traits and litter biochemistry mediate decay rate.

    Science.gov (United States)

    Cline, Lauren C; Zak, Donald R

    2015-10-01

    Priority effects are an important ecological force shaping biotic communities and ecosystem processes, in which the establishment of early colonists alters the colonization success of later-arriving organisms via competitive exclusion and habitat modification. However, we do not understand which biotic and abiotic conditions lead to strong priority effects and lasting historical contingencies. Using saprotrophic fungi in a model leaf decomposition system, we investigated whether compositional and functional consequences of initial colonization were dependent on initial colonizer traits, resource availability or a combination thereof. To test these ideas, we factorially manipulated leaf litter biochemistry and initial fungal colonist identity, quantifying subsequent community composition, using neutral genetic markers, and community functional characteristics, including enzyme potential and leaf decay rates. During the first 3 months, initial colonist respiration rate and physiological capacity to degrade plant detritus were significant determinants of fungal community composition and leaf decay, indicating that rapid growth and lignolytic potential of early colonists contributed to altered trajectories of community assembly. Further, initial colonization on oak leaves generated increasingly divergent trajectories of fungal community composition and enzyme potential, indicating stronger initial colonizer effects on energy-poor substrates. Together, these observations provide evidence that initial colonization effects, and subsequent consequences on litter decay, are dependent upon substrate biochemistry and physiological traits within a regional species pool. Because microbial decay of plant detritus is important to global C storage, our results demonstrate that understanding the mechanisms by which initial conditions alter priority effects during community assembly may be key to understanding the drivers of ecosystem-level processes. © 2015 John Wiley & Sons Ltd.

  11. Shaping of the fungal communities isolated from yellow lupin seeds (Lupinus luteus L. throughout storage time

    Directory of Open Access Journals (Sweden)

    Bożena Cwalina-Ambroziak

    2012-12-01

    Full Text Available The object of the experiment were seeds of two traditional cultivars of yellow lupin (Juno and Amulet cultivated in 1999 in two crop-rotation with 20% and 33% yellow lupine contribution. The quantitative and qualitative composition of the fungal community colonizing the seeds were determined in the laboratory conditions after 0.5-, 1.5- and 2.5-year of storage time. In total 1077 fungal colonies were isolated from the lupin seeds. Fungi representing the species of Penicillium - 29.3%, Alternaria alternata - 26.7% and Rhizopus nigricans - 12.7% were isolated most widely. Among the fungi pathogenic to lupin, the species of Colletotrichum gloeosporioides (16.3% isolates was dominant. The crop rotation with 20% lupin reduced the number of fungal colonies colonizing the seeds including the pathogens from the species of C. gloeosporioides. Seed disinfection decreased the total number of fungal colonies isolated from both cultivars. Higher number of C. gloeosporioides isolates was found in the combination with disinfected seeds. More fungal colonies were obtained from seeds of cv. Amulet than from those of cv. Juno. The storage duration had an effect on the population and the composition of species of fungi isolated from seeds of yellow lupine. With longer storage population of Penicillium spp. and Rhizopus spp. increased, whereas the population of C. gloeosporioides decreased.

  12. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

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    Cedar N Hesse

    2015-04-01

    Full Text Available Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 75,000 carbohydrate active enzyme transcript sequences (CAZymes in each metatranscriptome. Parallel ribosomal RNA surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  13. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests.

    Science.gov (United States)

    Hesse, Cedar N; Mueller, Rebecca C; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D; Zak, Donald R; Kuske, Cheryl R

    2015-01-01

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  14. 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities

    DEFF Research Database (Denmark)

    Lekberg, Karin Ylva Margareta; Schnoor, Tim; Kjøller, Rasmus

    2012-01-01

    1. Disturbance is assumed to be a major driver of plant community composition, but whether similar processes operate on associated soil microbial communities is less known. Based on the assumed trade-off between disturbance tolerance and competiveness, we hypothesize that a severe disturbance......, disturbance did not significantly alter the community composition and OTU richness. Instead, OTU abundances were positively correlated across treatments; i.e., common OTUs in undisturbed soil were also common after the severe disturbance. However, the distribution of OTUs within and between plots was largely...... applied within a semi-natural grassland would shift the arbuscular mycorrhizal (AM) fungal community towards disturbance-tolerant fungi that are rare in undisturbed soils. 2. We used 454-sequencing of the large subunit rDNAregion to characterizeAMfungal communities in Plantago lanceolata roots grown...

  15. Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing.

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    C Ryan Penton

    Full Text Available Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼ 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.

  16. Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change.

    Science.gov (United States)

    Gehring, Catherine; Flores-Rentería, Dulce; Sthultz, Christopher M; Leonard, Tierra M; Flores-Rentería, Lluvia; Whipple, Amy V; Whitham, Thomas G

    2014-03-01

    Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary. © 2013 John Wiley & Sons Ltd.

  17. Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Folwell, Benjamin D; McGenity, Terry J; Whitby, Corinne

    2016-04-01

    High-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs) are natural components of fossil fuels that are carcinogenic and persistent in the environment, particularly in oil sands process-affected water (OSPW). Their hydrophobicity and tendency to adsorb to organic matter result in low bioavailability and high recalcitrance to degradation. Despite the importance of microbes for environmental remediation, little is known about those involved in HMW-PAH transformations. Here, we investigated the transformation of HMW-PAHs using samples of OSPW and compared the bacterial and fungal community compositions attached to hydrophobic filters and in suspension. It was anticipated that the hydrophobic filters with sorbed HMW-PAHs would select for microbes that specialize in adhesion. Over 33 days, more pyrene was removed (75% ± 11.7%) than the five-ring PAHs benzo[a]pyrene (44% ± 13.6%) and benzo[b]fluoranthene (41% ± 12.6%). For both bacteria and fungi, the addition of PAHs led to a shift in community composition, but thereafter the major factor determining the fungal community composition was whether it was in the planktonic phase or attached to filters. In contrast, the major determinant of the bacterial community composition was the nature of the PAH serving as the carbon source. The main bacteria enriched by HMW-PAHs were Pseudomonas, Bacillus, and Microbacterium species. This report demonstrates that OSPW harbors microbial communities with the capacity to transform HMW-PAHs. Furthermore, the provision of suitable surfaces that encourage PAH sorption and microbial adhesion select for different fungal and bacterial species with the potential for HMW-PAH degradation.

  18. Fungal communities respond to long-term CO2 elevation by community reassembly.

    Science.gov (United States)

    Tu, Qichao; Yuan, Mengting; He, Zhili; Deng, Ye; Xue, Kai; Wu, Liyou; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

    2015-04-01

    Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO2 (eCO2), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO2, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO2 for 12 years. Long-term eCO2 did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO2 were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO2 increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO2 network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO2, especially with increased plant biomass and NH4 (+) availability. This study provided novel insights into how eCO2 shapes soil fungal communities in grassland ecosystems.

  19. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs

    NARCIS (Netherlands)

    Van der Wal, A.; Klein Gunnewiek, P.J.A.; Cornelissen, J.H.C.; Crowther, Thomas W.; De Boer, W.

    2016-01-01

    Community assembly processes do not only influence community structure, but can also affect ecosystem processes. To understand the effect of initial community development on ecosystem processes, we studied natural fungal community dynamics during initial wood decay. We hypothesize that fungal commun

  20. Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs

    NARCIS (Netherlands)

    Wal, van der Annemieke; Klein Gunnewiek, P.J.A.; Cornelissen, J.H.C.; Crowther, Thomas W.; Boer, de Wietse

    2016-01-01

    Community assembly processes do not only influence community structure, but can also affect ecosystem processes. To understand the effect of initial community development on ecosystem processes, we studied natural fungal community dynamics during initial wood decay. We hypothesize that fungal com

  1. Short-term impacts of energy wood harvesting on ectomycorrhizal fungal communities of Norway spruce saplings.

    Science.gov (United States)

    Huusko, Karoliina; Tarvainen, Oili; Saravesi, Karita; Pennanen, Taina; Fritze, Hannu; Kubin, Eero; Markkola, Annamari

    2015-03-01

    The increased demand for harvesting energy wood raises questions about its effects on the functioning of the forest ecosystems, soil processes and biodiversity. Impacts of tree stump removal on ectomycorrhizal fungal (EMF) communities of Norway spruce saplings were studied with 454-pyrosequencing in a 3-year field experiment replicated in 3 geographical areas. This is possibly the most thorough investigation of EMF communities associated with saplings grown on sites subjected to energy wood harvesting. To separate impacts of tree stump and logging residue removal on EMF and plant variables, we used three harvesting treatments with increasing complexity from patch mounding alone (P) to patch mounding combined with logging residue removal (RP), and patch mounding combined with both logging residue and stump removal (SRP). Saplings grown in uncut forests (F) served as references for harvesting treatments. A majority of sequences (>92%) and operational taxonomic units (OTUs, 55%) were assigned as EMF. EMF OTU richness, fungal community composition or sapling growth did not differ between harvesting treatments (P, RP and SRP), while EMF OTU richness, diversity and evenness were highest and sapling growth lowest in the undisturbed reference forests (F). The short study period may partially explain the similarities in fungal and sapling variables in different harvesting treatments. In conclusion, our results indicate that neither stump removal nor logging residue removal have significant additional negative impacts on EMF communities or growth of Norway spruce saplings in the short-term compared with the impacts of more conventional harvesting methods, including clear cutting and patch mounding.

  2. Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation

    Directory of Open Access Journals (Sweden)

    Ping eHu

    2015-01-01

    Full Text Available The meals from many oilseed crops have potential for biofumigation due to their release of biocidal compounds such as isothiocyanates (ITCs. Various ITCs are known to inhibit numerous pathogens; however, much less is known about how the soil microbial community responds to the different types of ITCs released from oilseed meals (SMs. To simulate applying ITC-releasing SMs to soil, we amended soil with 1% flax SM (contains no biocidal chemicals along with four types of ITCs (allyl, butyl, phenyl, and benzyl ITC in order to determine their effects on soil fungal and bacterial communities in a replicated microcosm study. Microbial communities were analyzed based on the ITS region for fungi and 16S rRNA gene for bacteria using qPCR and tag-pyrosequencing with 454 GS FLX titanium technology. A dramatic decrease in fungal populations (~85% reduction was observed after allyl ITC addition. Fungal community compositions also shifted following ITC amendments (e.g., Humicola increased in allyl and Mortierella in butyl ITC amendments. Bacterial populations were less impacted by ITCs, although there was atransient increase in the proportion of Firmicutes, related to bacteria know to be antagonistic to plant pathogens, following amendment with allyl ITC. Our results indicate that the type of ITC released from SMs can result in differential impacts on soil microorganisms. This information will aid selection and breeding of plants for biofumigation-based control of soil-borne pathogens while minimizing the impacts on non-target microorganisms.

  3. Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities.

    Science.gov (United States)

    Rojas, Xavier; Guo, Jingqi; Leff, Jonathan W; McNear, David H; Fierer, Noah; McCulley, Rebecca L

    2016-07-01

    Tall fescue (Schedonorus arundinaceus) is a widespread grass that can form a symbiotic relationship with a shoot-specific fungal endophyte (Epichloë coenophiala). While the effects of fungal endophyte infection on fescue physiology and ecology have been relatively well studied, less attention has been given to how this relationship may impact the soil microbial community. We used high-throughput DNA sequencing and phospholipid fatty acid analysis to determine the structure and biomass of microbial communities in both bulk and rhizosphere soils from tall fescue stands that were either uninfected with E. coenophiala or were infected with the common toxic strain or one of several novel strains of the endophyte. We found that rhizosphere and bulk soils harbored distinct microbial communities. Endophyte presence, regardless of strain, significantly influenced soil fungal communities, but endophyte effects were less pronounced in prokaryotic communities. E. coenophiala presence did not change total fungal biomass but caused a shift in soil and rhizosphere fungal community composition, increasing the relative abundance of taxa within the Glomeromycota phylum and decreasing the relative abundance of genera in the Ascomycota phylum, including Lecanicillium, Volutella, Lipomyces, Pochonia, and Rhizoctonia. Our data suggests that tripartite interactions exist between the shoot endophyte E. coenophiala, tall fescue, and soil fungi that may have important implications for the functioning of soils, such as carbon storage, in fescue-dominated grasslands.

  4. Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands.

    Science.gov (United States)

    Kyaschenko, Julia; Clemmensen, Karina E; Hagenbo, Andreas; Karltun, Erik; Lindahl, Björn D

    2017-04-01

    Forestry reshapes ecosystems with respect to tree age structure, soil properties and vegetation composition. These changes are likely to be paralleled by shifts in microbial community composition with potential feedbacks on ecosystem functioning. Here, we assessed fungal communities across a chronosequence of managed Pinus sylvestris stands and investigated correlations between taxonomic composition and extracellular enzyme activities. Not surprisingly, clear-cutting had a negative effect on ectomycorrhizal fungal abundance and diversity. In contrast, clear-cutting favoured proliferation of saprotrophic fungi correlated with enzymes involved in holocellulose decomposition. During stand development, the re-establishing ectomycorrhizal fungal community shifted in composition from dominance by Atheliaceae in younger stands to Cortinarius and Russula species in older stands. Late successional ectomycorrhizal taxa correlated with enzymes involved in mobilisation of nutrients from organic matter, indicating intensified nutrient limitation. Our results suggest that maintenance of functional diversity in the ectomycorrhizal fungal community may sustain long-term forest production by retaining a capacity for symbiosis-driven recycling of organic nutrient pools.

  5. High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity.

    Science.gov (United States)

    Xia, Fei; Chen, Xin; Guo, Meng-Yuan; Bai, Xiao-Hui; Liu, Yan; Shen, Guang-Rong; Li, Yu-Ling; Lin, Juan; Zhou, Xuan-Wei

    2016-09-14

    Chinese Cordyceps, known in Chinese as "DongChong XiaCao", is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats.

  6. Regional scale gradients of climate and nitrogen deposition drive variation in ectomycorrhizal fungal communities associated with native Scots pine.

    Science.gov (United States)

    Jarvis, S; Woodward, S; Alexander, I J; Taylor, A F S

    2013-06-01

    Ectomycorrhizal fungi commonly associate with the roots of forest trees where they enhance nutrient and water uptake, promote seedling establishment and have an important role in forest nutrient cycling. Predicting the response of ectomycorrhizal fungi to environmental change is an important step to maintaining forest productivity in the future. These predictions are currently limited by an incomplete understanding of the relative significance of environmental drivers in determining the community composition of ectomycorrhizal (ECM) fungi at large spatial scales. To identify patterns of community composition in ECM fungi along regional scale gradients of climate and nitrogen deposition in Scotland, fungal communities were analysed from 15 seminatural Scots pine (Pinus sylvestris L.) forests. Fungal taxa were identified by sequencing of the ITS rDNA region using fungal-specific primers. Nonmetric multidimensional scaling was used to assess the significance of 16 climatic, pollutant and edaphic variables on community composition. Vector fitting showed that there was a strong influence of rainfall and soil moisture on community composition at the species level, and a smaller impact of temperature on the abundance of ectomycorrhizal exploration types. Nitrogen deposition was also found to be important in determining community composition, but only when the forest experiencing the highest deposition (9.8 kg N ha(-1)  yr(-1) ) was included in the analysis. This finding supports previously published critical load estimates for ectomycorrhizal fungi of 5-10 kg N ha(-1)  yr(-1) . This work demonstrates that both climate and nitrogen deposition can drive gradients of fungal community composition at a regional scale.

  7. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

    Science.gov (United States)

    Hannula, S. Emilia; van Veen, Johannes A.

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose. PMID:27965632

  8. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils.

    Science.gov (United States)

    Hannula, S Emilia; van Veen, Johannes A

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in carbon cycling were designed and/or validated and the functioning of soil fungal communities along a chronosequence of land abandonment from agriculture was evaluated using them. We hypothesized that changes in fungal community structure during secondary succession would lead to difference in the types of genes present in soils and that these changes would be directional. We expected an increase in genes involved in degradation of recalcitrant organic matter in time since agriculture. Out of the investigated genes, the richness of the genes related to carbon cycling was significantly higher in fields abandoned for longer time. The composition of six of the genes analyzed revealed significant differences between fields abandoned for shorter and longer time. However, all genes revealed significant variance over the fields studied, and this could be related to other parameters than the time since agriculture such as pH, organic matter, and the amount of available nitrogen. Contrary to our initial hypothesis, the genes significantly different between fields were not related to the decomposition of more recalcitrant matter but rather involved in degradation of cellulose and hemicellulose.

  9. Fungal composition on leaves explains pollutant-mediated indirect effects on amphipod feeding.

    Science.gov (United States)

    Bundschuh, Mirco; Zubrod, Jochen P; Kosol, Sujitra; Maltby, Lorraine; Stang, Christoph; Duester, Lars; Schulz, Ralf

    2011-07-01

    The energy stored in coarse particulate organic matter, e.g. leaf litter, is released to aquatic ecosystems by breakdown processes involving microorganisms and leaf shredding invertebrates. The palatability of leaves and thus the feeding of shredders on leaf material are highly influenced by microorganisms. However, implications in the colonization of leaves by microorganisms (=conditioning) caused by chemical stressors are rarely studied. Our laboratory experiments, therefore, investigated for the first time effects of a fungicide on the conditioning process of leaf material by means of food-choice experiments using Gammarus fossarum (Crustacea: Amphipoda). Additionally, microbial analyses were conducted to facilitate the mechanistic understanding of the observed behavior. Gammarids significantly preferred control leaf discs over those conditioned in presence of the fungicide tebuconazole at concentrations of 50 and 500 μg/L. Besides the decrease of fungal biomass with increasing fungicide concentration, also the leaf associated fungal community composition showed that species preferred by gammarids, such as Alatospora acumunata, Clavariopsis aquatica, or Flagellospora curvula, were more frequent in the control. Tetracladium marchalianum, however, which is rejected by gammarids, was abundant in all treatments suggesting an increasing importance of this species for the lower leaf palatability--as other more palatable fungal species were almost absent--in the fungicide treatments. Hence, the food-choice behavior of G. fossarum seems to be a suitable indicator for alterations in leaf associated microbial communities, especially fungal species composition, caused by chemical stressors. Finally, this or similar test systems may be a reasonable supplement to the environmental risk assessment of chemicals in order to achieve its protection goals, as on the one hand, indirect effects may occur far below concentrations known to affect gammarids directly, and on the other

  10. Diversity of an ectomycorrhizal fungal community studied by a root tip and total soil DNA approach

    NARCIS (Netherlands)

    Landeweert, R.; Leeflang, P.; Smit, E.; Kuyper, T.W.

    2005-01-01

    Molecular methods based on soil DNA extracts are increasingly being used to study the fungal diversity of ectomycorrhizal (EM) fungal communities in soil. Contrary to EM root tip identification, the use of molecular methods enables identification of extramatrical mycelia in soil. To compare fungal d

  11. Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica

    Science.gov (United States)

    The diversity of fungal communities from different substrates in Antarctica were studied and their capability to produce bioactive compounds. A one hundred and one fungal isolates were identified by molecular analysis in 35 different fungal taxa from 20 genera. Pseudogymnoascus sp. 3, Pseudogymnoasc...

  12. Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny

    Science.gov (United States)

    Bell, Terrence H; El-Din Hassan, Saad; Lauron-Moreau, Aurélien; Al-Otaibi, Fahad; Hijri, Mohamed; Yergeau, Etienne; St-Arnaud, Marc

    2014-01-01

    Phytoremediation is an attractive alternative to excavating and chemically treating contaminated soils. Certain plants can directly bioremediate by sequestering and/or transforming pollutants, but plants may also enhance bioremediation by promoting contaminant-degrading microorganisms in soils. In this study, we used high-throughput sequencing of bacterial 16S rRNA genes and the fungal internal transcribed spacer (ITS) region to compare the community composition of 66 soil samples from the rhizosphere of planted willows (Salix spp.) and six unplanted control samples at the site of a former petrochemical plant. The Bray–Curtis distance between bacterial communities across willow cultivars was significantly correlated with the distance between fungal communities in uncontaminated and moderately contaminated soils but not in highly contaminated (HC) soils (>2000 mg kg−1 hydrocarbons). The mean dissimilarity between fungal, but not bacterial, communities from the rhizosphere of different cultivars increased substantially in the HC blocks. This divergence was partly related to high fungal sensitivity to hydrocarbon contaminants, as demonstrated by reduced Shannon diversity, but also to a stronger influence of willows on fungal communities. Abundance of the fungal class Pezizomycetes in HC soils was directly related to willow phylogeny, with Pezizomycetes dominating the rhizosphere of a monophyletic cluster of cultivars, while remaining in low relative abundance in other soils. This has implications for plant selection in phytoremediation, as fungal associations may affect the health of introduced plants and the success of co-inoculated microbial strains. An integrated understanding of the relationships between fungi, bacteria and plants will enable the design of treatments that specifically promote effective bioremediating communities. PMID:23985744

  13. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

    Science.gov (United States)

    Porter, Teresita M.; Shokralla, Shadi; Baird, Donald; Golding, G. Brian; Hajibabaei, Mehrdad

    2016-01-01

    Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence. PMID:26731732

  14. Isolation and identification of fungal communities in compost and vermicompost.

    Science.gov (United States)

    Anastasi, Antonella; Varese, Giovanna Cristina; Marchisio, Valeria Filipello

    2005-01-01

    This research illustrates the qualitative and quantitative composition of the mycoflora of both a green compost (thermophilically produced from plant debris) and a vermicompost (mesophilically produced by the action of earthworms on plant and animal wastes after thermophilic preconditioning). Fungi were isolated using three media (PDA, CMC, PDA plus cycloheximide), incubated at three temperatures (24, 37 and 45 C). Substantial qualiquantitative differences in the species composition of the two composts were observed. The total fungal load was up to 8.2 X 10(5) CFU/g dwt in compost and 4.0 x 10(5) CFU/g dwt in vermicompost. A total of 194 entities were isolated: 118 from green compost, 142 from vermicompost; 66 were common to both. Structural characterization of this kind is necessary to determine the most appropriate application of a compost and its hygienic quality.

  15. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum and sagebrush (Artemisia tridentata-associated soils.

    Directory of Open Access Journals (Sweden)

    Carolyn F Wiber

    Full Text Available Nonnative Bromus tectorum (cheatgrass is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF, whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene in the 0-4 cm and 4-8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0-4 cm contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP, which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales, which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass

  16. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum and sagebrush (Artemisia tridentate-associated soils.

    Directory of Open Access Journals (Sweden)

    Carolyn F Weber

    Full Text Available Nonnative Bromus tectorum (cheatgrass is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF, whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene in the 0-4 cm and 4-8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0-4 cm contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP, which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales, which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass

  17. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum) and sagebrush (Artemisia tridentate)-associated soils.

    Science.gov (United States)

    Weber, Carolyn F; King, Gary M; Aho, Ken

    2015-01-01

    Nonnative Bromus tectorum (cheatgrass) is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF), whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C)-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene) in the 0-4 cm and 4-8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0-4 cm) contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP), which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales), which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass- and

  18. Relative abundance of and composition within fungal orders differ between cheatgrass (Bromus tectorum) and sagebrush (Artemisia tridentata)-associated soils.

    Science.gov (United States)

    Wiber, Carolyn F; King, Gary M; Aho, Ken

    2015-01-01

    Nonnative Bromus tectorum (cheatgrass) is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF), whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C)-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene) in the 0-4 cm and 4-8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0-4 cm) contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP), which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales), which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass- and

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

    Directory of Open Access Journals (Sweden)

    Dorsaf Kerfahi

    Full Text Available 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.

  20. Ectomycorrhizal fungal communities in urban parks are similar to those in natural forests but shaped by vegetation and park age.

    Science.gov (United States)

    Hui, Nan; Liu, Xinxin; Kotze, D Johan; Jumpponen, Ari; Francini, Gaia; Setälä, Heikki

    2017-09-29

    Ectomycorrhizal (ECM) fungi are important mutualists for growth and health of most boreal trees. Forest age and its host species composition can impact the composition of ECM fungal communities. Although plentiful empirical data exist for forested environments, the effects of established vegetation and its successional trajectories on ECM fungi in urban greenspaces remain poorly understood. We analyzed ECM fungi in 5 control forests and 41 urban parks of two plant functional groups (conifer and broadleaf trees) and in three age categories (10, ∼50 and >100 years old) in southern Finland. Our results show that although ECM fungal richness was marginally greater in forests than in urban parks, urban parks still hosted rich and diverse ECM communities. ECM community composition differed between the two habitats, but was driven by taxon rank order reordering, as key ECM taxa remained largely the same. In parks, the ECM communities differed between conifer and broadleaf trees. The successional trajectories of ECM fungi -- as inferred in relation to the time since park construction -- differed among the conifers and broadleaf trees: the ECM fungal communities changed over time under the conifers, whereas communities under broadleaf trees provided no evidence for such age related effects. Our data show that plant-ECM interactions in urban parks, in spite of being constructed environments, are surprisingly similar in richness to those in natural forests. This suggests that the presence of host trees, rather than soil characteristics or even disturbance regime of the system, determine ECM fungal community structure and diversity.Importance In urban environments soil and trees improve environmental quality and provide essential ecosystem services. Ectomycorrhizal (ECM) fungi enhance plant growth and performance, increasing plant nutrient acquisition and protecting plants against toxic compounds. Recent evidence indicates that soil-inhabiting fungal communities - including

  1. Characterization of arbuscular mycorrhizal fungal communities with respect to zonal vegetation in a coastal dune ecosystem.

    Science.gov (United States)

    Kawahara, Ai; Ezawa, Tatsuhiro

    2013-10-01

    Coastal dune vegetation distributes zonally along the environmental gradients of, e.g., soil disturbance. In the preset study, arbuscular mycorrhizal fungal communities in a coastal dune ecosystem were characterized with respect to tolerance to soil disturbance. Two grass species, Elymus mollis and Miscanthus sinensis, are distributed zonally in the seaward and landward slopes, respectively, in the primary dunes in Ishikari, Japan. The seaward slope is severely disturbed by wind, while the landward slope is stabilized by the thick root system of M. sinensis. The roots and rhizosphere soils of the two grasses were collected from the slopes. The soils were sieved to destruct the fungal hyphal networks, and soil trap culture was conducted to assess tolerance of the communities to disturbance, with parallel analysis of the field communities using a molecular ecological tool. In the landward communities, large shifts in the composition and increases in diversity were observed in the trap culture compared with the field, but in the seaward communities, the impact of trap culture was minimal. The landward field community was significantly nested within the landward trap culture community, implying that most members in the field community did not disappear in the trap culture. No nestedness was observed in the seaward communities. These observations suggest that disturbance-tolerant fungi have been preferentially selected in the seaward slope due to severe disturbance in the habitat. Whereas a limited number of fungi, which are not necessarily disturbance-sensitive, dominate in the stable landward slope, but high-potential diversity has been maintained in the habitat.

  2. Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest

    Science.gov (United States)

    Cullings, Ken; Raleigh, Christopher; New, Michael H.; Henson, Joan

    2005-01-01

    Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

  3. Ectomycorrhizal fungal communities associated with Masson pine (Pinus massoniana Lamb.) in Pb-Zn mine sites of central south China.

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    Huang, Jian; Nara, Kazuhide; Lian, Chunlan; Zong, Kun; Peng, Kejian; Xue, Shengguo; Shen, Zhenguo

    2012-11-01

    To advance our understanding of ectomycorrhizal fungal communities in mining areas, the diversity and composition of ectomycorrhizal fungi associated with Masson pine (Pinus massoniana Lamb.) and soil chemistry were investigated in Taolin lead-zinc (Pb-Zn) mine tailings (TLT), two fragmented forest patches in a Huayuan Pb-Zn mineland (HY1 and HY2), and a non-polluted forest in Taolin in central south China. Ectomycorrhizal fungal species were identified by morphotyping and sequence analyses of the internally transcribed spacer regions of ribosomal DNA. The two study sites in the Huayuan mineland (HY1 and HY2) were significantly different in soil Pb, Zn, and cadmium (Cd) concentrations, but no significant difference was observed in ectomycorrhizal colonization, ectomycorrhizal fungal richness, diversity, or rank-abundance. In addition, the similarity of ectomycorrhizal fungal communities between HY1 and HY2 was quite high (Sørensen similarity index = 0.47). Thus, the concentration of heavy metals may not be determining factors in the structure of these communities. In the tailings, however, significantly lower ectomycorrhizal colonization and ectomycorrhizal fungal richness were observed. The amounts of Pb and Zn in the tailing sand were higher than the non-polluted forest but far lower than in HY1. Thus, these heavy metals did not account for the reduced colonization and ectomycorrhizal fungal richness in TLT. The ectomycorrhizal fungal community in TLT was dominated by four pioneer species (Rhizopogon buenoi, Tomentella ellisii, Inocybe curvipes, and Suillus granulatus), which collectively accounted for 93.2 % of root tip colonization. The immature soil conditions in tailing (low N and P, sand texture, and lack of organic matter) may only allow certain pioneer ectomycorrhizal fungal species to colonize the site. When soil samples from four sites were combined, we found that the occurrences of major ectomycorrhizal fungal taxa were not clearly related to the

  4. Fungal communities in gardens of the leafcutter ant Atta cephalotes in forest and cabruca agrosystems of southern Bahia State (Brazil).

    Science.gov (United States)

    Reis, Bárbara Monique dos Santos; Silva, Aline; Alvarez, Martín Roberto; Oliveira, Tássio Brito de; Rodrigues, Andre

    2015-12-01

    Leaf-cutting ants interact with several fungi in addition to the fungal symbiont they cultivate for food. Here, we assessed alien fungal communities in colonies of Atta cephalotes. Fungus garden fragments were sampled from colonies in the Atlantic Rainforest and in a cabruca agrosystem in the state of Bahia (Brazil) in two distinct periods to evaluate whether differences in nest habitat influence the diversity of fungi in the ant colonies. We recovered a total of 403 alien fungi isolates from 628 garden fragments. The prevalent taxa found in these samples were Escovopsis sp. (26 %), Escovopsioides nivea (24 %), and Trichoderma spirale (10.9 %). Fungal diversity was similar between the colonies sampled in both areas suggesting that ants focus on reducing loads of alien fungi in the fungus gardens instead of avoiding specific fungi. However, fungal taxa composition differed between colonies sampled in the two areas and between the sampling periods. These differences are likely explained by the availability of plant substrates available for foraging over habitats and periods. Ordination analysis further supported that sampling period was the main attribute for community structuring but also revealed that additional factors may explain the structuring of fungal communities in colonies of A. cephalotes.

  5. Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests.

    Science.gov (United States)

    Clemmensen, Karina E; Finlay, Roger D; Dahlberg, Anders; Stenlid, Jan; Wardle, David A; Lindahl, Björn D

    2015-03-01

    Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems. We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration. In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition. Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

  6. Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism and susceptibility to herbivory: Consequences for fungi and host plants

    Directory of Open Access Journals (Sweden)

    Catherine A. Gehring

    2014-06-01

    Full Text Available Plants and mycorrhizal fungi influence each other’s abundance, diversity and distribution. How other biotic interactions affect the mycorrhizal symbiosis is less well understood. Likewise, we know little about the effects of climate change on the fungal component of the symbiosis or its function. We synthesized our long-term studies on the influence of mistletoe parasites, insect herbivores, competing trees, and drought on the ectomycorrhizal fungal communities associated with a foundation tree species of the southwestern United States, pinyon pine (Pinus edulis, and described how these changes feed back to affect host plant performance. We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa. Ectomycorrhizal fungi responded similarly to each of these stressors resulting in a predictable trajectory of community disassembly, consistent with ecological theory. Although we predicted that the fungal communities associated with trees stressed by drought, herbivory, competition, and parasitism would be poor mutualists, we found the opposite pattern in field studies. Our results suggest that climate change and the increased importance of herbivores, competitors and parasites that can be associated with it, may ultimately lead to reductions in ectomycorrhizal fungal diversity, but that the remaining fungal community may be beneficial to host trees under the current climate and the warmer, drier climate predicted for the future.

  7. Ectomycorrhizal fungal communities of Coccoloba uvifera (L.) L. mature trees and seedlings in the neotropical coastal forests of Guadeloupe (Lesser Antilles).

    Science.gov (United States)

    Séne, Seynabou; Avril, Raymond; Chaintreuil, Clémence; Geoffroy, Alexandre; Ndiaye, Cheikh; Diédhiou, Abdala Gamby; Sadio, Oumar; Courtecuisse, Régis; Sylla, Samba Ndao; Selosse, Marc-André; Bâ, Amadou

    2015-10-01

    We studied belowground and aboveground diversity and distribution of ectomycorrhizal (EM) fungal species colonizing Coccoloba uvifera (L.) L. (seagrape) mature trees and seedlings naturally regenerating in four littoral forests of the Guadeloupe island (Lesser Antilles). We collected 546 sporocarps, 49 sclerotia, and morphotyped 26,722 root tips from mature trees and seedlings. Seven EM fungal species only were recovered among sporocarps (Cantharellus cinnabarinus, Amanita arenicola, Russula cremeolilacina, Inocybe littoralis, Inocybe xerophytica, Melanogaster sp., and Scleroderma bermudense) and one EM fungal species from sclerotia (Cenococcum geophilum). After internal transcribed spacer (ITS) sequencing, the EM root tips fell into 15 EM fungal taxa including 14 basidiomycetes and 1 ascomycete identified. Sporocarp survey only weakly reflected belowground assessment of the EM fungal community, although 5 fruiting species were found on roots. Seagrape seedlings and mature trees had very similar communities of EM fungi, dominated by S. bermudense, R. cremeolilacina, and two Thelephoraceae: shared species represented 93 % of the taxonomic EM fungal diversity and 74 % of the sampled EM root tips. Furthermore, some significant differences were observed between the frequencies of EM fungal taxa on mature trees and seedlings. The EM fungal community composition also varied between the four investigated sites. We discuss the reasons for such a species-poor community and the possible role of common mycorrhizal networks linking seagrape seedlings and mature trees in regeneration of coastal forests.

  8. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

    Science.gov (United States)

    Mueller, Rebecca C; Belnap, Jayne; Kuske, Cheryl R

    2015-01-01

    Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha−1 yr−1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

  9. Soil bacterial and fungal community responses to nitrogen addition across soil depths and microhabitat in an arid shrubland

    Directory of Open Access Journals (Sweden)

    Rebecca C Mueller

    2015-09-01

    Full Text Available Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 cm or 0-10 cm across the N-amendment gradient (0, 7 and 15 kg ha-1 yr-1. We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

  10. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland.

    Science.gov (United States)

    Mueller, Rebecca C; Belnap, Jayne; Kuske, Cheryl R

    2015-01-01

    Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

  11. Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens.

    Science.gov (United States)

    Girvan, Martina S; Bullimore, Juliet; Ball, Andrew S; Pretty, Jules N; Osborn, A Mark

    2004-05-01

    The composition of the active microbial (bacterial and fungal) soil community in an arable wheat field subjected to different management practices was examined at five times during a 1-year period. Field sections were fertilized either at good agricultural practice (GAP) levels or at reduced levels (0.5x GAP) and were inoculated with vesicular arbuscular mycorrhizae (VAM) at the same time. Field subsections were treated either with or without pesticides. Changes in the active microbial communities were investigated by denaturing gradient gel electrophoresis analysis of reverse transcription-PCR-amplified 16S and 18S rRNA. Microbial community structure was primarily determined by season, and the seasonal trends were similar for the fungal and bacterial components. Between-sample microbial heterogeneity decreased under a mature crop in the summer but increased following harvesting and plowing. Although similar overall trends were seen for the two microbial components, sample variability was greater for the fungal community than for the bacterial community. The greatest management effects were due to GAP fertilization, which caused increases in the bacterial numbers in the total and culturable communities. Microbial biomass similarly increased. GAP fertilization also caused large shifts in both the active bacterial community structure and the active fungal community structure and additionally resulted in a decrease in the heterogeneity of the active bacterial community. Pesticide addition did not significantly affect bacterial numbers or heterogeneity, but it led to major shifts in the active soil bacterial community structure. PCR primers specific for Glomales 25S rRNA genes were used to monitor the VAM population following inoculation. Glomales were detected initially only in VAM-inoculated field sections but were subsequently detected in noninoculated field sections as the season progressed. After plowing, the level of Glomales was reduced in noninoculated field

  12. Loss of diversity in wood-inhabiting fungal communities affects decomposition activity in Norway spruce wood

    Directory of Open Access Journals (Sweden)

    Lara eValentin

    2014-05-01

    Full Text Available Hundreds of wood-inhabiting fungal species are now threatened, principally due to a lack of dead wood in intensively managed forests, but the consequences of reduced fungal diversity on ecosystem functioning are not known. Several experiments have shown that primary productivity is negatively affected by a loss of species, but the effects of microbial diversity on decomposition are less studied. We studied the relationship between fungal diversity and the in vitro decomposition rate of slightly, moderately and heavily decayed Picea abies wood with indigenous fungal communities that were diluted to examine the influence of diversity. Respiration rate, wood-degrading hydrolytic enzymes and fungal community structure were assessed during a 16-week incubation. Respiration rate increased between early- and late-decay stages. Reduced fungal diversity was associated with lower respiration rates during intermediate stages of decay, but no effects were detected at later stages. The activity of hydrolytic enzymes varied among decay stages and fungal dilutions. Our results suggest that functioning of highly diverse communities of the late-decay stage were more resistant to the loss of diversity than less diverse communities of early decomposers. This indicates the accumulation of functional redundancy during the succession of the fungal community in decomposing substrates.

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

    Energy Technology Data Exchange (ETDEWEB)

    Jasrotia, Puja [Florida State University, Tallahassee; Green, Stefan [University of Illinois, Chicago; Canion, Andy [Florida State University, Tallahassee; Overholt, Will [Florida State University, Tallahassee; Prakash, Om [Florida State University, Tallahassee; Wafula, Dennis [Georgia Institute of Technology, Atlanta; Hubbard, Daniela [Florida State University, Tallahassee; Watson, David B [ORNL; Schadt, Christopher Warren [ORNL; Brooks, Scott C [ORNL; Kostka, [Georgia Institute of Technology, Atlanta

    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 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 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.

  14. Edaphic factors trigger diverse AM fungal communities associated to exotic camellias in closely located Lake Maggiore (Italy) sites.

    Science.gov (United States)

    Borriello, Roberto; Berruti, Andrea; Lumini, Erica; Della Beffa, Maria Teresa; Scariot, Valentina; Bianciotto, Valeria

    2015-05-01

    Camellia japonica L. is an acidophilic ornamental shrub of high economic value that has its center of origin in Japan and has been introduced in several European environmental niches. This exotic species forms arbuscular mycorrhizas (AM), known for their ability to positively affect plant growth. However, AM fungal communities associated to C. japonica in the field have never been characterized. For the first time, the AM fungal community naturally selected by C. japonica was screened in three sites located on the shores of Lake Maggiore (Italy), where specimens of this plant were introduced in the nineteenth century. Mycorrhizal levels were assessed, and the AM fungal communities associated to roots and soil were molecularly characterized based on the small subunit (SSU) rDNA region. The frequency of mycorrhizal roots was high in all sampled root systems (>90 %). Overall, 39 Operational Taxonomic Units (OTUs; 22 Glomerales, 9 Paraglomerales, 7 Archaeosporales, and 1 Diversisporales) were found in the root and soil samples. OTU richness did not significantly differ between the root and the soil niche (5.7 ± 0.6 and 8.0 ± 1.1 average OTUs per sample, respectively) and the three sites analyzed (7.5 ± 0.7, 5.2 ± 1.0, and 7.8 ± 1.5 average OTUs per sample in the three sites, respectively). The AM fungal community composition significantly differed between root-colonizing and soil-dwelling communities and among the three sites under study. Data show a major involvement of edaphic factors, such as available N sources, P, Mg, and K content in soil and soil compaction, in the structuring of the AM fungal communities.

  15. Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska.

    Science.gov (United States)

    Morgado, Luis N; Semenova, Tatiana A; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József

    2015-02-01

    Arctic regions are experiencing the greatest rates of climate warming on the planet and marked changes have already been observed in terrestrial arctic ecosystems. While most studies have focused on the effects of warming on arctic vegetation and nutrient cycling, little is known about how belowground communities, such as fungi root-associated, respond to warming. Here, we investigate how long-term summer warming affects ectomycorrhizal (ECM) fungal communities. We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra. Cortinarius was the most OTU-rich genus in the moist tundra, while the most diverse genus in the dry tundra was Tomentella. On the diversity level, in the moist tundra we found significant differences in community composition, and a sharp decrease in the richness of ECM fungi due to warming. On the functional level, our results indicate that warming induces shifts in the extramatrical properties of the communities, where the species with medium-distance exploration type seem to be favored with potential implications for the mobilization of different nutrient pools in the soil. In the dry tundra, neither community richness nor community composition was significantly altered by warming, similar to what had been observed in ECM host plants. There was, however, a marginally significant increase in OTUs identified as ECM fungi with the medium-distance exploration type in the warmed plots. Linking our findings of decreasing richness with previous results of increasing ECM fungal biomass suggests that certain ECM species are favored by warming and may become more abundant, while many other species may go locally extinct due to direct or indirect effects of warming. Such compositional shifts in the community might affect nutrient cycling and soil organic C storage. © 2014 The Authors. Global Change

  16. Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities

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    Anthony Stuart Amend

    2015-02-01

    Full Text Available Fungi play a critical role in the degradation of organic matter. Because different combinations of fungi result in different rates of decomposition, determining how climate change will affect microbial composition and function is fundamental to predicting future environments. Fungal response to global change is patterned by genetic relatedness, resulting in communities with comparatively low phylogenetic diversity. This may have important implications for the functional capacity of disturbed communities if lineages sensitive to disturbance also contain unique traits important for litter decomposition. Here we tested the relationship between phylogenetic diversity and decomposition rates. Leaf litter fungi were isolated from the field and deployed in microcosms as mock communities along a gradient of initial phylogenetic diversity, while species richness was held constant. Replicate communities were subject to nitrogen fertilization comparable to anthropogenic deposition levels. Carbon mineralization rates were measured over the course of sixty-six days. We found that nitrogen fertilization increased cumulative respiration by 24.8%, and that differences in respiration between fertilized and ambient communities diminished over the course of the experiment. Initial phylogenetic diversity failed to predict respiration rates or their change in response to nitrogen fertilization, and there was no correlation between community similarity and respiration rates. Last, we detected no phylogenetic signal in the contributions of individual isolates to respiration rates. Our results suggest that the degree to which phylogenetic diversity predicts ecosystem function will depend on environmental context.

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

    Science.gov (United States)

    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.

  18. The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management.

    Directory of Open Access Journals (Sweden)

    Laurence Delhaes

    Full Text Available BACKGROUND: Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF, it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways. METHODOLOGY AND PRINCIPAL FINDINGS: Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values. Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus. CONCLUSIONS: In light of the recent concept of CF lung microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential

  19. Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities

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    Peter Kennedy

    2014-12-01

    Full Text Available A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e., antagonistic, neutral, or positive was assessed using taxon co-occurrence and DNA sequence abundance correlational analyses. ECM fungal communities were sampled from root tips or mesh in-growth bags in three monodominant A. rubra plots at a site in Oregon, USA and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 175 ECM fungal taxa; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead, the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.

  20. Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions.

    Science.gov (United States)

    Pérez, María Laura; Collavino, Mónica Mariana; Sansberro, Pedro Alfonso; Mroginski, Luis Amado; Galdeano, Ernestina

    2016-04-01

    The composition and diversity of the endophytic community associated with yerba mate (Ilex paraguariensis) was investigated using culture-depending methods. Fungi were identified based on their micromorphological characteristics and internal transcribed spacer rDNA sequence analysis; for bacteria 16S rDNA sequence analysis was used. Fungal and bacterial diversity did not show significant differences between organ age. The highest fungal diversity was registered during fall season and the lowest in winter. Bacterial diversity was higher in stems and increased from summer to winter, in contrast with leaves, which decreased. The most frequently isolated fungus was Fusarium, followed by Colletotrichum; they were both present in all the sampling seasons and organ types assayed. Actinobacteria represented 57.5 % of all bacterial isolates. The most dominant bacterial taxa were Curtobacterium and Microbacterium. Other bacteria frequently found were Methylobacterium, Sphingomonas, Herbiconiux and Bacillus. Nitrogen fixation and phosphate solubilization activity, ACC deaminase production and antagonism against plant fungal pathogens were assayed in endophytic bacterial strains. In the case of fungi, strains of Trichoderma, Penicillium and Aspergillus were assayed for antagonism against pathogenic Fusarium sp. All microbial isolates assayed showed at least one growth promoting activity. Strains of Bacillus, Pantoea, Curtobacterium, Methylobacterium, Brevundimonas and Paenibacillus had at least two growth-promoting activities, and Bacillus, Paenibacillus and the three endophytic fungi showed high antagonistic activity against Fusarium sp. In this work we have made a wide study of the culturable endophytic community within yerba mate plants and found that several microbial isolates could be considered as potential inoculants useful for improving yerba mate production.

  1. Rapid response of soil fungal communities to low and high intensity fire

    Science.gov (United States)

    Smith, Jane E.; Cowan, Ariel D.; Reazin, Chris; Jumpponen, Ari

    2016-04-01

    Contemporary fires have created high-severity burn areas exceeding historical distributions in forests in the western United States. Until recently, the response of soil ecosystems to high intensity burns has been largely unknown. In complementary studies, we investigated the environmental effect of extreme soil heating, such that occurs with the complete combustion of large down wood during wildfires, on soil fungi and nutrients. We used TRFLP and next generation sequencing (Illumina MiSeq) to investigate the fungal communities. During the burning of large down wood, temperatures lethal to fungi were detected at 0-cm, 5-cm, and 10-cm depths in soils compared to 0-cm depth in soils receiving low intensity broadcast burns. We compared the soil fungal diversity in ten high intensity burned plots paired with adjacent low intensity burned plots before and one week after at 0-10 cm soil depth. Nonmetric Multidimensional Scaling (NMS) ordinations and analyses of taxon frequencies reveal a substantial community turnover and corresponding near complete replacement of the dominant basidiomycetes by ascomycetes in high intensity burns. These coarse-level taxonomic responses were primarily attributable to a few fire-responsive (phoenicoid) fungi, particularly Pyronema sp. and Morchella sp., whose frequencies increased more than 100-fold following high intensity burns. Pinus ponderosa seedlings planted one week post-burn were harvested after four months for EMF root tip analysis. We found: a) greater differences in soil properties and nutrients in high intensity burned soils compared to low intensity burned and unburned soils; b) no differences in EMF richness and diversity; and c) weak differences in community composition based on relative abundance between unburned and either burn treatments. These results confirm the combustion of large downed wood can alter the soil environment directly beneath it. However, an EMF community similar to low burned soils recolonized high

  2. New perspectives towards analising fungal communities in terrestrial environments

    NARCIS (Netherlands)

    Kowalchuk, G.A.

    1999-01-01

    Fungi play key roles in numerous ecosystem functions, and recent advances in the study of fungal diversity and ecology have led to a greater appreciation of this group of microeukaryotes. The application of a variety of nucleic acid techniques to fungal classification and phylogeny has led to a numb

  3. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems

    Directory of Open Access Journals (Sweden)

    Kezia eGoldmann

    2015-11-01

    Full Text Available Fungal communities have been shown to be highly sensitive towards shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L., with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L. or spruce (Picea abies Karst. which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure.We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal OTU richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera.This study extends our knowledge

  4. The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient.

    Science.gov (United States)

    Cordier, Tristan; Robin, Cécile; Capdevielle, Xavier; Fabreguettes, Olivier; Desprez-Loustau, Marie-Laure; Vacher, Corinne

    2012-10-01

    Little is known about the potential effect of climate warming on phyllosphere fungi, despite their important impact on the dynamics and diversity of plant communities. The structure of phyllosphere fungal assemblages along elevation gradients may provide information about this potential effect, because elevation gradients correspond to temperature gradients over short geographic distances. We thus investigated variations in the composition of fungal assemblages inhabiting the phyllosphere of European beech (Fagus sylvatica) at four sites over a gradient of 1000 m of elevation in the French Pyrénées Mountains, by using tag-encoded 454 pyrosequencing. Our results show that the composition of fungal assemblages varied significantly between elevation sites, in terms of both the relative abundance and the presence-absence of species, and that the variations in assemblage composition were well correlated with variations in the average temperatures. Our results therefore suggest that climate warming might alter both the incidence and the abundance of phyllosphere fungal species, including potential pathogens. For example, Mycosphaerella punctiformis, a causal agent of leaf spots, showed decreasing abundance with elevation and might therefore shift to higher elevations in response to warming.

  5. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

    Science.gov (United States)

    Shakya, Migun; Gottel, Neil; Castro, Hector; Yang, Zamin K; Gunter, Lee; Labbé, Jessy; Muchero, Wellington; Bonito, Gregory; Vilgalys, Rytas; Tuskan, Gerald; Podar, Mircea; Schadt, Christopher W

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities that

  6. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees.

    Directory of Open Access Journals (Sweden)

    Migun Shakya

    Full Text Available Bacterial and fungal communities associated with plant roots are central to the host health, survival and growth. However, a robust understanding of the root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings, host plant genotype (Simple Sequence Repeat (SSR markers, season (Spring vs. Fall and geographic setting (at scales from regional watersheds to local riparian zones on microbial community structure. Each of the trees sampled displayed unique aspects to its associated community structure with high numbers of Operational Taxonomic Units (OTUs specific to an individual trees (bacteria >90%, fungi >60%. Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal and endosphere (1 bacterial and 1 fungal microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50% while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%. While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina and seasons (Spring vs. Fall. SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall host genotypic distances did not have a significant effect on corresponding communities

  7. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

    Energy Technology Data Exchange (ETDEWEB)

    Shakya, Migun [ORNL; Gottel, Neil R [ORNL; Castro Gonzalez, Hector F [ORNL; Yang, Zamin [ORNL; Gunter, Lee E [ORNL; Labbe, Jessy L [ORNL; Muchero, Wellington [ORNL; Bonito, Gregory [Duke University; Vilgalys, Rytas [Duke University; Tuskan, Gerald A [ORNL; Podar, Mircea [ORNL; Schadt, Christopher Warren [ORNL

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that could be

  8. Diversity and bioprospecting of fungal communities associated with endemic and cold-adapted macroalgae in Antarctica.

    Science.gov (United States)

    Godinho, Valéria M; Furbino, Laura E; Santiago, Iara F; Pellizzari, Franciane M; Yokoya, Nair S; Pupo, Diclá; Alves, Tânia M A; Junior, Policarpo A S; Romanha, Alvaro J; Zani, Carlos L; Cantrell, Charles L; Rosa, Carlos A; Rosa, Luiz H

    2013-07-01

    We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates, which were identified using molecular methods as belonging to 21 genera and 50 taxa. The most frequent taxa were Geomyces species (sp.), Penicillium sp. and Metschnikowia australis. Seven fungal isolates associated with the endemic Antarctic macroalgae Monostroma hariotii (Chlorophyte) displayed high internal transcribed spacer sequences similarities with the psychrophilic pathogenic fungus Geomyces destructans. Thirty-three fungal singletons (66%) were identified, representing rare components of the fungal communities. The fungal communities displayed high diversity, richness and dominance indices; however, rarefaction curves indicated that not all of the fungal diversity present was recovered. Penicillium sp. UFMGCB 6034 and Penicillium sp. UFMGCB 6120, recovered from the endemic species Palmaria decipiens (Rhodophyte) and M. hariotii, respectively, yielded extracts with high and selective antifungal and/or trypanocidal activities, in which a preliminary spectral analysis using proton nuclear magnetic resonance spectroscopy indicated the presence of highly functionalised aromatic compounds. These results suggest that the endemic and cold-adapted macroalgae of Antarctica shelter a rich, diversity and complex fungal communities consisting of a few dominant indigenous or mesophilic cold-adapted species, and a large number of rare and/or endemic taxa, which may provide an interesting model of algal-fungal interactions under extreme conditions as well as a potential source of bioactive compounds.

  9. A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district, eastern Japan.

    Science.gov (United States)

    Matsumura, Emi; Fukuda, Kenji

    2013-03-01

    To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and CMH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.

  10. Geographic locality greatly influences fungal endophyte communities in Cephalotaxus harringtonia.

    Science.gov (United States)

    Langenfeld, Aude; Prado, Soizic; Nay, Bastien; Cruaud, Corine; Lacoste, Sandrine; Bury, Edith; Hachette, François; Hosoya, Tsuyoshi; Dupont, Joëlle

    2013-02-01

    Although endophytes of conifers have been extensively studied, few data are available on Cephalotaxaceae. We examined foliar and stem endophytes of Cephalotaxus harringtonia, within its natural range in Japan and outside its natural range in France to study the effect of geography on endophyte community composition. In Japan, rapidly growing endophytes were dominant and may have masked the real diversity, in comparison to France where most endophytes were growing slowly. Analyses of ITS rDNA revealed 104 different Blast Groups among 554 isolates. Almost no overlap between endophyte assemblages of C. harringtonia from the two countries was observed. It seems that Japanese C. harringtonia trees, which should be well adapted to their native site, would host a specific, endemic endophyte community, while trees that have been introduced recently to a foreign site, in France, should have captured existing cosmopolitan and more generalist taxa. In Japan the majority of xylariaceous taxa, which dominated the communities, were unknown and, although closely related to Asian taxa, may be new to science. Dothideomycetes were more prevalent in France. Locally, urban environment, particularly in Japan, may have introduced some perturbations in the native endophyte community of C. harringtonia, with an abundance of generalist fungi such as Nigrospora and Colletotrichum. Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  11. Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales.

    Science.gov (United States)

    Horn, Sebastian; Caruso, Tancredi; Verbruggen, Erik; Rillig, Matthias C; Hempel, Stefan

    2014-11-01

    Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Elina eSohlberg

    2015-06-01

    Full Text Available 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 m 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.

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

    Science.gov (United States)

    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. PMID:26106376

  16. Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque.

    Science.gov (United States)

    Hayward, Jeremy; Horton, Thomas R; Nuñez, Martin A

    2015-10-01

    Coinvasive ectomycorrhizal (ECM) fungi allow Pinaceae species to invade regions otherwise lacking compatible symbionts, but ECM fungal communities permitting Pinaceae invasions are poorly understood. In the context of Pinaceae invasions on Isla Victoria, Nahuel Huapi National Park, Argentina, we asked: what ECM fungi are coinvading with Pinaceae hosts on Isla Victoria; are some ECM fungal species or genera more prone to invade than others; and are all ECM fungal species that associate with Northern Hemisphere hosts also nonnative, or are some native fungi compatible with nonnative plants? We sampled ECMs from 226 Pinaceae host plant individuals, both planted individuals and recruits, growing inside and invading from plantations. We used molecular techniques to examine ECM fungal communities associating with these trees. A distinctive subset of the ECM fungal community predominated far from plantations, indicating differences between highly invasive and less invasive ECM fungi. Some fungal invaders reported here have been detected in other locations around the world, suggesting strong invasion potential. Fungi that were frequently detected far from plantations are often found in early-successional sites in the native range, while fungi identified as late-successional species in the native range are rarely found far from plantations, suggesting a means for predicting potential fungal coinvaders.

  17. Relationship between the decomposition process of coarse woody debris and fungal community structure as detected by high-throughput sequencing in a deciduous broad-leaved forest in Japan.

    Directory of Open Access Journals (Sweden)

    Satoshi Yamashita

    Full Text Available We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris

  18. Comparison of Arbuscular Mycorrhizal Fungal Community in Roots and Rhizosphere of Invasive Cenchrus incertus and Native Plant in Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    Dan XIANG; Baodong CHEN; Huan LI; Ruojuan LI; Xin ZHANG

    2016-01-01

    Plant invasions could significantly alter arbuscular mycorrhizal (AM) fungal communities, but the effect may vary with plant species and local environments. Identifying changes in the AM fungal community due to plant invasion could improve our understanding of the invasion processes. Here, we examined the AM fungal community composition both in roots and rhizo-sphere soils of the invasive plant Cenchrus incertus and the dominant native plant Setaria viridis in a typical steppe in Inner Mongolia by using terminal restriction fragment length polymorphism analyses (T-RFLP). The results showed that AM fungal abundance in the rhizosphere soils of C. incertus was significantly lower than that of S. viridis. The AM fungal community com-position in the rhizosphere soils of the two plant species also largely differed. In general, AM fungal community structures in roots corresponded very wel to that in rhizosphere soils for both plant species. The dominant AM fungal type both in invasive and native plants was T-RFLP 524bp, which represents Glomus sp. (Virtual taxa 109 and 287). Three specific T-RF types (280, 190 and 141bp) were significantly more abundant in C. incertus, representing three clusters in Glomus which also named as VT (virtual taxa) 287, 64 and 214, Rhizophagus intraradices (VT 113) and Diversispora sp. (VT 60). While the specific T-RF types, 189 and 279bp, for S. viridis, only existed in Glomus cluster 1 (VT 156), were significantly less abundant in C. incertus. These results indicated that AM fungi might play an important role in the invasion process of C. incertus, which stil remains to be fur-ther investigated.

  19. Repression of fungal plant pathogens and fungal-related contaminants: Selected ecosystem services by soil fauna communities in agroecosystems

    Science.gov (United States)

    Meyer-Wolfarth, Friederike; Schrader, Stefan; Oldenburg, Elisabeth; Brunotte, Joachim; Weinert, Joachim

    2017-04-01

    In agroecosystems soil-borne fungal plant diseases are major yield-limiting factors which are difficult to control. Fungal plant pathogens, like Fusarium species, survive as a saprophyte in infected tissue like crop residues and endanger the health of the following crop by increasing the infection risk for specific plant diseases. In infected plant organs, these pathogens are able to produce mycotoxins. Mycotoxins like deoxynivalenol (DON) persist during storage, are heat resistant and of major concern for human and animal health after consumption of contaminated food and feed, respectively. Among fungivorous soil organisms, there are representatives of the soil fauna which are obviously antagonistic to a Fusarium infection and the contamination with mycotoxins. Specific members of the soil macro-, meso-, and microfauna provide a wide range of ecosystem services including the stimulation of decomposition processes which may result in the regulation of plant pathogens and the degradation of environmental contaminants. Investigations under laboratory conditions and in field were conducted to assess the functional linkage between soil faunal communities and plant pathogenic fungi (Fusarium culmorum). The aim was to examine if Fusarium biomass and the content of its mycotoxin DON decrease substantially in the presence of soil fauna (earthworms: Lumbricus terrestris, collembolans: Folsomia candida and nematodes: Aphelenchoides saprophilus) in a commercial cropping system managed with conservation tillage located in Northern Germany. The results of our investigations pointed out that the degradation performance of the introduced soil fauna must be considered as an important contribution to the biodegradation of fungal plant diseases and fungal-related contaminants. Different size classes within functional groups and the traits of keystone species appear to be significant for soil function and the provision of ecosystem services as in particular L. terrestris revealed to

  20. Bacterial and Fungal Community Structures in Loess Plateau Grasslands with Different Grazing Intensities

    Directory of Open Access Journals (Sweden)

    Huhe

    2017-04-01

    Full Text Available The Loess Plateau of China is one of the most fragile ecosystems worldwide; thus, human production activities need to be conducted very cautiously. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and changes in vegetation and soil physical and chemical properties induced by grazing, in four grasslands with different levels of grazing intensity (0, 2.67, 5.33, and 8.67 sheep/ha in the semiarid region of the Loess Plateau. The relative abundances of the bacterial community in the grasslands with 2.67 and 5.33 sheep/ha were significantly higher than those in grasslands with 0 and 8.67 sheep/ha, and the fungal diversity was significantly lower for grasslands with 2.67 sheep/ha than for the other grasslands. Redundancy analysis (RDA showed that plant biomass, nitrate, and total nitrogen have significant effects on bacterial community structure, whereas nitrate and total nitrogen also significantly affect fungal community structure. Variation partitioning showed that soil and plant characteristics influence the bacterial and fungal community structures; these characteristics explained 51.9 and 52.9% of the variation, respectively. Thus, bacterial and fungal community structures are very sensitive to grazing activity and change to different extents with different grazing intensities. Based on our findings, a grazing intensity of about 2.67 sheep/ha is considered the most appropriate in semiarid grassland of the Loess Plateau.

  1. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    Full Text Available This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs. Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.

  2. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes

    DEFF Research Database (Denmark)

    Barnes, Christopher James; Maldonado Goyzueta, Carla Brenda; Frøslev, Tobias Guldberg

    2016-01-01

    in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography...... in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß......-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of -0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 % and 7.2 % of community...

  3. Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore-associated microbes.

    Science.gov (United States)

    Iffis, Bachir; St-Arnaud, Marc; Hijri, Mohamed

    2016-09-01

    The root-associated microbiome is a key determinant of pollutant degradation, soil nutrient availability and plant biomass productivity, but could not be examined in depth prior to recent advances in high-throughput sequencing. Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of vascular plants. They are known to enhance mineral uptake and promote plant growth and are postulated to influence the processes involved in phytoremediation. Amplicon sequencing approaches have previously shown that petroleum hydrocarbon pollutant (PHP) concentration strongly influences AMF community structure in in situ phytoremediation experiments. We examined how AMF communities and their spore-associated microbiomes were structured within the rhizosphere of three plant species growing spontaneously in three distinct waste decantation basins of a former petrochemical plant. Our results show that the AMF community was only affected by PHP concentrations, while the AMF-associated fungal and bacterial communities were significantly affected by both PHP concentrations and plant species identity. We also found that some AMF taxa were either positively or negatively correlated with some fungal and bacterial groups. Our results suggest that in addition to PHP concentrations and plant species identity, AMF community composition may also shape the community structure of bacteria and fungi associated with AMF spores. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  4. Investigation of the indigenous fungal community populating barley grains: Secretomes and xylanolytic potential

    DEFF Research Database (Denmark)

    Sultan, Abida; Frisvad, Jens Christian; Andersen, Birgit

    2017-01-01

    The indigenous fungal species populating cereal grains produce numerous plant cell wall-degrading enzymes including xylanases, which could play important role in plant-pathogen interactions and in adaptation of the fungi to varying carbon sources. To gain more insight into the grain surface......-associated enzyme activity, members of the populating fungal community were isolated, and their secretomes and xylanolytic activities assessed. Twenty-seven different fungal species were isolated from grains of six barley cultivars over different harvest years and growing sites. The isolated fungi were grown...

  5. Moisture parameters and fungal communities associated with gypsum drywall in buildings

    OpenAIRE

    Dedesko, Sandra; Siegel, Jeffrey A.

    2015-01-01

    Uncontrolled excess moisture in buildings is a common problem that can lead to changes in fungal communities. In buildings, moisture parameters can be classified by location and include assessments of moisture in the air, at a surface, or within a material. These parameters are not equivalent in dynamic indoor environments, which makes moisture-induced fungal growth in buildings a complex occurrence. In order to determine the circumstances that lead to such growth, it is essential to have a t...

  6. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons.

    Science.gov (United States)

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-11-28

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

  7. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

    Science.gov (United States)

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-11-01

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

  8. Continuous fungal treatment of non-sterile veterinary hospital effluent: pharmaceuticals removal and microbial community assessment.

    Science.gov (United States)

    Badia-Fabregat, Marina; Lucas, Daniel; Pereira, Maria Alcina; Alves, Madalena; Pennanen, Taina; Fritze, Hannu; Rodríguez-Mozaz, Sara; Barceló, Damià; Vicent, Teresa; Caminal, Glòria

    2016-03-01

    Source point treatment of effluents with a high load of pharmaceutical active compounds (PhACs), such as hospital wastewater, is a matter of discussion among the scientific community. Fungal treatments have been reported to be successful in degrading this type of pollutants and, therefore, the white-rot fungus Trametes versicolor was applied for the removal of PhACs from veterinary hospital wastewater. Sixty-six percent removal was achieved in a non-sterile batch bioreactor inoculated with T. versicolor pellets. On the other hand, the study of microbial communities by means of DGGE and phylogenetic analyses led us to identify some microbial interactions and helped us moving to a continuous process. PhAC removal efficiency achieved in the fungal treatment operated in non-sterile continuous mode was 44 % after adjusting the C/N ratio with respect to the previously calculated one for sterile treatments. Fungal and bacterial communities in the continuous bioreactors were monitored as well.

  9. Biodegradation of polyester polyurethane during commercial composting and analysis of associated fungal communities.

    Science.gov (United States)

    Zafar, Urooj; Nzeram, Petrus; Langarica-Fuentes, Adrian; Houlden, Ashley; Heyworth, Alan; Saiani, Alberto; Robson, Geoff D

    2014-04-01

    In this study the biodegradation of polyurethane (PU) during the maturation stage of a commercial composting process was investigated. PU coupons were buried in the centre and at the surface of a 10 m high compost pile. Fungal communities colonising polyester PU coupons were compared with the native compost communities using culture based and molecular techniques. Putative polyester PU degrading fungi were ubiquitous in compost and rapidly colonised the surface of polyester PU coupons with significant deterioration. As the temperature decreased, fungal diversity in the compost and on the surface of the polyester PU coupons increased and selection of fungal community on the polyester PU coupons occurs that is different from the surrounding compost. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. AM fungal communities inhabiting the roots of submerged aquatic plant Lobelia dortmanna are diverse and include a high proportion of novel taxa.

    Science.gov (United States)

    Moora, Mari; Öpik, Maarja; Davison, John; Jairus, Teele; Vasar, Martti; Zobel, Martin; Eckstein, R Lutz

    2016-10-01

    While the arbuscular mycorrhizal (AM) symbiosis is known to be widespread in terrestrial ecosystems, there is growing evidence that aquatic plants also form the symbiosis. It has been suggested that symbiosis with AM fungi may represent an important adaptation for isoëtid plants growing on nutrient-poor sediments in oligotrophic lakes. In this study, we address AM fungal root colonization intensity, richness and community composition (based on small subunit (SSU) ribosomal RNA (rRNA) gene sequencing) in five populations of the isoëtid plant species Lobelia dortmanna inhabiting oligotrophic lakes in Southern Sweden. We found that the roots of L. dortmanna hosted rich AM fungal communities and about 15 % of the detected molecular taxa were previously unrecorded. AM fungal root colonization intensity and taxon richness varied along an environmental gradient, being higher in oligotrophic and lower in mesotrophic lakes. The overall phylogenetic structure of this aquatic fungal community differed from that described in terrestrial systems: The roots of L. dortmanna hosted more Archaeosporaceae and fewer Glomeraceae taxa than would be expected based on global data from terrestrial AM fungal communities.

  11. Identification of Fungal Communities Associated with the Biodeterioration of Waterlogged Archeological Wood in a Han Dynasty Tomb in China

    Directory of Open Access Journals (Sweden)

    Zijun Liu

    2017-08-01

    Full Text Available The Mausoleum of the Dingtao King (termed ‘M2’ is a large-scale huangchang ticou tomb that dates to the Western Han Dynasty (206 B.C.–25 A.D.. It is the highest-ranking Han Dynasty tomb discovered to date. However, biodeterioration on the surface of the tomb M2 is causing severe damage to its wooden materials. The aim of the present study was to give insight into the fungal communities colonized the wooden tomb. For this purpose, seven samples were collected from different sections of the tomb M2 which exhibited obvious biodeterioration in the form of white spots. Microbial structures associated with the white spots were observed with scanning electron microscopy. Fungal community structures were assessed for seven samples via a combination of high-throughput sequencing and culture-dependent techniques. Sequencing analyses identified 114 total genera that belonged to five fungal phyla. Hypochnicium was the most abundant genus across all samples and accounted for 98.61–99.45% of the total community composition. Further, Hypochnicium sp. and Mortierella sp. cultures were successfully isolated from the tomb samples, and were distinguished as Hypochnicium sp. WY-DT1 and Mortierella sp. NK-DT1, respectively. Cultivation-dependent experiments indicated that the dominant member, Hypochnicium sp. WY- DT1, could grow at low temperatures and significantly degraded cellulose and lignin. Thus, our results taken together suggest that this fungal strain must be regarded as a serious threat to the preservation of the wooden tomb M2. The results reported here are useful for informing future contamination mitigation efforts for the tomb M2 as well as other similar cultural artifacts.

  12. Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons.

    Science.gov (United States)

    McGuire, Krista L; Allison, Steven D; Fierer, Noah; Treseder, Kathleen K

    2013-01-01

    Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0-20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.

  13. Unravelling soil fungal communities from different Mediterranean land-use backgrounds.

    Directory of Open Access Journals (Sweden)

    Alberto Orgiazzi

    Full Text Available BACKGROUND: Fungi strongly influence ecosystem structure and functioning, playing a key role in many ecological services as decomposers, plant mutualists and pathogens. The Mediterranean area is a biodiversity hotspot that is increasingly threatened by intense land use. Therefore, to achieve a balance between conservation and human development, a better understanding of the impact of land use on the underlying fungal communities is needed. METHODOLOGY/PRINCIPAL FINDINGS: We used parallel pyrosequencing of the nuclear ribosomal its regions to characterize the fungal communities in five soils subjected to different anthropogenic impact in a typical mediterranean landscape: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards. Marked differences in the distribution of taxon assemblages among the different sites and communities were found. Data analyses consistently indicated a sharp distinction of the fungal community of the cork oak forest soil from those described in the other soils. Each soil showed features of the fungal assemblages retrieved which can be easily related to the above-ground settings: ectomycorrhizal phylotypes were numerous in natural sites covered by trees, but were nearly completely missing from the anthropogenic and grass-covered sites; similarly, coprophilous fungi were common in grazed sites. CONCLUSIONS/SIGNIFICANCE: Data suggest that investigation on the below-ground fungal community may provide useful elements on the above-ground features such as vegetation coverage and agronomic procedures, allowing to assess the cost of anthropogenic land use to hidden diversity in soil. Datasets provided in this study may contribute to future searches for fungal bio-indicators as biodiversity markers of a specific site or a land-use degree.

  14. [Effects of wheat root exudates on cucumber growth and soil fungal community structure].

    Science.gov (United States)

    Wu, Feng-Zhi; Li, Min; Cao, Peng; Ma, Ya-Fei; Wang, Li-Li

    2014-10-01

    With wheat as the donor plant and cucumber as the receptor plant, this study investigated the effects of root exudates from wheat cultivars with different allelopathic potentials (positive or negative) and companion cropping with wheat on soil fungal community structure by PCR-DGGE method and cucumber growth. Results showed that the wheat root exudates with positive allelopathic potential increased height and stem diameter of cucumber seedlings significantly, compared to the control seedlings (W) after 6 days and 12 days treatment, respectively. Also, wheat root exudates with both positive and negative allelopathic potential increased the seedling height of cucumber significantly after 18 days treatment. The wheat root exudates with different allelopathic potentials decreased the band number, Shannon and evenness indices of soil fungal community significantly in cucumber seedling rhizosphere, and those in the soil with the control seedlings (W) were also significantly higher than that in the control soil without seedlings (Wn) after 6 days treatment. The band number, Shannon and evenness indices in all the treatments were significantly higher than those in the control soil without seedlings (Wn) after 18 days treatment. Companion cropping with negative allelopathic potential wheat decreased the Shannon and evenness indices of soil fungi community significantly in the cucumber seedling rhizosphere, suggesting the wheat root exudates and companion cropping with wheat changed soil fungal community structure in the cucumber seedling rhizosphere. The results of DGGE map and the principal component analysis showed that companion cropping with wheat cultivars with different allelopathic potentials changed soil fungal community structure in cucumber seedling rhizosphere.

  15. Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.

    Directory of Open Access Journals (Sweden)

    Teresita M Porter

    Full Text Available Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1 a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN; 2 a composition-based method (Ribosomal Database Project naïve bayesian classifier, NBC; and, 3 a phylogeny-based method (Statistical Assignment Package, SAP. We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50-100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys.

  16. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    Science.gov (United States)

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-03-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects-direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.

  17. Fungal Community Associated with Dactylopius (Hemiptera: Coccoidea: Dactylopiidae) and Its Role in Uric Acid Metabolism.

    Science.gov (United States)

    Vera-Ponce de León, Arturo; Sanchez-Flores, Alejandro; Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2016-01-01

    We studied fungal species associated with the carmine cochineal Dactylopius coccus and other non-domesticated Dactylopius species using culture-dependent and -independent methods. Thirty seven fungi were isolated in various culture media from insect males and females from different developmental stages and Dactylopius species. 26S rRNA genes and ITS sequences, from cultured fungal isolates revealed different species of Cryptococcus, Rhodotorula, Debaryomyces, Trametes, and Penicillium, which are genera newly associated with Dactylopius. Uric acid (UA) and uricase activity were detected in tissues extracts from different insect developmental stages. However, accumulation of high UA levels and low uricase activities were found only after antifungal treatments, suggesting an important role of fungal species in its metabolism. Additionally, uricolytic fungal isolates were identified and characterized that presumably are involved in nitrogen recycling metabolism. After metagenomic analyses from D. coccus gut and hemolymph DNA and from two published data sets, we confirmed the presence of fungal genes involved in UA catabolism, suggesting that fungi help in the nitrogen recycling process in Dactylopius by uricolysis. All these results show the importance of fungal communities in scale insects such as Dactylopius.

  18. Antibacterial, antifungal and antiprotozoal activities of fungal communities present in different substrates from Antarctica

    Science.gov (United States)

    Antarctica is a pristine and extreme environment that represents a unique opportunity for taxonomic, ecological and biotechnological studies of the microorganisms. In the present work, the fungal communities of rhizosphere soil of Deschampsia antarctica, soil, ornithogenic soil, marine and lake sedi...

  19. Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils

    NARCIS (Netherlands)

    Hannula, S.E.; van Veen, J.A.

    2016-01-01

    Phylogenetic diversity of soil microbes is a hot topic at the moment. However, the molecular tools for the assessment of functional diversity in the fungal community are less developed than tools based on genes encoding the ribosomal operon. Here 20 sets of primers targeting genes involved mainly in

  20. Belowground ectomycorrhizal fungal communities respond to liming in three southern Swedish coniferous forest stands

    DEFF Research Database (Denmark)

    Kjøller, Rasmus; Clemmensen, Karina

    2009-01-01

    In this study we report on changes in the belowground ectomycorrhizal fungal communities in southern Swedish coniferous forests as a consequence of liming with 3-7 ton limestone per hectare 16 years prior to the study. A total of 107 ectomycorrhizal fungi were identified from 969 independently...

  1. A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest.

    Science.gov (United States)

    Walker, Donald M; Lawrence, Brandy R; Esterline, Dakota; Graham, Sean P; Edelbrock, Michael A; Wooten, Jessica A

    2014-11-01

    The flow of energy within an ecosystem can be considered either top-down, where predators influence consumers, or bottom-up, where producers influence consumers. Plethodon cinereus (Red-backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics-based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.

  2. Anthropization Effects on the Filamentous Fungal Community of the Brazilian Catimbau National Park

    Directory of Open Access Journals (Sweden)

    Roberta Cruz

    2017-08-01

    Full Text Available ABSTRACT The Caatinga biome features an exclusive endemic biodiversity, and is characterized by the presence of xerophytic, deciduous vegetation, high temperatures, and low rainfall. This important park has undergone anthropization, especially through extraction of firewood and timber and growing plants for raising goats. The objectives of this study were to compare the communities of filamentous fungi present in the preserved area and in the anthropized soil of the Catimbau National Park in Buíque, PE, Brazil, and to evaluate the impacts of anthropization on such communities. A total of 12 collections of soil samples were made, six in the preserved area and six in the anthropic area, and the physicochemical properties of the soil samples were analyzed. Fungi were isolated through suspension and serial dilution methods. After growth, the samples were purified and identified based on classical taxonomy, according to specific literature. The diversity, evenness, richness, dominance, frequency, and similarity among the species of filamentous fungi in both areas were assessed based on ecological indexes. A total of 4,488 colony-forming units of filamentous fungi were obtained, which were distributed into 65 species belonging to 15 genera. In the preserved area, higher abundance and richness of species were observed, with predominance of the genera Aspergillus and Penicillium. In both areas, diversity and equitability were high, demonstrating that the species are well distributed in these areas. In the preserved area, the dominant genera were Aspergillus, Gongronella, and Penicillium, whereas Aspergillus was the dominant genus in the anthropic area. Two distinct communities were observed in the areas analyzed. Principal component analysis showed that Penicillium simplicissimum influences the total diversity of both communities. The anthropization that occurred in the Catimbau National Park has changed the composition of the filamentous fungal

  3. Fungal endophytic communities on twigs of fast and slow growing Scots pine (Pinus sylvestris L.) in northern Spain.

    Science.gov (United States)

    Sanz-Ros, Antonio V; Müller, Michael M; San Martín, Roberto; Diez, Julio J

    2015-10-01

    Most plant species harbour a diverse community of endophytic, but their role is still unknown in most cases, including ecologically and economically important tree species. This study describes the culturable fungal endophytic community of Pinus sylvestris L. twigs in northern Spain and its relationship with diametric growth of the host. In all, 360 twig samples were collected from 30 Scots pines in fifteen stands. Isolates were obtained from all twig samples and 43 fungal taxa were identified by morphogrouping and subsequent ITS rDNA sequencing. All isolates were Ascomycetes, being Dothideomycetes and Sordariomycetes the most abundant classes. Half of the species were host generalists while the others were conifer or pine specialists. We found three new endophytic species for the Pinaceae: Biscogniauxia mediterranea, Phaeomoniella effusa and Plectania milleri, and additional six new species for P. sylvestris: Daldinia fissa, Hypocrea viridescens, Nigrospora oryzae, Ophiostoma nigrocarpum, Penicillium melinii and Penicillium polonicum. The endophytic community of fast and slow growing trees showed differences in species composition, abundance and evenness, but not in diversity. Phoma herbarum was associated to fast growing trees and Hypocrea lixii to those growing slow. Our results support the hypothesis that some endophytic species may affect growth of P. sylvestris.

  4. Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

    Science.gov (United States)

    Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris; Belnap, Jayne; Kuske, Cheryl R.

    2013-01-01

    Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO2 Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO2 did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.

  5. Light structures phototroph, bacterial and fungal communities at the soil surface.

    Directory of Open Access Journals (Sweden)

    Lawrence O Davies

    Full Text Available The upper few millimeters of soil harbour photosynthetic microbial communities that are structurally distinct from those of underlying bulk soil due to the presence of light. Previous studies in arid zones have demonstrated functional importance of these communities in reducing soil erosion, and enhancing carbon and nitrogen fixation. Despite being widely distributed, comparative understanding of the biodiversity of the soil surface and underlying soil is lacking, particularly in temperate zones. We investigated the establishment of soil surface communities on pasture soil in microcosms exposed to light or dark conditions, focusing on changes in phototroph, bacterial and fungal communities at the soil surface (0-3 mm and bulk soil (3-12 mm using ribosomal marker gene analyses. Microbial community structure changed with time and structurally similar phototrophic communities were found at the soil surface and in bulk soil in the light exposed microcosms suggesting that light can influence phototroph community structure even in the underlying bulk soil. 454 pyrosequencing showed a significant selection for diazotrophic cyanobacteria such as Nostoc punctiforme and Anabaena spp., in addition to the green alga Scenedesmus obliquus. The soil surface also harboured distinct heterotrophic bacterial and fungal communities in the presence of light, in particular, the selection for the phylum Firmicutes. However, these light driven changes in bacterial community structure did not extend to the underlying soil suggesting a discrete zone of influence, analogous to the rhizosphere.

  6. Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B [ORNL; Schadt, Christopher Warren [ORNL; Palumbo, Anthony Vito [ORNL; Ansley, R J [Texas A& M University; Boutton, Thomas W [Texas A& M University

    2010-01-01

    In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

  7. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community.

    Science.gov (United States)

    Raja, Huzefa A; Miller, Andrew N; Pearce, Cedric J; Oberlies, Nicholas H

    2017-03-24

    Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.

  8. Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities.

    Science.gov (United States)

    Traven, Ana; Jänicke, Amrei; Harrison, Paul; Swaminathan, Angavai; Seemann, Torsten; Beilharz, Traude H

    2012-01-01

    Understanding multicellular fungal structures is important for designing better strategies against human fungal pathogens. For example, the ability to form multicellular biofilms is a key virulence property of the yeast Candida albicans. C. albicans biofilms form on indwelling medical devices and are drug resistant, causing serious infections in hospital settings. Multicellular fungal communities are heterogeneous, consisting of cells experiencing different environments. Heterogeneity is likely important for the phenotypic characteristics of communities, yet it is poorly understood. Here we used colonies of the yeast Saccharomyces cerevisiae as a model fungal multicellular structure. We fractionated the outside colony layers from the cells in the center by FACS, using a Cit1-GFP marker expressed exclusively on the outside. Transcriptomics analysis of the two subpopulations revealed that the outside colony layers are actively growing by fermentative metabolism, while the cells residing on the inside are in a resting state and experience changes to mitochondrial activity. Our data shows several parallels with C. albicans biofilms providing insight into the contributions of heterogeneity to biofilm phenotypes. Hallmarks of C. albicans biofilms - the expression of ribosome and translation functions and activation of glycolysis and ergosterol biosynthesis occur on the outside of colonies, while expression of genes associates with sulfur assimilation is observed in the colony center. Cell wall restructuring occurs in biofilms, and cell wall functions are enriched in both fractions: the outside cells display enrichment of cell wall biosynthesis enzymes and cell wall proteins, while the inside cells express cell wall degrading enzymes. Our study also suggests that noncoding transcription and posttranscriptional mRNA regulation play important roles during growth of yeast in colonies, setting the scene for investigating these pathways in the development of multicellular

  9. Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities.

    Directory of Open Access Journals (Sweden)

    Ana Traven

    Full Text Available Understanding multicellular fungal structures is important for designing better strategies against human fungal pathogens. For example, the ability to form multicellular biofilms is a key virulence property of the yeast Candida albicans. C. albicans biofilms form on indwelling medical devices and are drug resistant, causing serious infections in hospital settings. Multicellular fungal communities are heterogeneous, consisting of cells experiencing different environments. Heterogeneity is likely important for the phenotypic characteristics of communities, yet it is poorly understood. Here we used colonies of the yeast Saccharomyces cerevisiae as a model fungal multicellular structure. We fractionated the outside colony layers from the cells in the center by FACS, using a Cit1-GFP marker expressed exclusively on the outside. Transcriptomics analysis of the two subpopulations revealed that the outside colony layers are actively growing by fermentative metabolism, while the cells residing on the inside are in a resting state and experience changes to mitochondrial activity. Our data shows several parallels with C. albicans biofilms providing insight into the contributions of heterogeneity to biofilm phenotypes. Hallmarks of C. albicans biofilms - the expression of ribosome and translation functions and activation of glycolysis and ergosterol biosynthesis occur on the outside of colonies, while expression of genes associates with sulfur assimilation is observed in the colony center. Cell wall restructuring occurs in biofilms, and cell wall functions are enriched in both fractions: the outside cells display enrichment of cell wall biosynthesis enzymes and cell wall proteins, while the inside cells express cell wall degrading enzymes. Our study also suggests that noncoding transcription and posttranscriptional mRNA regulation play important roles during growth of yeast in colonies, setting the scene for investigating these pathways in the development

  10. Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica.

    Science.gov (United States)

    Godinho, Valéria M; Gonçalves, Vívian N; Santiago, Iara F; Figueredo, Hebert M; Vitoreli, Gislaine A; Schaefer, Carlos E G R; Barbosa, Emerson C; Oliveira, Jaquelline G; Alves, Tânia M A; Zani, Carlos L; Junior, Policarpo A S; Murta, Silvane M F; Romanha, Alvaro J; Kroon, Erna Geessien; Cantrell, Charles L; Wedge, David E; Duke, Stephen O; Ali, Abbas; Rosa, Carlos A; Rosa, Luiz H

    2015-05-01

    We surveyed the diversity and capability of producing bioactive compounds from a cultivable fungal community isolated from oligotrophic soil of continental Antarctica. A total of 115 fungal isolates were obtained and identified in 11 taxa of Aspergillus, Debaryomyces, Cladosporium, Pseudogymnoascus, Penicillium and Hypocreales. The fungal community showed low diversity and richness, and high dominance indices. The extracts of Aspergillus sydowii, Penicillium allii-sativi, Penicillium brevicompactum, Penicillium chrysogenum and Penicillium rubens possess antiviral, antibacterial, antifungal, antitumoral, herbicidal and antiprotozoal activities. Bioactive extracts were examined using (1)H NMR spectroscopy and detected the presence of secondary metabolites with chemical shifts. Our results show that the fungi present in cold-oligotrophic soil from Antarctica included few dominant species, which may have important implications for understanding eukaryotic survival in cold-arid oligotrophic soils. We hypothesize that detailed further investigations may provide a greater understanding of the evolution of Antarctic fungi and their relationships with other organisms described in that region. Additionally, different wild pristine bioactive fungal isolates found in continental Antarctic soil may represent a unique source to discover prototype molecules for use in drug and biopesticide discovery studies.

  11. Molecular diversity of fungal and bacterial communities in the marine sponge Dragmacidon reticulatum.

    Science.gov (United States)

    Passarini, Michel R Z; Miqueletto, Paula B; de Oliveira, Valéria M; Sette, Lara D

    2015-02-01

    The present work aimed to investigate the diversity of bacteria and filamentous fungi of southern Atlantic Ocean marine sponge Dragmacidon reticulatum using cultivation-independent approaches. Fungal ITS rDNA and 18S gene analyses (DGGE and direct sequencing approaches) showed the presence of representatives of three order (Polyporales, Malasseziales, and Agaricales) from the phylum Basidiomycota and seven orders belonging to the phylum Ascomycota (Arthoniales, Capnodiales, Dothideales, Eurotiales, Hypocreales, Pleosporales, and Saccharomycetales). On the other hand, bacterial 16S rDNA gene analyses by direct sequencing approach revealed the presence of representatives of seven bacterial phyla (Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Lentisphaerae, Chloroflexi, and Planctomycetes). Results from statistical analyses (rarefaction curves) suggested that the sampled clones covered the fungal diversity in the sponge samples studied, while for the bacterial community additional sampling would be necessary for saturation. This is the first report related to the molecular analyses of fungal and bacterial communities by cultivation-independent approaches in the marine sponges D. reticulatum. Additionally, the present work broadening the knowledge of microbial diversity associated to marine sponges and reports innovative data on the presence of some fungal genera in marine samples. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Diversity of soil fungal communities of Cerrado and its closely surrounding agriculture fields.

    Science.gov (United States)

    de Castro, Alinne Pereira; Quirino, Betania Ferraz; Pappas, Georgios; Kurokawa, Adriane Silva; Neto, Eduardo Leonardecz; Krüger, Ricardo Henrique

    2008-08-01

    Cerrado is a savanna-like region that covers a large area of Brazil. Despite its biological importance, the Cerrado has been the focus of few microbial diversity studies. A molecular approach was chosen to characterize the soil fungal communities in four areas of the Cerrado biome: a native Cerrado, a riverbank forest, an area converted to a soybean plantation, and an area converted to pasture. Global diversity of fungal communities in each area was assessed through Ribosomal intergenic spacer analysis which revealed remarkable differences among the areas studied. Sequencing of approximately 200 clones containing 18S rDNA sequences from each library was performed and, according to the genetic distance between sequences, these were assigned to operational taxonomic units (OTUs). A total of 75, 85, 85, and 70 OTUs were identified for the native Cerrado, riverbank forest, pasture, and soybean plantation, respectively. Analysis of sequences using a similarity cutoff value of 1% showed that the number of OTUs for the native Cerrado area was reduced by 35%; for the soybean plantation, a reduction by more than 50% was observed, indicating a reduction in fungal biodiversity associated with anthropogenic activity. This is the first study demonstrating the anthropogenic impact on Cerrado soil fungal diversity.

  13. Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities

    Science.gov (United States)

    Nawaz, Ali; Purahong, Witoon; Lehmann, Robert; Herrmann, Martina; Küsel, Kirsten; Totsche, Kai U.; Buscot, François; Wubet, Tesfaye

    2016-01-01

    Fungi are one important group of eukaryotic microorganisms in a diverse range of ecosystems, but their diversity in groundwater ecosystems is largely unknown. We used DNA-based pyro-tag sequencing of the fungal internal transcribed spacer (ITS) rDNA gene to investigate the presence and community structure of fungi at different sampling sites of two superimposed limestone aquifers ranging from 8.5 to 84 m depth in the newly established Hainich Critical Zone Exploratory (Hainich CZE). We detected a diversity of fungal OTUs in groundwater samples of all sampling sites. The relative percentage abundance of Basidiomycota was higher in the upper aquifer assemblage, whilst Ascomycota dominated the lower one. In parallel to differences in the hydrochemistry we found distinct fungal communities at all sampling sites. Classification into functional groups revealed an overwhelming majority of saprotrophs. Finding taxa common to all analyzed groundwater sites, point to a groundwater specific fungal microbiome. The presence of different functional groups and, in particular plant and cattle pathogens that are not typical of subsurface habitats, suggests links between the surface and subsurface biogeosphere due to rapid transportation across the fracture networks typical of karstic regions during recharge episodes. However, further studies including sampling series extended in both time and space are necessary to confirm this hypothesis. PMID:27242696

  14. Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

    Science.gov (United States)

    Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

    2017-01-01

    Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  15. Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

    Science.gov (United States)

    David, Aaron S; Seabloom, Eric W; May, Georgiana

    2016-05-01

    Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

  16. Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

    Science.gov (United States)

    Barnes, Christopher J.; Maldonado, Carla; Frøslev, Tobias G.; Antonelli, Alexandre; Rønsted, Nina

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography in regulating fungal community assembly. We show that α-diversity for these fungal communities was similar to temperate and arid ecosystems, averaging 90.1 operational taxonomic units (OTUs) per sample, with reads predominantly assigned to the Ascomycota phylum and with a saprotrophic lifestyle. ß-diversity was calculated as the distance-decay rate, and in contrast to α-diversity, was exceptionally high with a rate of −0.407. Soil properties (pH and P) principally regulated fungal community assembly in an analogous manner to temperate environments, with pH and phosphorus explaining 7.8 and 7.2% of community variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's “hidden biodiversity.” PMID:27630629

  17. Moisture parameters and fungal communities associated with gypsum drywall in buildings.

    Science.gov (United States)

    Dedesko, Sandra; Siegel, Jeffrey A

    2015-12-08

    Uncontrolled excess moisture in buildings is a common problem that can lead to changes in fungal communities. In buildings, moisture parameters can be classified by location and include assessments of moisture in the air, at a surface, or within a material. These parameters are not equivalent in dynamic indoor environments, which makes moisture-induced fungal growth in buildings a complex occurrence. In order to determine the circumstances that lead to such growth, it is essential to have a thorough understanding of in situ moisture measurement, the influence of building factors on moisture parameters, and the levels of these moisture parameters that lead to indoor fungal growth. Currently, there are disagreements in the literature on this topic. A literature review was conducted specifically on moisture-induced fungal growth on gypsum drywall. This review revealed that there is no consistent measurement approach used to characterize moisture in laboratory and field studies, with relative humidity measurements being most common. Additionally, many studies identify a critical moisture value, below which fungal growth will not occur. The values defined by relative humidity encompassed the largest range, while those defined by moisture content exhibited the highest variation. Critical values defined by equilibrium relative humidity were most consistent, and this is likely due to equilibrium relative humidity being the most relevant moisture parameter to microbial growth, since it is a reasonable measure of moisture available at surfaces, where fungi often proliferate. Several sources concur that surface moisture, particularly liquid water, is the prominent factor influencing microbial changes and that moisture in the air and within a material are of lesser importance. However, even if surface moisture is assessed, a single critical moisture level to prevent fungal growth cannot be defined, due to a number of factors, including variations in fungal genera and

  18. Using molecular biology to study mycorrhizal fungal community ecology: Limits and perspectives.

    Science.gov (United States)

    Chagnon, Pierre-Luc; Bainard, Luke D

    2015-01-01

    Molecular tools have progressively replaced morphological approaches to characterize microbial communities in nature. Arbuscular mycorrhizal (AM) fungi are no exception to this rule. Yet, one challenge posed by these symbionts is that they colonize simultaneously both plant roots and soil, which complicates their detection and quantification. In most studies conducted to date, AM fungal communities have been characterized from roots only, soil only or spores only. Here, we discuss the pitfalls associated to drawing ecological inferences using such datasets. We also conclude by arguing that molecular biology will contribute most to advance knowledge in AM fungal ecology if it is integrated into broader perspectives taking into account the natural history of these organisms. This calls for a better merging of molecular and morphological approaches, and the establishment of intensive, long-term research programs.

  19. Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing

    Directory of Open Access Journals (Sweden)

    Lindsay Kalan

    2016-09-01

    Full Text Available Chronic nonhealing wounds have been heralded as a silent epidemic, causing significant morbidity and mortality especially in elderly, diabetic, and obese populations. Polymicrobial biofilms in the wound bed are hypothesized to disrupt the highly coordinated and sequential events of cutaneous healing. Both culture-dependent and -independent studies of the chronic-wound microbiome have almost exclusively focused on bacteria, omitting what we hypothesize are important fungal contributions to impaired healing and the development of complications. Here we show for the first time that fungal communities (the mycobiome in chronic wounds are predictive of healing time, associated with poor outcomes, and form mixed fungal-bacterial biofilms. We longitudinally profiled 100, nonhealing diabetic-foot ulcers with high-throughput sequencing of the pan-fungal internal transcribed spacer 1 (ITS1 locus, estimating that up to 80% of wounds contain fungi, whereas cultures performed in parallel captured only 5% of colonized wounds. The “mycobiome” was highly heterogeneous over time and between subjects. Fungal diversity increased with antibiotic administration and onset of a clinical complication. The proportions of the phylum Ascomycota were significantly greater (P = 0.015 at the beginning of the study in wounds that took >8 weeks to heal. Wound necrosis was distinctly associated with pathogenic fungal species, while taxa identified as allergenic filamentous fungi were associated with low levels of systemic inflammation. Directed culturing of wounds stably colonized by pathogens revealed that interkingdom biofilms formed between yeasts and coisolated bacteria. Combined, our analyses provide enhanced resolution of the mycobiome during impaired wound healing, its role in chronic disease, and impact on clinical outcomes.

  20. Development and validation of an oligonucleotide microarray to characterise ectomycorrhizal fungal communities

    Directory of Open Access Journals (Sweden)

    Reich Marlis

    2009-01-01

    Full Text Available Abstract Background In forest ecosystems, communities of ectomycorrhizal fungi (ECM are influenced by several biotic and abiotic factors. To understand their underlying dynamics, ECM communities have been surveyed with ribosomal DNA-based sequencing methods. However, most identification methods are both time-consuming and limited by the number of samples that can be treated in a realistic time frame. As a result of ongoing implementation, the array technique has gained throughput capacity in terms of the number of samples and the capacity for parallel identification of several species. Thus far, although phylochips (microarrays that are used to detect species have been mostly developed to trace bacterial communities or groups of specific fungi, no phylochip has been developed to carry oligonucleotides for several ectomycorrhizal species that belong to different genera. Results We have constructed a custom ribosomal DNA phylochip to identify ECM fungi. Specific oligonucleotide probes were targeted to the nuclear internal transcribed spacer (ITS regions from 95 fungal species belonging to 21 ECM fungal genera. The phylochip was first validated using PCR amplicons of reference species. Ninety-nine percent of the tested oligonucleotides generated positive hybridisation signals with their corresponding amplicons. Cross-hybridisation was mainly restricted at the genus level, particularly for Cortinarius and Lactarius species. The phylochip was subsequently tested with environmental samples that were composed of ECM fungal DNA from spruce and beech plantation fungal communities. The results were in concordance with the ITS sequencing of morphotypes and the ITS clone library sequencing results that were obtained using the same PCR products. Conclusion For the first time, we developed a custom phylochip that is specific for several ectomycorrhizal fungi. To overcome cross-hybridisation problems, specific filter and evaluation strategies that used spot

  1. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    Energy Technology Data Exchange (ETDEWEB)

    Widenfalk, Anneli [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)], E-mail: anneli.widenfalk@kemi.se; Bertilsson, Stefan [Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 20, SE-752 36 Uppsala (Sweden); Sundh, Ingvar [Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07 Uppsala (Sweden); Goedkoop, Willem [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)

    2008-04-15

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points.

  2. Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland.

    Science.gov (United States)

    Eldridge, David J; Woodhouse, Jason N; Curlevski, Nathalie J A; Hayward, Matthew; Brown, Mark V; Neilan, Brett A

    2015-12-01

    Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance.

  3. Land-use change and soil type are drivers of fungal and archaeal communities in the Pampa biome.

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    Lupatini, Manoeli; Jacques, Rodrigo Josemar Seminoti; Antoniolli, Zaida Inês; Suleiman, Afnan Khalil Ahmad; Fulthorpe, Roberta R; Roesch, Luiz Fernando Würdig

    2013-02-01

    The current study aimed to test the hypothesis that both land-use change and soil type are responsible for the major changes in the fungal and archaeal community structure and functioning of the soil microbial community in Brazilian Pampa biome. Soil samples were collected at sites with different land-uses (native grassland, native forest, Eucalyptus and Acacia plantation, soybean and watermelon field) and in a typical toposequence in Pampa biome formed by Paleudult, Albaqualf and alluvial soils. The structure of soil microbial community (archaeal and fungal) was evaluated by ribosomal intergenic spacer analysis and soil functional capabilities were measured by microbial biomass carbon and metabolic quotient. We detected different patterns in microbial community driven by land-use change and soil type, showing that both factors are significant drivers of fungal and archaeal community structure and biomass and microbial activity. Fungal community structure was more affected by land-use and archaeal community was more affected by soil type. Irrespective of the land-use or soil type, a large percentage of operational taxonomic unit were shared among the soils. We accepted the hypothesis that both land-use change and soil type are drivers of archaeal and fungal community structure and soil functional capabilities. Moreover, we also suggest the existence of a soil microbial core.

  4. Rapid change of AM fungal community in a rain-fed wheat field with short-term plastic film mulching practice.

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    Liu, Yongjun; Mao, Lin; He, Xinhua; Cheng, Gang; Ma, Xiaojun; An, Lizhe; Feng, Huyuan

    2012-01-01

    Plastic film mulching (PFM) is a widely used agricultural practice in the temperate semi-arid Loess Plateau of China. However, how beneficial soil microbes, arbuscular mycorrhizal (AM) fungi in particular, respond to the PFM practice is not known. Here, a field experiment was performed to study the effects of a 3-month short-term PFM practice on AM fungi in plots planted with spring wheat (Triticum aestivum L. cv. Dingxi-2) in the Loess Plateau. AM colonization, spore density, wheat spike weight, and grain phosphorus (P) content were significantly increased in the PFM treatments, and these changes were mainly attributable to changes in soil properties such as available P and soil moisture. Alkaline phosphatase activity was significantly higher in PFM soils, but levels of AM fungal-related glomalin were similar between treatments. A total of nine AM fungal phylotypes were detected in root samples based on AM fungal SSU rDNA analyses, with six and five phylotypes in PFM and no-PFM plots, respectively. Although AM fungal phylotype richness was not statistically different between treatments, the community compositions were different, with four and three specific phylotypes in the PFM and no-PFM plots, respectively. A significant and rapid change in AM fungal, wheat, and soil variables following PFM suggested that the functioning of the AM symbiosis had been changed in the wheat field under PFM. Future studies are needed to investigate whether PFM applied over a longer term has a similar effect on the AM fungal community and their functioning in an agricultural ecosystem.

  5. Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

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    Akihiro eKoyama

    2014-10-01

    Full Text Available The pool of soil organic carbon (SOC in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-proteobacteria and β-proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming.

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

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    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.

  7. High compatibility between arbuscular mycorrhizal fungal communities and seedlings of different land use types in a tropical dry ecosystem.

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    Gavito, Mayra E; Pérez-Castillo, Daniel; González-Monterrubio, César F; Vieyra-Hernández, Teresa; Martínez-Trujillo, Miguel

    2008-12-01

    We conducted this study to explore limitations for the establishment of mycorrhizal associations in disturbed areas of the tropical dry ecosystem in the Chamela region of Jalisco, Mexico. Specifically, we: (1) assessed the diversity and composition of arbuscular mycorrhizal fungal (AMF) communities through spore morphospecies identification in three common land uses (primary forest, secondary forest, and pasture), (2) tested the inoculum potential of the AMF communities and the effect of water stress on the establishment of mycorrhizal associations in seedlings of various plant species, and (3) explored the importance of AMF community composition on early seedling development. Soil and root samples were taken from 15 random points in each of three plots established in two primary forests, two 26-year-old secondary forests, and two 26-year-old pastures. We expected that because of soil degradation and management, pastures would have the lowest and primary forests the highest AMF species richness. We found evidence for changes in AMF species composition due to land use and for higher morphospecies richness in primary forests than in secondary forests and pastures. We expected also that water stress limited plant and mycorrhizal development and that plants and AMF communities from secondary forests and pastures would be less affected by (better adapted to) water stress than those from the primary forest. We found that although all plant species showed biomass reductions under water stress, only some of the plant species had lower mycorrhizal development under water stress, and this was regardless of the AMF community inoculated. The third hypothesis was that plant species common to all land use types would respond similarly to all AMF communities, whereas plant species found mainly in one land use type would grow better when inoculated with the AMF community of that specific land use type. All plant species were however equally responsive to the three AMF communities

  8. Soil fungal community shift evaluation as a potential cadaver decomposition indicator.

    Science.gov (United States)

    Chimutsa, Monica; Olakanye, Ayodeji O; Thompson, Tim J U; Ralebitso-Senior, T Komang

    2015-12-01

    Fungi metabolise organic matter in situ and so alter both the bio-/physico-chemical properties and microbial community structure of the ecosystem. In particular, they are responsible reportedly for specific stages of decomposition. Therefore, this study aimed to extend previous bacteria-based forensic ecogenomics research by investigating soil fungal community and cadaver decomposition interactions in microcosms with garden soil (20 kg, fresh weight) and domestic pig (Sus scrofa domesticus) carcass (5 kg, leg). Soil samples were collected at depths of 0-10 cm, 10-20 cm and 20-30 cm on days 3, 28 and 77 in the absence (control -Pg) and presence (experimental +Pg) of Sus scrofa domesticus and used for total DNA extraction and nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) profiling of the 18S rRNA gene. The Shannon-Wiener (H') community diversity indices were 1.25±0.21 and 1.49±0.30 for the control and experimental microcosms, respectively, while comparable Simpson species dominance (S) values were 0.65±0.109 and 0.75±0.015. Generally, and in contrast to parallel studies of the bacterial 16S rRNA and 16S rDNA profiles, statistical analysis (t-test) of the 18S dynamics showed no mathematically significant shifts in fungal community diversity (H'; p=0.142) and dominance (S; p=0.392) during carcass decomposition, necessitating further investigations.

  9. High diversity of the fungal community structure in naturally-occurring Ophiocordyceps sinensis.

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    Yongjie Zhang

    Full Text Available BACKGROUND: Ophiocordyceps sinensis (syn. Cordyceps sinensis, which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable medicinal fungi in the world. "Natural O. sinensis specimens" harbor various other fungi. Several of these other fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS: Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP, the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. CONCLUSIONS/SIGNIFICANCE: A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our

  10. Molecular profiling of fungal communities in moisture damaged buildings before and after remediation - a comparison of culture-dependent and culture-independent methods

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    Auvinen Petri

    2011-10-01

    Full Text Available Abstract Background Indoor microbial contamination due to excess moisture is an important contributor to human illness in both residential and occupational settings. However, the census of microorganisms in the indoor environment is limited by the use of selective, culture-based detection techniques. By using clone library sequencing of full-length internal transcribed spacer region combined with quantitative polymerase chain reaction (qPCR for 69 fungal species or assay groups and cultivation, we have been able to generate a more comprehensive description of the total indoor mycoflora. Using this suite of methods, we assessed the impact of moisture damage on the fungal community composition of settled dust and building material samples (n = 8 and 16, correspondingly. Water-damaged buildings (n = 2 were examined pre- and post- remediation, and compared with undamaged reference buildings (n = 2. Results Culture-dependent and independent methods were consistent in the dominant fungal taxa in dust, but sequencing revealed a five to ten times higher diversity at the genus level than culture or qPCR. Previously unknown, verified fungal phylotypes were detected in dust, accounting for 12% of all diversity. Fungal diversity, especially within classes Dothideomycetes and Agaricomycetes tended to be higher in the water damaged buildings. Fungal phylotypes detected in building materials were present in dust samples, but their proportion of total fungi was similar for damaged and reference buildings. The quantitative correlation between clone library phylotype frequencies and qPCR counts was moderate (r = 0.59, p Conclusions We examined a small number of target buildings and found indications of elevated fungal diversity associated with water damage. Some of the fungi in dust were attributable to building growth, but more information on the material-associated communities is needed in order to understand the dynamics of microbial communities between

  11. Neighboring Deschampsia flexuosa and Trientalis europaea harbor contrasting root fungal endophytic communities.

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    Tejesvi, Mysore V; Sauvola, Tiina; Pirttilä, Anna Maria; Ruotsalainen, Anna Liisa

    2013-01-01

    Fungal endophytic communities and potential host preference of root-inhabiting fungi of boreal forest understory plants are poorly known. The objective of this study was to find out whether two neighboring plant species, Deschampsia flexuosa (Poaceae) and Trientalis europaea (Primulaceae), share similar root fungal endophytic communities and whether the communities differ between two sites. The study was carried out by analysis of pure culture isolates and root fungal colonization percentages. A total of 84 isolates from D. flexuosa and 27 isolates from T. europaea were obtained. The roots of D. flexuosa harbored 16 different isolate types based on macromorphological characteristics, whereas only 4 isolate types were found in T. europaea. The root colonization by dark septate and hyaline septate hyphae correlated with isolate numbers being higher in D. flexuosa compared to T. europaea. The different isolate types were further identified on the basis of internal transcribed spacer sequence and phylogenetic analysis. An isolate type identified as dark septate endophyte Phialocephala fortinii colonized 50 % of the T. europaea and 21 % of the D. flexuosa specimens. In addition, Meliniomyces variabilis, Phialocephala sphaeroides, and Umbelopsis isabellina were found colonizing the grass, D. flexuosa, for the first time and Mycena sp. was confirmed as an endophyte of D. flexuosa. Site-specific differences were observed in the abundance and diversity of endophytic fungi in the roots of both study plants, but the differences were not as predominant as those between plant species. It is concluded that D. flexuosa harbors both higher amount and more diverse community of endophytic fungi in its roots compared to T. europaea.

  12. Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.

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    Alan J Marsh

    Full Text Available Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

  13. Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources.

    Science.gov (United States)

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2013-01-01

    Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

  14. Different degrees of plant invasion significantly affect the richness of the soil fungal community.

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    Chuncan Si

    Full Text Available Several studies have shown that soil microorganisms play a key role in the success of plant invasion. Thus, ecologists have become increasingly interested in understanding the ecological effects of biological invasion on soil microbial communities given continuing increase in the effects of invasive plants on native ecosystems. This paper aims to provide a relatively complete depiction of the characteristics of soil microbial communities under different degrees of plant invasion. Rhizospheric soils of the notorious invasive plant Wedelia trilobata with different degrees of invasion (uninvaded, low-degree, and high-degree using its coverage in the invaded ecosystems were collected from five discrete areas in Hainan Province, P. R. China. Soil physicochemical properties and community structure of soil microorganisms were assessed. Low degrees of W. trilobata invasion significantly increased soil pH values whereas high degrees of invasion did not significantly affected soil pH values. Moreover, the degree of W. trilobata invasion exerted significant effects on soil Ca concentration but did not significantly change other indices of soil physicochemical properties. Low and high degrees of W. trilobata invasion increased the richness of the soil fungal community but did not pose obvious effects on the soil bacterial community. W. trilobata invasion also exerted obvious effects on the community structure of soil microorganisms that take part in soil nitrogen cycling. These changes in soil physicochemical properties and community structure of soil microbial communities mediated by different degrees of W. trilobata invasion may present significant functions in further facilitating the invasion process.

  15. Different degrees of plant invasion significantly affect the richness of the soil fungal community.

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    Si, Chuncan; Liu, Xueyan; Wang, Congyan; Wang, Lei; Dai, Zhicong; Qi, Shanshan; Du, Daolin

    2013-01-01

    Several studies have shown that soil microorganisms play a key role in the success of plant invasion. Thus, ecologists have become increasingly interested in understanding the ecological effects of biological invasion on soil microbial communities given continuing increase in the effects of invasive plants on native ecosystems. This paper aims to provide a relatively complete depiction of the characteristics of soil microbial communities under different degrees of plant invasion. Rhizospheric soils of the notorious invasive plant Wedelia trilobata with different degrees of invasion (uninvaded, low-degree, and high-degree using its coverage in the invaded ecosystems) were collected from five discrete areas in Hainan Province, P. R. China. Soil physicochemical properties and community structure of soil microorganisms were assessed. Low degrees of W. trilobata invasion significantly increased soil pH values whereas high degrees of invasion did not significantly affected soil pH values. Moreover, the degree of W. trilobata invasion exerted significant effects on soil Ca concentration but did not significantly change other indices of soil physicochemical properties. Low and high degrees of W. trilobata invasion increased the richness of the soil fungal community but did not pose obvious effects on the soil bacterial community. W. trilobata invasion also exerted obvious effects on the community structure of soil microorganisms that take part in soil nitrogen cycling. These changes in soil physicochemical properties and community structure of soil microbial communities mediated by different degrees of W. trilobata invasion may present significant functions in further facilitating the invasion process.

  16. Response of compost maturity and microbial community composition to pentachlorophenol (PCP)-contaminated soil during composting.

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    Zeng, Guangming; Yu, Zhen; Chen, Yaoning; Zhang, Jiachao; Li, Hui; Yu, Man; Zhao, Mingjie

    2011-05-01

    Two composting piles were prepared by adding to a mixture of rice straw, vegetables and bran: (i) raw soil free from pentachlorophenol (PCP) contamination (pile A) and (ii) PCP-contaminated soil (pile B). It was shown by the results that compost maturity characterized by water soluble carbon (WSC), TOC/TN ratio, germination index (GI) and dehydrogenase activity (DA) was significantly affected by PCP exposure, which resulted in an inferior degree of maturity for pile B. DGGE analysis revealed an inhibited effect of PCP on compost microbial abundance. The bacteria community shifts were mainly consistent with composting factors such as temperature, pH, moisture content and substrates. By contrast, the fungal communities were more sensitive to PCP contamination due to the significant correlation between fungal community shifts and PCP removal. Therefore, the different microbial community compositions for properly evaluating the degree of maturity and PCP contamination were suggested.

  17. Dysbiotic bacterial and fungal communities not restricted to clinically affected skin sites in dandruff

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    Renan Cardoso Soares

    2016-11-01

    Full Text Available Dandruff is a prevalent chronic inflammatory skin condition of the scalp that has been associated with Malassezia yeasts. However, the microbial role has not been elucidated yet, and the etiology of the disorder remains poorly understood. Using high-throughput 16S rDNA and ITS1 sequencing, we characterized cutaneous bacterial and fungal microbiotas from healthy and dandruff subjects, comparing scalp and forehead (lesional and non-lesional skin sites. Bacterial and fungal communities from dandruff analyzed at genus level differed in comparison with healthy ones, presenting higher diversity and greater intragroup variation. The microbial shift was observed also in non-lesional sites from dandruff subjects, suggesting that dandruff is related to a systemic process that is not restricted to the site exhibiting clinical symptoms. In contrast, Malassezia microbiota analyzed at species level did not differ according to health status. A 2-step OTU assignment using combined databases substantially increased fungal assigned sequences, and revealed the presence of highly prevalent uncharacterized Malassezia organisms (>37% of the reads. Although clinical symptoms of dandruff manifest locally, microbial dysbiosis beyond clinically affected skin sites suggests that subjects undergo systemic alterations, which could be considered for redefining therapeutic approaches.

  18. Fungal communities of the rhizosphere and the rhizoplane of yellow lupine in a crop rotation system

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    Bożena Cwalina-Abroziak

    2014-08-01

    Full Text Available Fungal community populating the rhizosphere and lhe rhizoplane of yellow lupine Juno and Markiz cultivated in the crop rotation with the 20% and 33% portion of lupine was analyzed. The total fungus number was reduced when the participation of lupine in the crop rotation was established at level 20%. Then the pathogenic fungi were replaced by more frequently appeared saprofitic species representing the following genera: Trichoderma, Paecilomyces and Penicillium. Pathogenic Fusarium were more frequently isolated from the lupine rhizoplane cultivated in combination with its 33% participation.

  19. Mycorrhizal fungal communities respond to experimental elevation of soil pH and P availability in temperate hardwood forests.

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    Carrino-Kyker, Sarah R; Kluber, Laurel A; Petersen, Sheryl M; Coyle, Kaitlin P; Hewins, Charlotte R; DeForest, Jared L; Smemo, Kurt A; Burke, David J

    2016-03-01

    Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here, we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454-pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.

  20. Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists.

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    Kawahara, Ai; An, Gi-Hong; Miyakawa, Sachie; Sonoda, Jun; Ezawa, Tatsuhiro

    2016-01-01

    Soil acidity is a major constraint on plant productivity. Arbuscular mycorrhizal (AM) fungi support plant colonization in acidic soil, but soil acidity also constrains fungal growth and diversity. Fungi in extreme environments generally evolve towards specialists, suggesting that AM fungi in acidic soil are acidic-soil specialists. In our previous surveys, however, some AM fungi detected in strongly acidic soils could also be detected in a soil with moderate pH, which raised a hypothesis that the fungi in acidic soils are pH generalists. To test the hypothesis, we conducted a pH-manipulation experiment and also analyzed AM fungal distribution along a pH gradient in the field using a synthesized dataset of the previous and recent surveys. Rhizosphere soils of the generalist plant Miscanthus sinensis were collected both from a neutral soil and an acidic soil, and M. sinensis seedlings were grown at three different pH. For the analysis of field communities, rhizosphere soils of M. sinensis were collected from six field sites across Japan, which covered a soil pH range of 3.0-7.4, and subjected to soil trap culture. AM fungal community compositions were determined based on LSU rDNA sequences. In the pH-manipulation experiment the acidification of medium had a significant impact on the compositions of the community from the neutral soil, but the neutralization of the medium had no effect on those of the community from the acidic soil. Furthermore, the communities in lower -pH soils were subsets of (nested in) those in higher-pH soils. In the field communities a significant nestedness pattern was observed along the pH gradient. These observations suggest that the fungi in strongly acidic soils are pH generalists that occur not only in acidic soil but also in wide ranges of soil pH. Nestedness in AM fungal community along pH gradients may have important implications for plant community resilience and early primary succession after disturbance in acidic soils.

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

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    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.

  2. Fungal community associated with fermentation and storage of Fuzhuan brick-tea.

    Science.gov (United States)

    Xu, Aiqing; Wang, Yuanliang; Wen, Jieyu; Liu, Ping; Liu, Ziyin; Li, Zongjun

    2011-03-15

    Chinese Fuzhuan brick-tea is a unique microbial fermented tea characterized by a period of fungal growth during its manufacturing process. The aim of the present study was to characterize, both physicochemically and microbiologically, traditional industrial production processes of Fuzhuan brick-tea. Fermenting tea samples were collected from the largest manufacturer. Physicochemical analyses showed that the low water content in the tea substrates provided optimal growth conditions for xerophilic fungi. The fungal communities existing in tea materials, fermenting tea, and stored teas were monitored by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) targeting the D1 region of the 26S rRNA genes, followed by sequencing of the amplicons. Results revealed that the microorganisms were from, or closely related to, the genera Eurotium, Debaryomyces, Aspergillus, Verticillium, Pichia, Pestalotiopsis, Rhizomucor and Beauveria. This is the first report of Debaryomyces participating in the processing of Fuzhuan brick-tea. We concluded that the dominant genera Eurotium, Debaryomyces and Aspergillus are beneficial fungi associated with the fermentation of Fuzhuan brick-tea. The genus Beauveria was present in the stored Fuzhuan brick-tea, which may help protect tea products from insect spoilage. The remaining four genera were of minor importance in the manufacturing of Fuzhuan brick-tea. The predominant Eurotium species, a strain named Eurotium sp. FZ, was phenotypically and genotypically identified as Eurotium cristatum. High performance thin layer chromatography analysis of anthraquinones showed that emodin existed in all the dark tea samples, but physcion was only detectable in the tea fermented by E. cristatum. The PCR-DGGE approach was an effective and convenient means for profiling the fungal communities in Fuzhuan brick-tea. These results may help promote the use of microbial consortia as starter cultures to stabilize and improve the quality

  3. Spatial and temporal escape from fungal parasitism in natural communities of anciently asexual bdelloid rotifers.

    Science.gov (United States)

    Wilson, Christopher G; Sherman, Paul W

    2013-08-22

    Sexual reproduction is costly, but it is nearly ubiquitous among plants and animals, whereas obligately asexual taxa are rare and almost always short-lived. The Red Queen hypothesis proposes that sex overcomes its costs by enabling organisms to keep pace with coevolving parasites and pathogens. If so, the few cases of stable long-term asexuality ought to be found in groups whose coevolutionary interactions with parasites are unusually weak. In theory, antagonistic coevolution will be attenuated if hosts disperse among patches within a metapopulation separately from parasites and more rapidly. We examined whether these conditions are met in natural communities of bdelloid rotifers, one of the longest-lived asexual lineages. At any life stage, these microscopic invertebrates can tolerate the complete desiccation of their ephemeral freshwater habitats, surviving as dormant propagules that are readily carried by the wind. In our field experiments, desiccation and wind transport enabled bdelloids to disperse independently of multiple fungal parasites, in both time and space. Surveys of bdelloid communities in unmanipulated moss patches confirmed that fungal parasitism was negatively correlated with extended drought and increasing height (exposure to wind). Bdelloid ecology therefore matches a key condition of models in which asexuals persist through spatio-temporal decoupling from coevolving enemies.

  4. Stream hydrological fragmentation drives bacterioplankton community composition.

    Directory of Open Access Journals (Sweden)

    Stefano Fazi

    Full Text Available In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow re-convergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain, at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter tightly shaping the bacterioplankton community composition.

  5. Fungal treatment of lignocellulosic biomass: Importance of fungal species, colonization and time on chemical composition and in vitro rumen degradability

    NARCIS (Netherlands)

    Kuijk, van S.J.A.; Sonnenberg, A.S.M.; Baars, J.J.P.; Hendriks, W.H.; Cone, J.W.

    2015-01-01

    The aim of this study is to evaluate fungal treatments to improve in vitro rumen degradability of lignocellulosic biomass. In this study four selective lignin degrading fungi, Ganoderma lucidum, Lentinula edodes, Pleurotus eryngii and Pleurotus ostreatus, were used to pre-treat lignocellulosic bioma

  6. Fungal treatment of lignocellulosic biomass: Importance of fungal species, colonization and time on chemical composition and in vitro rumen degradability

    NARCIS (Netherlands)

    Kuijk, van S.J.A.; Sonnenberg, A.S.M.; Baars, J.J.P.; Hendriks, W.H.; Cone, J.W.

    2015-01-01

    The aim of this study is to evaluate fungal treatments to improve in vitro rumen degradability of lignocellulosic biomass. In this study four selective lignin degrading fungi, Ganoderma lucidum, Lentinula edodes, Pleurotus eryngii and Pleurotus ostreatus, were used to pre-treat lignocellulosic

  7. Effects of sugar beet chitinase IV on root-associated fungal community of transgenic silver birch in a field trial.

    Science.gov (United States)

    Pasonen, Hanna-Leena; Lu, Jinrong; Niskanen, Anna-Maija; Seppänen, Sanna-Kaisa; Rytkönen, Anna; Raunio, Janne; Pappinen, Ari; Kasanen, Risto; Timonen, Sari

    2009-10-01

    Heterogenous chitinases have been introduced in many plant species with the aim to increase the resistance of plants to fungal diseases. We studied the effects of the heterologous expression of sugar beet chitinase IV on the intensity of ectomycorrhizal (ECM) colonization and the structure of fungal communities in the field trial of 15 transgenic and 8 wild-type silver birch (Betula pendula Roth) genotypes. Fungal sequences were separated in denaturing gradient gel electrophoresis and identified by sequencing the ITS1 region to reveal the operational taxonomic units. ECM colonization was less intense in 7 out of 15 transgenic lines than in the corresponding non-transgenic control plants, but the slight decrease in overall ECM colonization in transgenic lines could not be related to sugar beet chitinase IV expression or total endochitinase activity. One transgenic line showing fairly weak sugar beet chitinase IV expression without significantly increased total endochitinase activity differed significantly from the non-transgenic controls in the structure of fungal community. Five sequences belonging to three different fungal genera (Hebeloma, Inocybe, Laccaria) were indicative of wild-type genotypes, and one sequence (Lactarius) indicated one transgenic line. In cluster analysis, the non-transgenic control grouped together with the transgenic lines indicating that genotype was a more important factor determining the structure of fungal communities than the transgenic status of the plants. With the tested birch lines, no clear evidence for the effect of the heterologous expression of sugar beet chitinase IV on ECM colonization or the structure of fungal community was found.

  8. Plant pathogens but not antagonists change in soil fungal communities across a land abandonment gradient in a Mediterranean landscape

    Science.gov (United States)

    Bosso, L.; Lacatena, F.; Varlese, R.; Nocerino, S.; Cristinzio, G.; Russo, D.

    2017-01-01

    We assessed whether the presence and abundance of plant pathogens and antagonists change in soil fungal communities along a land abandonment gradient. The study was carried out in the Cilento area (Southern Italy) at a site with three different habitats found along a land abandonment gradient: agricultural land, Mediterranean shrubland and woodland. For all microbiological substrates the colony forming units were about 3.1 × 106 g-1 soil for agricultural land and about 1.1 × 106 g-1 soil for Mediterranean shrubland and woodland. We found the following genera in all habitats: Cladosporium, Mortierella, Penicillium and Trichoderma. In agricultural land, the significantly most abundant fungus genera were Aspergillus, Fusarium, Cylindrocarpon and Nectria; in Mediterranean shrubland, Rhizopus and Trichoderma; and in woodland, Bionectria, Mortierella, Cladosporium, Diplodia, Paecilomyces, Penicillium and Trichoderma. We found a total of 8, 8 and 9 species of fungal antagonist, and 16, 6 and 6 species of fungal plant pathogens in agricultural land, Mediterranean shrubland and woodland respectively. Fungal plant pathogens decreased significantly over a land abandonment gradient, while we no found significant differences among fungal antagonists in the three habitats. We conclude that a decrease in the number of fungal pathogen species occurs when formerly cultivated areas are abandoned. On the other hand, fungal antagonists seem not to be affected by this process.

  9. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

    Directory of Open Access Journals (Sweden)

    Koen Illeghems

    Full Text Available This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni. Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

  10. Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient.

    Science.gov (United States)

    Geml, József; Pastor, Nicolás; Fernandez, Lisandro; Pacheco, Silvia; Semenova, Tatiana A; Becerra, Alejandra G; Wicaksono, Christian Y; Nouhra, Eduardo R

    2014-05-01

    The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g. agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the entire latitudinal extent of the Yungas in Argentina. The sampled sites represent the three altitudinal forest types: the piedmont (400-700 m a.s.l.), montane (700-1500 m a.s.l.) and montane cloud (1500-3000 m a.s.l.) forests. The deep sequence data presented here (i.e. 4 108 126 quality-filtered sequences) indicate that fungal community composition correlates most strongly with elevation, with many fungi showing preference for a certain altitudinal forest type. For example, ectomycorrhizal and root endophytic fungi were most diverse in the montane cloud forests, particularly at sites dominated by Alnus acuminata, while the diversity values of various saprobic groups were highest at lower elevations. Despite the strong altitudinal community turnover, fungal diversity was comparable across the different zonal forest types. Besides elevation, soil pH, N, P, and organic matter contents correlated with fungal community structure as well, although most of these variables were co-correlated with elevation. Our data provide an unprecedented insight into the high diversity and spatial distribution of fungi in the Yungas forests. © 2014 John Wiley & Sons Ltd.

  11. Ectomycorrhizal Fungal Communities of Red Pine (Pinus densiflora) Seedlings in Disturbed Sites and Undisturbed Old Forest Sites.

    Science.gov (United States)

    Lee, Eun-Hwa; Eom, Ahn-Heum

    2013-06-01

    This study aimed to investigate differences in ectomycorrhizal (ECM) fungal communities between disturbed sites and undisturbed old forest sites. ECM root tips of Pinus densiflora were collected from 4 sites disturbed by human activities and 3 undisturbed old forest sites adjacent to the disturbed sites. Results in this study showed that the number of ECM root tips, species diversity, and number of species were significantly higher in the disturbed sites than in the undisturbed sites, suggesting that the ECM fungal community structure was affected by the degree of disturbance.

  12. Predicting community composition from pairwise interactions

    Science.gov (United States)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

  13. Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition.

    Science.gov (United States)

    Guo, Jingqi; McCulley, Rebecca L; McNear, David H

    2015-01-01

    Tall fescue [Lolium arundinaceum (Schreb.)] is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a shoot-specific fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stresses. Because alkaloids produced by the common variety of the endophyte cause severe animal health issues, focus has been on replacing the common-toxic strain with novel varieties that do not produce the mammal-toxic alkaloids but maintain abiotic and biotic stress tolerance benefits. Little attention has been given to the influence of the plant-fungal symbiosis on rhizosphere processes. Therefore, our objective was to study the influence of this relationship on plant biomass production and root exudate composition in tall fescue cultivars PDF and 97TF1, which were either not infected with the endophyte (E-), infected with the common toxic endophyte (CTE+) strain or with one of two novel endophytes (AR542E+, AR584E+). Plants were grown sterile for 3 weeks after which plant biomass, total organic carbon, total phenolic content and detailed chemical composition of root exudates were determined. Plant biomass production and exudate phenolic and organic carbon content were influenced by endophyte status, tall fescue cultivar, and their interaction. GC-TOF MS identified 132 compounds, including lipids, carbohydrates and carboxylic acids. Cluster analysis showed that the interaction between endophyte and cultivar resulted in unique exudate profiles. This is the first detailed study to assess how endophyte infection, notably with novel endophytes, and tall fescue cultivar interact to influence root exudate composition. Our results illustrate that tall fescue cultivar and endophyte status can influence plant growth and root exudate composition, which may help explain the observed influence of this symbiosis on rhizosphere biogeochemical processes.

  14. Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition

    Directory of Open Access Journals (Sweden)

    Jingqi eGuo

    2015-04-01

    Full Text Available Tall fescue (Lolium arundinaceum (Schreb. is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a shoot-specific fungal endophyte (Epichloë coenophiala thought to provide the plant with enhanced resistance to biotic and abiotic stresses. Because alkaloids produced by the common variety of the endophyte cause severe animal health issues, focus has been on replacing the common-toxic strain with novel varieties that do not produce the mammal-toxic alkaloids but maintain abiotic and biotic stress tolerance benefits. Little attention has been given to the influence of the plant-fungal symbiosis on rhizosphere processes. Therefore, our objective was to study the influence of this relationship on plant biomass production and root exudate composition in tall fescue cultivars PDF and 97TF1, which were either not infected with the endophyte (E-, infected with the common toxic endophyte (CTE+ strain or with one of two novel endophytes (AR542E+, AR584E+. Plants were grown sterile for three weeks after which plant biomass, total organic carbon, total phenolic content and detailed chemical composition of root exudates were determined. Plant biomass production and exudate phenolic and organic carbon content were influenced by endophyte status, tall fescue cultivar, and their interaction. GC-TOF MS identified 132 compounds, including lipids, carbohydrates and carboxylic acids. Cluster analysis showed that the interaction between endophyte and cultivar resulted in unique exudate profiles. This is the first detailed study to assess how endophyte infection, notably with novel endophytes, and tall fescue cultivar interact to influence root exudate composition. Our results illustrate that tall fescue cultivar and endophyte status can influence plant growth and root exudate composition, which may help explain the observed influence of this symbiosis on rhizosphere biogeochemical processes.

  15. Temperature oscillation coupled with fungal community shifts can modulate warming effects on litter decomposition.

    Science.gov (United States)

    Dang, Christian K; Schindler, Markus; Chauvet, Eric; Gessner, Mark O

    2009-01-01

    Diel temperature oscillations are a nearly ubiquitous phenomenon, with amplitudes predicted to change along with mean temperatures under global-warming scenarios. Impact assessments of global warming have largely disregarded diel temperature oscillations, even though key processes in ecosystems, such as decomposition, may be affected. We tested the effect of a 5 degrees C temperature increase with and without diel oscillations on litter decomposition by fungal communities in stream microcosms. Five temperature regimes with identical thermal sums (degree days) were applied: constant 3 degrees and 8 degrees C; diel temperature oscillations of 5 degrees C around each mean; and oscillations of 9 degrees C around 8 degrees C. Temperature oscillations around 8 degrees C (warming scenario), but not 3 degrees C (ambient scenario), accelerated decomposition by 18% (5 degrees C oscillations) and 31% (9 degrees C oscillations), respectively, compared to the constant temperature regime at 8 degrees C. Community structure was not affected by oscillating temperatures, although the rise in mean temperature from 3 degrees to 8 degrees C consistently shifted the relative abundance of species. A simple model using temperature-growth responses of the dominant fungal decomposers accurately described the experimentally observed pattern, indicating that the effect of temperature oscillations on decomposition in our warming scenario was caused by strong curvilinear responses of species to warming at low temperature, particularly of the species becoming most abundant at 8 degrees C (Tetracladium marchalianum). These findings underscore the need to consider species-specific temperature characteristics in concert with changes in communities when assessing consequences of global warming on ecosystem processes.

  16. Comparison of fungal community in black pepper-vanilla and vanilla monoculture systems associated with vanilla Fusarium wilt disease

    Directory of Open Access Journals (Sweden)

    Qirong eShen

    2016-02-01

    Full Text Available Long-term vanilla monocropping often results in the occurrence of vanilla Fusarium wilt disease, seriously affecting its production all over the world. In the present study, vanilla exhibited significantly less Fusarium wilt disease in the soil of a long-term continuously cropped black pepper orchard. The entire fungal communities of bulk and rhizosphere soils between the black pepper-vanilla system (i.e., vanilla cropped in the soil of a continuously cropped black pepper orchard and vanilla monoculture system were compared through the deep pyrosequencing. The results showed that the black pepper-vanilla system revealed a significantly higher fungal diversity than the vanilla monoculture system in both bulk and rhizosphere soils. The UniFrac-weighted PCoA analysis revealed significant differences in bulk soil fungal community structures between the two cropping systems, and fungal community structures were seriously affected by the vanilla root system. In summary, the black pepper-vanilla system harboured a lower abundance of F. oxysporum in the vanilla rhizosphere soil and increased the putatively plant-beneficial fungal groups such as Trichoderma and Penicillium genus, which could explain the healthy growth of vanilla in the soil of the long-term continuously cropped black pepper field. Thus, cropping vanilla in the soil of continuously cropped black pepper fields for maintaining the vanilla industry is executable and meaningful as an agro-ecological system.

  17. Land use practices and ectomycorrhizal fungal communities from oak woodlands dominated by Quercus suber L. considering drought scenarios.

    Science.gov (United States)

    Azul, Anabela Marisa; Sousa, João Paulo; Agerer, Reinhard; Martín, María P; Freitas, Helena

    2010-02-01

    Oak woodlands in the Mediterranean basin have been traditionally converted into agro-silvo-pastoral systems and exemplified sustainable land use in Europe. In Portugal, in line with the trend of other European countries, profound changes in management options during the twentieth century have led to landscape simplification. Landscapes are dynamic and the knowledge of future management planning combining biological conservation and soil productivity is needed, especially under the actual scenarios of drought and increasing evidence of heavy oak mortality. We examined the ectomycorrhizal (ECM) fungal community associated with cork oak in managed oak woodlands (called montado) under different land use practices, during summer. ECM fungal richness and abundance were assessed in 15 stands established in nine montados located in the Alentejo region (southern Portugal), using morphotyping and ITS rDNA analysis. Parameters related to the montados landscape characteristics, land use history over the last 25 years, climatic and edaphic conditions were taken into account. Fifty-five ECM fungal taxa corresponding to the most abundant fungal symbionts were distinguished on cork oak roots. Cenococcum geophilum and the families Russulaceae and Thelephoraceae explained 56% of the whole ECM fungal community; other groups were represented among the community: Cortinariaceae, Boletaceae, Amanita, Genea, Pisolithus, Scleroderma, and Tuber. There were pronounced differences in ECM fungal community structure among the 15 montados stands: C. geophilum was the only species common to all stands, tomentelloid and russuloid species were detected in 87-93% of the stands, Cortinariaceae was detected in 60% of the stands, and the other groups were more unequally distributed. Ordination analysis revealed that ECM fungal richness was positively correlated with the silvo-pastoral exploitation regime and low mortality of cork oak, while ECM fungal abundance was positively correlated with extensive

  18. Arbuscular Mycorrhizal Fungal Mediation of Plant-Plant Interactions in a Marshland Plant Community

    Directory of Open Access Journals (Sweden)

    Qian Zhang

    2014-01-01

    Full Text Available Obligate aerobic AMF taxa have high species richness under waterlogged conditions, but their ecological role remains unclear. Here we focused on AM fungal mediation of plant interactions in a marshland plant community. Five cooccurring plant species were chosen for a neighbor removal experiment in which benomyl was used to suppress AMF colonization. A Phragmites australis removal experiment was also performed to study its role in promoting AMF colonization by increasing rhizosphere oxygen concentration. Mycorrhizal fungal effects on plant interactions were different for dominant and subdominant plant species. AMF colonization has driven positive neighbor effects for three subdominant plant species including Kummerowia striata, Leonurus artemisia, and Ixeris polycephala. In contrast, AMF colonization enhanced the negative effects of neighbors on the dominant Conyza canadensis and had no significant impact on the neighbor interaction to the dominant Polygonum pubescens. AM colonization was positively related to oxygen concentration. P. australis increased oxygen concentration, enhanced AMF colonization, and was thus indirectly capable of influencing plant interactions. Aerobic AM fungi appear to be ecologically relevant in this wetland ecosystem. They drive positive neighbor interactions for subdominant plant species, effectively increasing plant diversity. We suggest, therefore, that AM fungi may be ecologically important even under waterlogged conditions.

  19. Arbuscular mycorrhizal fungal mediation of plant-plant interactions in a marshland plant community.

    Science.gov (United States)

    Zhang, Qian; Sun, Qixiang; Koide, Roger T; Peng, Zhenhua; Zhou, Jinxing; Gu, Xungang; Gao, Weidong; Yu, Meng

    2014-01-01

    Obligate aerobic AMF taxa have high species richness under waterlogged conditions, but their ecological role remains unclear. Here we focused on AM fungal mediation of plant interactions in a marshland plant community. Five cooccurring plant species were chosen for a neighbor removal experiment in which benomyl was used to suppress AMF colonization. A Phragmites australis removal experiment was also performed to study its role in promoting AMF colonization by increasing rhizosphere oxygen concentration. Mycorrhizal fungal effects on plant interactions were different for dominant and subdominant plant species. AMF colonization has driven positive neighbor effects for three subdominant plant species including Kummerowia striata, Leonurus artemisia, and Ixeris polycephala. In contrast, AMF colonization enhanced the negative effects of neighbors on the dominant Conyza canadensis and had no significant impact on the neighbor interaction to the dominant Polygonum pubescens. AM colonization was positively related to oxygen concentration. P. australis increased oxygen concentration, enhanced AMF colonization, and was thus indirectly capable of influencing plant interactions. Aerobic AM fungi appear to be ecologically relevant in this wetland ecosystem. They drive positive neighbor interactions for subdominant plant species, effectively increasing plant diversity. We suggest, therefore, that AM fungi may be ecologically important even under waterlogged conditions.

  20. Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants.

    Science.gov (United States)

    Costa, Damien; Mercier, Anne; Gravouil, Kevin; Lesobre, Jérôme; Verdon, Julien; Imbert, Christine

    2016-10-01

    Chemical disinfectants are widely advocated to reduce the microbial contamination in dental unit waterlines (DUWL). However, until now their efficacy has been poorly examined after long-term application. In this study, through quantitative PCR and high-throughput sequencing, both bacterial and fungal communities were profiled from 8- to 12-year-old DUWL treated with disinfectants commonly used by European dentists. Water was collected from the tap water supplying units to the output exposure point of the turbine handpiece following a stagnation period and dental care activity. Results showed that (i) the unit itself is the principal source of microbial contamination and (ii) water stagnation, DU maintenance practices and quality of water supplying DU appeared as parameters driving the water quality. Despite disinfecting treatment combined to flushing process, the microbial contamination remained relevant in the studied output water, in association with a high bacterial and fungal diversity. The occurrence of potentially pathogenic microorganisms in these treated DUWL demonstrated a potential infectious risk for both patients and dental staff. A disinfectant shock before a prolonged stagnation period could limit the microbial proliferation inside DUWL. Necessity to proceed to regular water quality control of DUWL was highlighted.

  1. The community ecology of pathogens: coinfection, coexistence and community composition.

    Science.gov (United States)

    Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

    2015-04-01

    Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology. © 2015 John Wiley & Sons Ltd/CNRS.

  2. Fungal Communities Associated with the Biodegradation of Polyester Polyurethane Buried under Compost at Different Temperatures

    Science.gov (United States)

    Zafar, Urooj; Houlden, Ashley

    2013-01-01

    Plastics play an essential role in the modern world due to their low cost and durability. However, accumulation of plastic waste in the environment causes wide-scale pollution with long-lasting effects, making plastic waste management expensive and problematic. Polyurethanes (PUs) are heteropolymers that made up ca. 7% of the total plastic production in Europe in 2011. Polyester PUs in particular have been extensively reported as susceptible to microbial biodegradation in the environment, particularly by fungi. In this study, we investigated the impact of composting on PUs, as composting is a microbially rich process that is increasingly being used for the processing of green waste and food waste as an economically viable alternative to landfill disposal. PU coupons were incubated for 12 weeks in fresh compost at 25°C, 45°C, and 50°C to emulate the thermophilic and maturation stages of the composting process. Incubation at all temperatures caused significant physical deterioration of the polyester PU coupons and was associated with extensive fungal colonization. Terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of the fungal communities on the PU surface and in the surrounding compost revealed that the population on the surface of PU was different from the surrounding compost community, suggesting enrichment and selection. The most dominant fungi identified from the surfaces of PU coupons by pyrosequencing was Fusarium solani at 25°C, while at both 45°C and 50°C, Candida ethanolica was the dominant species. The results of this preliminary study suggest that the composting process has the potential to biodegrade PU waste if optimized further in the future. PMID:24056469

  3. Linking fungal communities in roots, rhizosphere, and soil to the health status of Pisum sativum

    DEFF Research Database (Denmark)

    Xu, Lihui; Ravnskov, Sabine; Larsen, John

    2012-01-01

    the three fields identified a number of OTUs that were more abundant in healthy roots. Pathogens such as Fusarium oxysporum were abundant in diseased roots in some fields. Patterns of disease and causal agents of root rot were different among the three fields, which were also reflected in fungal communities...

  4. Mycorrhizal fungal community relationship to root nitrogen concentration over a regional atmospheric nitrogen deposition gradient in the northeastern USA

    Science.gov (United States)

    Erik A. Lilleskov; Philip M. Wargo; Kristiina A. Vogt; Daniel J. Vogt

    2008-01-01

    Increased nitrogen (N) input has been found to alter ectomycorrhizal fungal communities over short deposition gradients and in fertilization experiments; however, its effects over larger spatial scales have not been determined. To address this gap, we reanalyzed data from a study originally designed to examine the effects of soil aluminum/calcium (Al/Ca) ratios on the...

  5. Unearthing carrion beetles' microbiome: characterization of bacterial and fungal hindgut communities across the Silphidae.

    Science.gov (United States)

    Kaltenpoth, Martin; Steiger, Sandra

    2014-03-01

    Carrion beetles (Coleoptera, Silphidae) are well known for their behaviour of exploiting vertebrate carcasses for nutrition. While species in the subfamily Silphinae feed on large carcasses and on larvae of competing scavengers, the Nicrophorinae are unique in monopolizing, burying and defending small carrion, and providing extensive biparental care. As a first step towards investigating whether microbial symbionts may aid in carcass utilization or defence, we characterized the microbial hindgut communities of six Nicrophorinae (Nicrophorus spp.) and two Silphinae species (Oiceoptoma noveboracense and Necrophila americana) by deep ribosomal RNA amplicon sequencing. Across all species, bacteria in the family Xanthomonadaceae, related to Ignatzschineriao larvae, were consistently common, and several other taxa were present in lower abundance (Enterobacteriales, Burkholderiales, Bacilli, Clostridiales and Bacteroidales). Additionally, the Nicrophorinae showed high numbers of unusual Clostridiales, while the Silphinae were characterized by Flavobacteriales and Rhizobiales (Bartonella sp.). In addition to the complex community of bacterial symbionts, each species of carrion beetle harboured a diversity of ascomycetous yeasts closely related to Yarrowia lipolytica. Despite the high degree of consistency in microbial communities across the Silphidae--specifically within the Nicrophorinae--both the fungal symbiont phylogeny and distance-based bacterial community clustering showed higher congruence with sampling locality than host phylogeny. Thus, despite the possibility for vertical transmission via anal secretions, the distinct hindgut microbiota of the Silphidae appears to be shaped by frequent horizontal exchange or environmental uptake of symbionts. The microbial community profiles, together with information on host ecology and the metabolic potential of related microorganisms, allow us to propose hypotheses on putative roles of the symbionts in carcass degradation

  6. Bacterial and fungal communities in a degraded ombrotrophic peatland undergoing natural and managed re-vegetation.

    Directory of Open Access Journals (Sweden)

    David R Elliott

    Full Text Available 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

  7. Functional Diversity of Fungal Communities in Soil Contaminated with Diesel Oil

    Directory of Open Access Journals (Sweden)

    Agata Borowik

    2017-09-01

    Full Text Available The widespread use and consumption of crude oil draws the public’s attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO, can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R and Shannon–Weaver (H indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2–3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD and Eco-physiological Diversity (EP indices] is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of

  8. Mycorrhizal Fungal Community of Poplars Growing on Pyrite Tailings Contaminated Site near the River Timok

    Directory of Open Access Journals (Sweden)

    Marina Katanić

    2015-06-01

    Full Text Available Background and Purpose: Mycorrhizal fungi are of high importance for functioning of forest ecosystems and they could be used as indicators of environmental stress. The aim of this research was to analyze ectomycorrhizal community structure and to determine root colonization rate with ectomycorrhizal, arbuscular mycorrhizal and endophytic fungi of poplars growing on pyrite tailings contaminated site near the river Timok (Eastern Serbia. Materials and Methods: Identification of ectomycorrhizal types was performed by combining morphological and anatomical characterization of ectomycorrhizae with molecular identification approach, based on sequencing of the nuclear ITS rRNA region. Also, colonization of poplar roots with ectomycorrhizal, arbuscular mycorrhizal and dark septated endophytic fungi were analysed with intersection method. Results and Conclusions: Physico-chemical analyses of soil from studied site showed unfavourable water properties of soil, relatively low pH and high content of heavy metals (copper and zinc. In investigated samples only four different ectomycorrhizal fungi were found. To the species level were identified Thelephora terrestris and Tomentella ellisi, while two types remained unidentified. Type Thelephora terrestris made up 89% of all ectomycorrhizal roots on studied site. Consequently total values of Species richness index and Shannon-Weaver diversity index were 0.80 and 0.43, respectively. No structures of arbuscular mycorrhizal fungi were recorded. Unfavourable environmental conditions prevailing on investigated site caused decrease of ectomycorrhizal types diversity. Our findings point out that mycorrhyzal fungal community could be used as an appropriate indicator of environmental changes.

  9. A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).

    Science.gov (United States)

    Oono, Ryoko; Lefèvre, Emilie; Simha, Anita; Lutzoni, François

    2015-10-01

    Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS-LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts.

  10. Effect of biocontrol agent Pseudomonas fluorescens 2P24 on soil fungal community in cucumber rhizosphere using T-RFLP and DGGE.

    Directory of Open Access Journals (Sweden)

    Guanpeng Gao

    Full Text Available Fungi and fungal community play important roles in the soil ecosystem, and the diversity of fungal community could act as natural antagonists of various plant pathogens. Biological control is a promising method to protect plants as chemical pesticides may cause environment pollution. Pseudomonas fluorescens 2P24 had strong inhibitory on Rastonia solanacearum, Fusarium oxysporum and Rhizoctonia solani, etc., and was isolated from the wheat rhizosphere take-all decline soils in Shandong province, China. However, its potential effect on soil fungal community was still unknown. In this study, the gfp-labeled P. fluorescens 2P24 was inoculated into cucumber rhizosphere, and the survival of 2P24 was monitored weekly. The amount decreased from 10(8 to 10(5 CFU/g dry soils. The effect of 2P24 on soil fungal community in cucumber rhizosphere was investigated using T-RFLP and DGGE. In T-RFLP analysis, principle component analysis showed that the soil fungal community was greatly influenced at first, digested with restriction enzyme Hinf I and Taq I. However, there was little difference as digested by different enzymes. DGGE results demonstrated that the soil fungal community was greatly shocked at the beginning, but it recovered slowly with the decline of P. fluorescens 2P24. Four weeks later, there was little difference between the treatment and control. Generally speaking, the effect of P. fluorescens 2P24 on soil fungal community in cucumber rhizosphere was just transient.

  11. Effects of Acetochlor and Methamidophos on Fungal Communities in Black Soils

    Institute of Scientific and Technical Information of China (English)

    LI Xin-Yu; ZHANG Hui-Wen; ZHOU Qi-Xing; SU Zhen-Cheng; ZHANG Cheng-Gang

    2005-01-01

    Using plate counting and ergosterol assay, single and joint effects of acetochlor and methamidophos on the dynamics of soil fungal population and total fungal biomass in the black soil zone of Northeast China were investigated. The results demonstrated that acetochlor at high concentration levels (150 and 250 mg kg-1) had an acute and mostly chronic toxicity on both the soil fungal population and total fungal biomass, but at a low concentration (50 mg kg-1) generally had a stimulating effect that was stronger with total fungal biomass than with the soil fungal population. Methamidophos at a high concentration level (250 mg kg-1) alone and almost all of its combinations with various dosages of acetochlor increased the soil fungal population, whereas at most sampling dates with 250 mg methamidophos kg-1 soil, total fungal biomass increased, but in combination with acetochlor it was decreased in the early period of incubation and then increased 28 days after incubation. Thus, through measuring the number of colony forming unit of the soil fungal population along with the total fungal biomass, a better understanding on effects of agrochemicals on soil fungi could be made.

  12. Urban greenness influences airborne bacterial community composition.

    Science.gov (United States)

    Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

    2016-11-15

    Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

  13. Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau

    Directory of Open Access Journals (Sweden)

    Xingjia Xiang

    2016-07-01

    Full Text Available Background: The Qinghai-Tibet Plateau (QTP is home to the vast grassland in China. The QTP grassland ecosystem has been seriously degraded by human land use practices and climate change. Fertilization is used in this region to increase vegetation yields for grazers. The impact of long-term fertilization on plant and microbial communities has been studied extensively. However, the influence of short-term fertilization on arbuscular mycorrhizal fungal (AMF communities in the QTP is largely unknown, despite their important functional role in grassland ecosystems. Methods: We investigated AMF community responses to three years of N and/or P addition at an experimental field site on the QTP, using the Illumina MiSeq platform (PE 300. Results: Fertilization resulted in a dramatic shift in AMF community composition and NP addition significantly increased AMF species richness and phylogenetic diversity. Aboveground biomass, available phosphorus, and NO3− were significantly correlated with changes in AMF community structure. Changes in these factors were driven by fertilization treatments. Thus, fertilization had a large impact on AMF communities, mediated by changes in aboveground productivity and soil chemistry. Discussion: Prior work has shown how plants often lower their reliance on AMF symbioses following fertilization, leading to decrease AMF abundance and diversity. However, our study reports a rise in AMF diversity with fertilization treatment. Because AMF can provide stress tolerance to their hosts, we suggest that extreme weather on the QTP may help drive a positive relationship between fertilizer amendment and AMF diversity.

  14. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

    Science.gov (United States)

    Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat

    2014-03-01

    Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community.

  15. Distribution and stable isotopic composition of amino acids from fungal peptaibiotics: assessing the potential for meteoritic contamination.

    Science.gov (United States)

    Elsila, Jamie E; Callahan, Michael P; Glavin, Daniel P; Dworkin, Jason P; Brückner, Hans

    2011-03-01

    The presence of nonprotein α-dialkyl-amino acids such as α-aminoisobutyric acid (α-AIB) and isovaline (Iva), which are considered to be relatively rare in the terrestrial biosphere, has long been used as an indication of the indigeneity of meteoritic amino acids. However, recent work showing the presence of α-AIB and Iva in peptides produced by a widespread group of filamentous fungi indicates the possibility of a terrestrial biotic source for the α-AIB observed in some meteorites. We measured the amino acid distribution and stable carbon and nitrogen isotopic composition of four α-AIB-containing fungal peptides and compared this data to similar meteoritic measurements. We show that the relatively simple distribution of the C(4) and C(5) amino acids in fungal peptides is distinct from the complex distribution observed in many carbonaceous chondrites. We also identify potentially diagnostic relationships between the stable isotopic compositions of pairs of amino acids from the fungal peptides that may aid in ruling out fungal contamination as a source of meteoritic amino acids.

  16. Linking fungal communities in roots, rhizosphere, and soil to the health status of Pisum sativum

    DEFF Research Database (Denmark)

    Xu, Lihui; Ravnskov, Sabine; Larsen, John;

    2012-01-01

    the three fields identified a number of OTUs that were more abundant in healthy roots. Pathogens such as Fusarium oxysporum were abundant in diseased roots in some fields. Patterns of disease and causal agents of root rot were different among the three fields, which were also reflected in fungal communities......Changes in fungal communities associated with healthy and diseased pea roots were investigated using deep amplicon pyrosequencing in three spatial compartments: roots, rhizosphere, and surrounding soil. Thirty root systems were collected from three fields, half of which showing clear symptoms...... of root rot. In total, 500 461 internal transcribed spacer-1 sequences were obtained that were clustered into 123 (roots), 271 (rhizosphere), and 440 (bulk soil) nonsingleton operational taxonomic units (OTUs). Species richness was highest in bulk soils and lowest in roots; however, no notable differences...

  17. Long-term effects of plant diversity and composition on soil nematode communities in model grasslands.

    Science.gov (United States)

    Viketoft, Maria; Bengtsson, Janne; Sohlenius, Björn; Berg, Matty P; Petchey, Owen; Palmborg, Cecilia; Huss-Danell, Kerstin

    2009-01-01

    An important component of plant-soil feedbacks is how plant species identity anddiversity influence soil organism communities. We examine the effects of grassland plant species growing alone and together up to a richness of 12 species on nematode diversity and feeding group composition, eight years after the establishment of experimental grassland plots at the BIODEPTH site in northern Sweden. This is a substantially longer time than most other experimental studies of plant effects on soil fauna. We address the hypotheses that (la) higher species or functional diversity of plants increases nematode diversity, as well as influences nematode community composition. Alternatively, (1b) individual plant species traits are most important for nematode diversity and community composition. (2) Plant effects on soil organisms will decrease with increasing number of trophic links between plants and soil fauna. Plant species identity was often more important than plant diversity for nematode community composition, supporting hypothesis 1b. There was a weak positive relation between plant and nematode richness;which could be attributed to the presence of the legume Trifolium pratense, but also to some other plant species, suggesting a selection or sampling effect. Several plant species in different functional groups affected nematode community composition. For example, we found that legumes increased bacterial-feeding nematodes, most notably r-selected Rhabditida, while fungal-feeding nematodes were enhanced by forbs. Other bacterial feeders and obligate root feeders were positively related to grasses. Plant effects were usually stronger on plant-, bacterial- and fungal-feeding nematodes than on omnivores/predators, which supports hypothesis 2. Our study suggests that plant identity has stronger effects than plant diversity on nematode community composition, but when comparing our results with similar previous studies the effects of particular plant species appear to vary. We

  18. The effects of weather on fungal abundance and richness among 25 communities in the Intermountain West

    Directory of Open Access Journals (Sweden)

    Coley Phyllis D

    2002-06-01

    Full Text Available Abstract Background Because moisture and temperature influence the growth of fungi, characterizing weather conditions favorable for fungi may be used to predict the abundance and richness of fungi in habitats with different climate conditions. To estimate habitat favorability to fungi, we examined the relationship of fungal abundance and species richness to various weather and environmental parameters in the Intermountain West. We cultured fungi from air and leaf surfaces, and collected continuous temperature and relative humidity measures over the growing season at 25 sites. Results Fungal richness was positively correlated with fungal abundance (r = 0.75. Measures of moisture availability, such as relative humidity and vapor pressure deficit, explained more of the variance in fungal abundance and richness than did temperature. Climate measurements from nearby weather stations were good predictors of fungal abundance and richness but not as good as weather measurements obtained in the field. Weather variables that took into account the proportion of time habitats experienced favorable or unfavorable relative humidity and temperatures were the best predictors, explaining up to 56% of the variation in fungal abundance and 72% for fungal richness. Conclusion Our results suggest that the abundance and richness of fungi in a habitat is limited by the duration of unfavorable weather conditions. Because fungal pathogens likely have similar abiotic requirements for growth as other fungi, characterizing weather conditions favorable for fungi also may be used to predict the selective pressures imposed by pathogenic fungi on plants in different habitats.

  19. Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic.

    Science.gov (United States)

    Timling, I; Walker, D A; Nusbaum, C; Lennon, N J; Taylor, D L

    2014-07-01

    Fungi are abundant and functionally important in the Arctic, yet comprehensive studies of their diversity in relation to geography and environment are not available. We sampled soils in paired plots along the North American Arctic Transect (NAAT), which spans all five bioclimatic subzones of the Arctic. Each pair of plots contrasted relatively bare, cryoturbated patterned-ground features (PGFs) and adjacent vegetated between patterned-ground features (bPGFs). Fungal communities were analysed via sequencing of 7834 ITS-LSU clones. We recorded 1834 OTUs - nearly half the fungal richness previously reported for the entire Arctic. These OTUs spanned eight phyla, 24 classes, 75 orders and 120 families, but were dominated by Ascomycota, with one-fifth belonging to lichens. Species richness did not decline with increasing latitude, although there was a decline in mycorrhizal taxa that was offset by an increase in lichen taxa. The dominant OTUs were widespread even beyond the Arctic, demonstrating no dispersal limitation. Yet fungal communities were distinct in each subzone and were correlated with soil pH, climate and vegetation. Communities in subzone E were distinct from the other subzones, but similar to those of the boreal forest. Fungal communities on disturbed PGFs differed significantly from those of paired stable areas in bPGFs. Indicator species for PGFs included lichens and saprotrophic fungi, while bPGFs were characterized by ectomycorrhizal and pathogenic fungi. Our results suggest that the Arctic does not host a unique mycoflora, while Arctic fungi are highly sensitive to climate and vegetation, with potential to migrate rapidly as global change unfolds.

  20. Inoculation effects on root-colonizing arbuscular mycorrhizal fungal communities spread beyond directly inoculated plants.

    Science.gov (United States)

    Janoušková, Martina; Krak, Karol; Vosátka, Miroslav; Püschel, David; Štorchová, Helena

    2017-01-01

    Inoculation with arbuscular mycorrhizal fungi (AMF) may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculation effects, and to which degree the inoculant and the inoculation-induced changes in AMF community composition spread into newly emerging seedlings that were not in direct contact with the introduced propagules. We addressed this topic in a greenhouse experiment based on the soil and native AMF community of a post-mining site. Plants were cultivated in compartmented pots with substrate containing the native AMF community, where AMF extraradical mycelium radiating from directly inoculated plants was allowed to inoculate neighboring plants. The abundances of the inoculated isolate and of native AMF taxa were monitored in the roots of the directly inoculated plants and the neighboring plants by quantitative real-time PCR. As expected, inoculation suppressed root colonization of the directly inoculated plants by other AMF taxa of the native AMF community and also by native genotypes of the same species as used for inoculation. In the neighboring plants, high abundance of the inoculant and the suppression of native AMF were maintained. Thus, we demonstrate that inoculation effects on native AMF propagate into plants that were not in direct contact with the introduced inoculum, and are therefore likely to persist at the site of inoculation.

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

    Science.gov (United States)

    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.

  2. Insights into deep-sea sediment fungal communities from the East Indian Ocean using targeted environmental sequencing combined with traditional cultivation

    National Research Council Canada - National Science Library

    Zhang, Xiao-yong; Tang, Gui-ling; Xu, Xin-ya; Nong, Xu-hua; Qi, Shu-hua

    2014-01-01

    .... We investigated the fungal community structure in five sediments from a depth of ∼ 4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation...

  3. A microcosmos study on the effects of Cd-containing wood ash on the coniferous humus fungal community and the Cd bioavailability

    Energy Technology Data Exchange (ETDEWEB)

    Fritze, H.; Perkioemaeki, J.; Pennanen, T. [Finnish Forest Research Inst., Vantaa (Finland); Petaenen, T.; Romantschuk, M.; Yrjaelae, K. [Dept. of Biosciences, Div. of General Microbiology, 56 (Biocenter 1 C), Univ. of Helsinki (Finland); Karp, M. [Dept. of Biotechnology, Univ. of Turku, Turku (Finland)

    2001-07-01

    Background and Aims. The use of wood ash in forestry has been questioned because the cadmium (Cd) concentration of ash, which varies between 1 and 20 mg kg{sup -1} ash, exceeds the level allowed for fertilizers (3 mg kg{sup -1}) used in agriculture. To investigate the effects of Cd and ash on the fungal community composition and Cd bioavailability of the humus layer of boreal, coniferous forests, pumice or wood ash, spiked with a water soluble (CdCl{sub 2}) or insoluble (CdO) form of Cd at three levels (0, 400 and 1000 mg kg{sup -1}), were applied at a fertilization level of 5000 kg ha{sup -1} in a laboratory microcosm study. Methods. After 2 months, the humus in the microcosms was sampled and extracted for total DNA to detect changes in the fungal community by using polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) techniques. PCR was performed using the fungal 18S rDNA primers FR1 + FF390 and FR1 + NS1. The bioavailability of Cd was measured with a bacterial biosensor (Bacillus subtilis BR 151/pT0024) emitting light in the presence of Cd. Results. Using the primer pairs FR1 + FF390 and FR1 + NS1, resulted in over 35 and 15 DGGE bands, respectively. Both primer pairs detected an ash, but no Cd effect. When using FR1 + FF390, a higher fluorescence was observed in one DGGE band of all ashed samples compared to the pumiced samples. With the primer pair FR1 + NS1, the ashed samples had a DGGE band which was not visible or only faintly visible in the pumiced samples. In addition, one DGGE band disappeared from the ashed samples. Humus layer water extracts showed that the Cd added with the pumice was in a bioavailable form. The luminescence intensity of the biosensor was dependent on the form and level of the Cd added. No luminescence was detected when the Cd was added with the ash. Conclusions. Ash fertilization altered the humus layer fungal community, whereas the level and form of additional Cd in the ash had no influence because it

  4. Microbial community composition affects soil fungistasis

    NARCIS (Netherlands)

    De Boer, W.; Verheggen, P.; Klein Gunnewiek, P.J.A.; Kowalchuk, G.A.; Van Veen, J.A.

    2003-01-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis)

  5. Effect of Biocontrol Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere Using T-RFLP and DGGE

    OpenAIRE

    Guanpeng Gao; Danhan Yin; Shengju Chen; Fei Xia; Jie Yang; Qing Li; Wei Wang

    2012-01-01

    Fungi and fungal community play important roles in the soil ecosystem, and the diversity of fungal community could act as natural antagonists of various plant pathogens. Biological control is a promising method to protect plants as chemical pesticides may cause environment pollution. Pseudomonas fluorescens 2P24 had strong inhibitory on Rastonia solanacearum, Fusarium oxysporum and Rhizoctonia solani, etc., and was isolated from the wheat rhizosphere take-all decline soils in Shandong provinc...

  6. Changes in Arbuscular Mycorrhizal Fungal Abundance and Community Structure in Response to the Long-Term Manipulation of Inorganic Nutrients in a Lowland Tropical Forest

    Science.gov (United States)

    Sheldrake, Merlin; Rosenstock, Nicholas; Tanner, Ed

    2014-05-01

    by N or P additions (~30% reduction) and heavily reduced by combined N and P addition (~50%), but not affected by K addition, despite K addition bringing about a strong reduction (~ 30%) in plant root biomass at this site. AMF biomass in roots was similarly affected, though the plant roots generally did not have a greater reduction in the +N,+P treatments than in either the +N or +P treatments. Phosphorus had the strongest effect on AMF community composition, although nitrogen also had a strong effect in roots; N and P interacted in their effect on both soil and root AMF communities. K addition did not have an effect on the AMF communities in soil or roots. These finding implicates AMF in plant acquisition of both N and P, particularly given that K addition had a marked effect on root growth but not on AMF community composition or biomass. Responses of AMF to fertilization differed between root and soil communities with some treatments; the reasons for these asymmetric changes in soil versus root AMF communities are discussed as are fungal and plant species-specific responses to fertilization.

  7. Mutualistic rhizobia reduce plant diversity and alter community composition.

    Science.gov (United States)

    Keller, Kane R

    2014-12-01

    Mutualistic interactions can be just as important to community dynamics as antagonistic species interactions like competition and predation. Because of their large effects on both abiotic and biotic environmental variables, resource mutualisms, in particular, have the potential to influence plant communities. Moreover, the effects of resource mutualists such as nitrogen-fixing rhizobia on diversity and community composition may be more pronounced in nutrient-limited environments. I experimentally manipulated the presence of rhizobia across a nitrogen gradient in early assembling mesocosm communities with identical starting species composition to test how the classic mutualism between nitrogen-fixing rhizobia and their legume host influence diversity and community composition. After harvest, I assessed changes in α-diversity, community composition, β-diversity, and ecosystem properties such as inorganic nitrogen availability and productivity as a result of rhizobia and nitrogen availability. The presence of rhizobia decreased plant community diversity, increased community convergence (reduced β-diversity), altered plant community composition, and increased total community productivity. These community-level effects resulted from rhizobia increasing the competitive dominance of their legume host Chamaecrista fasciculata. Moreover, different non-leguminous species responded both negatively and positively to the presence of rhizobia, indicating that rhizobia are driving both inhibitory and potentially facilitative effects in communities. These findings expand our understanding of plant communities by incorporating the effects of positive symbiotic interactions on plant diversity and composition. In particular, rhizobia that specialize on dominant plants may serve as keystone mutualists in terrestrial plant communities, reducing diversity by more than 40%.

  8. Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

    Science.gov (United States)

    Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

    2016-06-01

    A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

  9. Analysis of black fungal biofilms occurring at domestic water taps. I: compositional analysis using Tag-Encoded FLX Amplicon Pyrosequencing.

    Science.gov (United States)

    Heinrichs, Guido; Hübner, Iris; Schmidt, Carsten K; de Hoog, G Sybren; Haase, Gerhard

    2013-06-01

    Mass growth of dark fungal biofilms on water taps and associated habitats was observed in various German drinking water distribution systems recently. Customers of affected drinking water systems are anxious about potential and unknown health risks. These environments are known to harbour a fungal flora also comprising a variety of fungal opportunists that are well known to cause superficial mycoses in humans (Exophiala equina, Exophiala lecanii-corni) but are not known to establish dark biofilms so far. To gain profound insight on composition of respective biofilms, a metagenomic approach using Tag-Encoded FLX Amplicon Pyrosequencing (TEFAP) of the ribosomal internal transcribed spacer 2 region in comparison with a classical cultivation approach using Sabouraud agar with chloramphenicol and erythritol-chloramphenicol-agar was performed. E. lecanii-corni was found to be the major component in 10 of 13 biofilms analysed independently of the method used. Alternaria sp., E. equina, Fusarium spp. and Ochroconis spp. were also relatively abundant. As expected, TEFAP usually revealed a higher diversity than the cultivation approaches. For example, opportunistic species like Candida albicans or Exophiala dermatitidis were detected in very low amounts. In conclusion, TEFAP turned out to be a promising and powerful tool for the semi-quantitative analysis of fungal biofilms. Referring to relevant literature, potential biological hazards caused by fungi of the dark biofilms can be regarded as low.

  10. Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities.

    Science.gov (United States)

    Vesty, Anna; Biswas, Kristi; Taylor, Michael W; Gear, Kim; Douglas, Richard G

    2017-01-01

    The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3-V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome.

  11. Filamentous fungal diversity and community structure associated with the solid state fermentation of Chinese Maotai-flavor liquor.

    Science.gov (United States)

    Chen, Bi; Wu, Qun; Xu, Yan

    2014-06-02

    Maotai-flavor liquor is produced by simultaneous saccharification and fermentation (SSF) process under solid state conditions, including Daqu (starter) making, stacking fermentation and alcohol fermentation stages. Filamentous fungi produce many enzymes to degrade the starch material into fermentable sugar during liquor fermentation. This study investigated the filamentous fungal community associated with liquor making process. Eight and seven different fungal species were identified by using culture-dependent and -independent method (PCR-denaturing gradient gel electrophoresis, DGGE) analyses, respectively. The traditional enumeration method showed that Daqu provided 7 fungal species for stacking fermentation. The total population of filamentous fungi increased from 3.4 × 10(3)cfu/g to 1.28 × 10(4)cfu/g in the first 3 days of stacking fermentation, and then decreased till the end. In alcohol fermentation in pits, the population continuously decreased and few fungal species survived (lower than 1 × 10(3)cfu/g) after 10 days. Therefore, stacking fermentation is an essential stage for the growth of filamentous fungi. Paecilomyces variotii, Aspergillus oryzae and Aspergillus terreus were detected by both methods, and P. variotii and A. oryzae were the predominant species. Meanwhile, P. variotii possessed the highest glucoamylase (3252 ± 526 U/g) and A. oryzae exhibited the highest α-amylase (1491 ± 324 U/g) activity among the cultivable fungal species. Furthermore, the variation of starch and reducing sugar content was consistent with the growth of P. variotii and A. oryzae in Zaopei (fermented grains) during stacking fermentation, which implied that the two filamentous fungi played an important role in producing amylase for hydrolyzing the starch.

  12. Fungal biogeography. Global diversity and geography of soil fungi.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Põlme, Sergei; Kõljalg, Urmas; Yorou, Nourou S; Wijesundera, Ravi; Villarreal Ruiz, Luis; Vasco-Palacios, Aída M; Thu, Pham Quang; Suija, Ave; Smith, Matthew E; Sharp, Cathy; Saluveer, Erki; Saitta, Alessandro; Rosas, Miguel; Riit, Taavi; Ratkowsky, David; Pritsch, Karin; Põldmaa, Kadri; Piepenbring, Meike; Phosri, Cherdchai; Peterson, Marko; Parts, Kaarin; Pärtel, Kadri; Otsing, Eveli; Nouhra, Eduardo; Njouonkou, André L; Nilsson, R Henrik; Morgado, Luis N; Mayor, Jordan; May, Tom W; Majuakim, Luiza; Lodge, D Jean; Lee, Su See; Larsson, Karl-Henrik; Kohout, Petr; Hosaka, Kentaro; Hiiesalu, Indrek; Henkel, Terry W; Harend, Helery; Guo, Liang-dong; Greslebin, Alina; Grelet, Gwen; Geml, Jozsef; Gates, Genevieve; Dunstan, William; Dunk, Chris; Drenkhan, Rein; Dearnaley, John; De Kesel, André; Dang, Tan; Chen, Xin; Buegger, Franz; Brearley, Francis Q; Bonito, Gregory; Anslan, Sten; Abell, Sandra; Abarenkov, Kessy

    2014-11-28

    Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.

  13. Wood decomposition and fungal community dynamics mediated by temperature and endophytes

    Science.gov (United States)

    Song, Z.; Schilling, J. S.

    2013-12-01

    Wood decomposition is primarily fulfilled by brown rot and white rot fungi in temperate and boreal forests. The competition balance between these fungi determines the patterns of wood decomposition and carbon cycle in forests. But this balance may shift in a warmer future, especially in high latitude forests. Additionally, endophytes may assert influence over the fungal competition through priority effect and interact with the effect of climate change. In this study, we use paper birch and two common fungi to answer two questions 1) How does increased temperature affect the competition between brown rot and white rot fungi? 2) How do endophytes interact with fungi from the soil and influence wood decomposition? A microcosm system was used to simulate competition between Piptoporus betulinus (brown rot fungi) and Fomes fomentarius (white rot fungi) on small birch stem on the effect of increased temperature and endophytes. Activity of P. betulinus was slower in higher temperature, but F. fomentarius was not affected. Character of residue showed that when both fungi were present, wood tend to have white rot in higher temperature. Presence of endophytes significantly reduced the decay rate when they were competing with external fungi, indicating that part of their energy was allocated to interspecies antagonism from metabolizing wood. In the absence of external fungus, endophytes alone caused significant amount of wood decay. Higher temperature also tends to shift the community of endophyte toward more white rot fungi. Our results highlighted the role of endophytes in wood decomposition. Major wood decomposers, not just plant pathogen, may remain dormant in live trees and regain their activity right after tree death. The endophytes could be an important part of assembly history in forming microbial community in dead wood and may have complex interactions with fungi and bacteria in soil. An increased temperature obviously favors white rot fungi, which is in accordance

  14. Fucoidan-degrading fungal strains : screening, morphometric evaluation, and influence of medium composition

    OpenAIRE

    Rodríguez-Jasso, Rosa María; Mussatto, Solange I.; Pastrana, Lorenzo; Aguilar Gonzalez, Cristobal Noé; Teixeira, J.A.

    2010-01-01

    Ten different fungal strains from the genus Aspergillus, Penicillium, and Mucor were screened for fucoidan hydrolyzing ability aiming to find microorganisms able to produce sulfated fucan-degrading enzymes. Screening was carried out by measuring the strains kinetic and morphometric behavior over plate assays using Laminaria japonica fucoidan as only carbon source, testing three nitrogen sources (urea, peptone, and sodium nitrate). The selected fungal strains were subsequently u...

  15. Organic fertilization alters the community composition of root associated fungi in Pisum sativum

    DEFF Research Database (Denmark)

    Yu, L.; Nicolaisen, M.; Ravnskov, S.

    2013-01-01

    Organic fertilization is well known to affect individual functional groups of root associated fungi such as arbuscular mycorrhizal (AM) fungi and root pathogens, but limited information is available on the effect of organic fertilization at the fungal community composition level. The main objective...... of the present study was to examine the response of communities of root associated fungi in Pisum sativum to Protamylasse, an organic fertilizer used in pea production. Plants were grown in pots with field soil amended with four different levels of Protamylasse. 454 pyrosequencing was employed to examine......, the organic fertilizer Protamylasse clearly affects communities of root associated fungi, which seems to be linked to the life strategy of the different functional groups of root associated fungi. --------------------------------------------------------------------------------...

  16. Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.

    Science.gov (United States)

    Purahong, Witoon; Kapturska, Danuta; Pecyna, Marek J; Jariyavidyanont, Katalee; Kaunzner, Jennifer; Juncheed, Kantida; Uengwetwanit, Tanaporn; Rudloff, Renate; Schulz, Elke; Hofrichter, Martin; Schloter, Michael; Krüger, Dirk; Buscot, François

    2015-05-01

    Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.

  17. Fungal keratitis

    Directory of Open Access Journals (Sweden)

    Sonal S Tuli

    2011-02-01

    Full Text Available Sonal S TuliUniversity of Florida, Gainesville, FL, USA  Clinical question: What is the most appropriate management of fungal keratitis?Results: Traditionally, topical Natamycin is the most commonly used medication for filamentous fungi while Amphotericin B is most commonly used for yeast. Voriconazole is rapidly becoming the drug of choice for all fungal keratitis because of its wide spectrum of coverage and increased penetration into the cornea.Implementation: Repeated debridement of the ulcer is recommended for the penetration of topical medications. While small, peripheral ulcers may be treated in the community, larger or central ulcers, especially if associated with signs suggestive of anterior chamber penetration should be referred to a tertiary center. Prolonged therapy for approximately four weeks is usually necessary.Keywords: fungal keratitis, keratomycosis, antifungal medications, debridement

  18. Resource availability controls fungal diversity across a plant diversity gradient

    Science.gov (United States)

    Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

    2006-01-01

    Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

  19. Multi-element fingerprinting and high throughput sequencing identify multiple elements that affect fungal communities in Quercus macrocarpa foliage.

    Science.gov (United States)

    Jumpponen, Ari; Keating, Karen; Gadbury, Gary; Jones, Kenneth L; Mattox, J David

    2010-09-01

    Diverse fungal mutualists, pathogens and saprobes colonize plant leaves. These fungi face a complex environment, in which stochastic dispersal interplays with abiotic and biotic filters. However, identification of the specific factors that drive the community assembly seems unattainable. We mined two broad data sets and identified chemical elements, to which dominant molecular operational taxonomic units (OTUs) in the foliage of a native tree respond most extremely. While many associations could be identified, potential complicating issues emerged. Those were related to unevenly distributed OTU frequency data, a large number of potentially explanatory variables, and the disproportionate effects of outlier observations.

  20. Soil Microbial Community Composition During Natural Recovery in the Loess Plateau, China

    Institute of Scientific and Technical Information of China (English)

    XIAO Lie; LIU Guo-bin; XUE Sha; ZHANG Chao

    2013-01-01

    This study aimed to determine the characteristics of soil microbial community composition and its relationship with soil chemical properties during natural recovery in the Loess Plateau. The soil microbial community composition was analyzed by comparing the soil microbial phospholipid fatty acids (PLFAs) of eight croplands abandoned for 1, 3, 5, 10, 13, 15, 20, and 30 yr in the Dunshan watershed, northern Loess Plateau, China. The results showed that soil organic carbon, total nitrogen, soil microbial biomass carbon, and soil microbial biomass nitrogen signiifcantly increased with the abandonment duration, whereas the metabolic quotient signiifcantly decreased. The Shannon richness and Shannon evenness of PLFAs signiifcantly increased after 10 yr of abandonment. Gram-negative, Gram-positive, bacterial, fungal, and total PLFAs linearly increased with increased abandonment duration. Redundancy analysis showed that the abandonment duration was the most important environmental factor in determining the PLFA microbial community composition. The soil microbial PLFAs changed from anteiso-to iso-, unsaturated to saturated, and short-to long-chain during natural recovery. Therefore, in the Loess Plateau, cropland abandonment for natural recovery resulted in the increase of the soil microbial PLFA biomass and microbial PLFA species and changed the microbial from chemolithotrophic to a more heterotrophic community.

  1. A 3-year study reveals that plant growth stage, season and field site affect soil fungal communities while cultivar and GM-trait have minor effects.

    Science.gov (United States)

    Hannula, Silja Emilia; de Boer, Wietse; van Veen, Johannes

    2012-01-01

    In this three year field study the impact of different potato (Solanum tuberosum L.) cultivars including a genetically modified (GM) amylopectin-accumulating potato line on rhizosphere fungal communities are investigated using molecular microbiological methods. The effects of growth stage of a plant, soil type and year on the rhizosphere fungi were included in this study. To compare the effects, one GM cultivar, the parental isoline, and four non-related cultivars were planted in the fields and analysed using T-RFLP on the basis of fungal phylum specific primers combined with multivariate statistical methods. Additionally, fungal biomass and some extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) were quantified in order to gain insight into the function of the fungal communities. Plant growth stage and year (and agricultural management) had the strongest effect on both diversity and function of the fungal communities while the GM-trait studied was the least explanatory factor. The impact of cultivar and soil type was intermediate. Occasional differences between cultivars, the amylopectin-accumulating potato line, and its parental variety were detected, but these differences were mostly transient in nature and detected either only in one soil, one growth stage or one year.

  2. A 3-year study reveals that plant growth stage, season and field site affect soil fungal communities while cultivar and GM-trait have minor effects.

    Directory of Open Access Journals (Sweden)

    Silja Emilia Hannula

    Full Text Available In this three year field study the impact of different potato (Solanum tuberosum L. cultivars including a genetically modified (GM amylopectin-accumulating potato line on rhizosphere fungal communities are investigated using molecular microbiological methods. The effects of growth stage of a plant, soil type and year on the rhizosphere fungi were included in this study. To compare the effects, one GM cultivar, the parental isoline, and four non-related cultivars were planted in the fields and analysed using T-RFLP on the basis of fungal phylum specific primers combined with multivariate statistical methods. Additionally, fungal biomass and some extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases were quantified in order to gain insight into the function of the fungal communities. Plant growth stage and year (and agricultural management had the strongest effect on both diversity and function of the fungal communities while the GM-trait studied was the least explanatory factor. The impact of cultivar and soil type was intermediate. Occasional differences between cultivars, the amylopectin-accumulating potato line, and its parental variety were detected, but these differences were mostly transient in nature and detected either only in one soil, one growth stage or one year.

  3. Fucoidan-degrading fungal strains: screening, morphometric evaluation, and influence of medium composition.

    Science.gov (United States)

    Rodríguez-Jasso, Rosa M; Mussatto, Solange Inês; Pastrana, Lorenzo; Aguilar, Cristóbal N; Teixeira, José A

    2010-12-01

    Ten different fungal strains from the genus Aspergillus, Penicillium, and Mucor were screened for fucoidan hydrolyzing ability aiming to find microorganisms able to produce sulfated fucan-degrading enzymes. Screening was carried out by measuring the strains kinetic and morphometric behavior over plate assays using Laminaria japonica fucoidan as only carbon source, testing three nitrogen sources (urea, peptone, and sodium nitrate). The selected fungal strains were subsequently used in submerged fermentations, which were performed for (1) selection of the strains able to growth over fucoidan medium and (2) media selection, testing the synergy of fucoidan with other sugars for inducing high enzyme titles. Radial expansion and hyphae parameters were observed for Aspergillus niger PSH, Mucor sp. 3P, and Penicillium purpurogenum GH2 grown only over fucoidan-urea medium. A. niger PSH showed the maximum enzymatic activity values, which were significantly different (p < 0.05) from those achieved by the other selected fungi. Sucrose addition to fucoidan media proportioned the highest fucoidanase activity values for this fungal strain. This research allowed establishing optimal conditions for metabolites synthesis by fungal stains able to act toward fucoidan ramified matrix.

  4. Fungal Sinusitis

    Science.gov (United States)

    ... Marketplace Find an ENT Doctor Near You Fungal Sinusitis Fungal Sinusitis Patient Health Information News media interested ... sinusitis results. There Are Four Types Of Fungal Sinusitis: Mycetoma Fungal Sinusitis produces clumps of spores, a " ...

  5. Shifts in soil fungal communities in Tuber melanosporum plantations over a 20-year transition from agriculture fields to oak woodlands

    Directory of Open Access Journals (Sweden)

    Liu Bing

    2016-04-01

    Full Text Available Aim of study: To explore the diversity of soil fungi found in black truffle (Tuber melanosporum plantations following the introduction of the mycorrhizal-colonized host tree, (Quercus ilex, through the development of the brûlé and production of mature sporocarps.Area of study: This research was carried out province of Teruel, Aragon (central eastern Spain.Material and Methods: Soil samples from 6 plantations were collected beneath Q. ilex trees inoculated with T. melanosporum, of 3, 5, 7, 10, 14 and 20 years after out planting in truffle plantations. Soil DNA was extracted, PCR-amplified and sequenced to compare soil fungi present at different ages.Main results: As tree age increased, we observed an increased frequency of T. melanosporum (from 8% to 71% of sequenced colonies and concomitant decrease in the combined frequency of Fusarium spp. and Phoma spp. (from 64% to 3%.Research highlights: There are important shifts in species richness and in functional groups in the soil fungal communities in maturing black truffle-oak woodland plantations. The observed inverse relationship between the frequency of soil endophytic and/or pathogenic fungi and that of the mycorrhizal mutualist T. melanosporum provides support to continue a deeper analysis of shifts in fungal communities and functional groups where there is a transition from agriculture fields to woodlands.Abbreviations used: Ectomycorrhiza (ECM fungus; Vesicular arbuscular mycorrhiza (VAM; Operational taxonomic unit (OTU.

  6. Shifts in soil fungal communities in Tuber melanosporum plantations over a 20-year transition from agriculture fields to oak woodlands

    Energy Technology Data Exchange (ETDEWEB)

    Bing, L.; Fischer, C.R.; Bonet, J.A.; Castaño, C.; Colinas, C.

    2016-07-01

    Aim of study: To explore the diversity of soil fungi found in black truffle (Tuber melanosporum) plantations following the introduction of the mycorrhizal-colonized host tree, (Quercus ilex), through the development of the brûlé and production of mature sporocarps. Area of study: This research was carried out province of Teruel, Aragon (central eastern Spain). Material and Methods: Soil samples from 6 plantations were collected beneath Q. ilex trees inoculated with T. melanosporum, of 3, 5, 7, 10, 14 and 20 years after out planting in truffle plantations. Soil DNA was extracted, PCR-amplified and sequenced to compare soil fungi present at different ages. Main results: As tree age increased, we observed an increased frequency of T. melanosporum (from 8% to 71% of sequenced colonies) and concomitant decrease in the combined frequency of Fusarium spp. and Phoma spp. (from 64% to 3%). Research highlights: There are important shifts in species richness and in functional groups in the soil fungal communities in maturing black truffle-oak woodland plantations. The observed inverse relationship between the frequency of soil endophytic and/or pathogenic fungi and that of the mycorrhizal mutualist T. melanosporum provides support to continue a deeper analysis of shifts in fungal communities and functional groups where there is a transition from agriculture fields to woodlands. (Author)

  7. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes

    DEFF Research Database (Denmark)

    Barnes, Christopher James; Maldonado Goyzueta, Carla Brenda; Frøslev, Tobias Guldberg;

    2016-01-01

    Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected in mic...... root-associated fungal diversity in subtropical regions. This study sheds further light on the diversity and distribution of the world's "hidden biodiversity"....

  8. Spatial and Temporal Variation in Fungal Endophyte Communities Isolated from Cultivated Cotton (Gossypium hirsutum)

    OpenAIRE

    María J Ek-Ramos; Wenqing Zhou; Valencia, César U.; Antwi, Josephine B.; Kalns, Lauren L.; Gaylon D Morgan; David L. Kerns; Sword, Gregory A.

    2013-01-01

    Studies of fungi in upland cotton (Gossypium hirsutum) cultivated in the United States have largely focused on monitoring and controlling plant pathogens. Given increasing interest in asymptomatic fungal endophytes as potential biological control agents, surveys are needed to better characterize their diversity, distribution patterns and possible applications in integrated pest management. We sampled multiple varieties of cotton in Texas, USA and tested for temporal and spatial variation in f...

  9. Fungal community analysis in the deep-sea sediments of the Pacific Ocean assessed by comparison of ITS, 18S and 28S ribosomal DNA regions

    Science.gov (United States)

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

    2016-03-01

    We investigated the diversity of fungal communities in 6 different deep-sea sediment samples of the Pacific Ocean based on three different types of clone libraries, including internal transcribed spacer (ITS), 18S rDNA, and 28S rDNA regions. A total of 1978 clones were generated from 18 environmental clone libraries, resulting in 140 fungal operational taxonomic units (OTUs), including 18 OTUs from ITS, 44 OTUs from 18S rDNA, and 78 OTUs from 28S rDNA gene primer sets. The majority of the recovered sequences belonged to diverse phylotypes of the Ascomycota and Basidiomycota. Additionally, our study revealed a total of 46 novel fungal phylotypes, which showed low similarities (<97%) with available fungal sequences in the GenBank, including a novel Zygomycete lineage, suggesting possible new fungal taxa occurring in the deep-sea sediments. The results suggested that 28S rDNA is an efficient target gene to describe fungal community in deep-sea environment.

  10. Forestry impacts on the hidden fungal biodiversity associated with bryophytes.

    Science.gov (United States)

    Davey, Marie L; Kauserud, Håvard; Ohlson, Mikael

    2014-10-01

    Recent studies have revealed an unexpectedly high, cryptic diversity of fungi associated with boreal forest bryophytes. Forestry practices heavily influence the boreal forest and fundamentally transform the landscape. However, little is known about how bryophyte-associated fungal communities are affected by these large-scale habitat transformations. This study assesses to what degree bryophyte-associated fungal communities are structured across the forest successional stages created by current forestry practices. Shoots of Hylocomium splendens were collected in Picea abies dominated forests of different ages, and their associated fungal communities were surveyed by pyrosequencing of ITS2 amplicons. Although community richness, diversity and evenness were relatively stable across the forest types and all were consistently dominated by ascomycete taxa, there was a marked shift in fungal community composition between young and old forests. Numerous fungal operational taxonomic units (OTUs) showed distinct affinities for different forest ages. Spatial structure was also detected among the sites, suggesting that environmental gradients resulting from the topography of the study area and dispersal limitations may also significantly affect bryophyte-associated fungal community structure. This study confirms that Hylocomium splendens hosts an immense diversity of fungi and demonstrates that this community is structured in part by forest age, and as such is highly influenced by modern forestry practices.

  11. Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition

    OpenAIRE

    Jingqi eGuo; Rebecca Lynne McCulley; McNear, David H.

    2015-01-01

    Tall fescue (Lolium arundinaceum (Schreb.)) is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a shoot-specific fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stresses. Because alkaloids produced by the common variety of the endophyte cause severe animal health issues, focus has been on replacing the common-toxic strain with novel varieties that do not produce t...

  12. Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition

    OpenAIRE

    Guo, Jingqi; Rebecca L. McCulley; McNear, David H.

    2015-01-01

    Tall fescue [Lolium arundinaceum (Schreb.)] is a cool-season perennial grass used in pastures throughout the Southeastern United States. The grass can harbor a shoot-specific fungal endophyte (Epichloë coenophiala) thought to provide the plant with enhanced resistance to biotic and abiotic stresses. Because alkaloids produced by the common variety of the endophyte cause severe animal health issues, focus has been on replacing the common-toxic strain with novel varieties that do not produce th...

  13. The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests.

    Science.gov (United States)

    Rosenstock, Nicholas P; Berner, Christoffer; Smits, Mark M; Krám, Pavel; Wallander, Håkan

    2016-07-01

    We investigated fungal growth and community composition in buried meshbags, amended with apatite, biotite or hornblende, in Norway spruce (Picea abies) forests of varying nutrient status. Norway spruce needles and soil collected from forests overlying serpentinite had low levels of potassium and phosphorus, those from granite had low levels of magnesium, whereas those from amphibolite had comparably high levels of these nutrients. We assayed the fungal colonization of meshbags by measuring ergosterol content and fungal community with 454 sequencing of the internal transcribed spacer region. In addition, we measured fine root density. Fungal biomass was increased by apatite amendment across all plots and particularly on the K- and P-deficient serpentinite plots, whereas hornblende and biotite had no effect on fungal biomass on any plots. Fungal community (total fungal and ectomycorrhizal) composition was affected strongly by sampling location and soil depth, whereas mineral amendments had no effect on community composition. Fine root biomass was significantly correlated with fungal biomass. Ectomycorrhizal communities may respond to increased host-tree phosphorus demand by increased colonization of phosphorus-containing minerals, but this does not appear to translate to a shift in ectomycorrhizal community composition. This growth response to nutrient demand does not appear to exist for potassium or magnesium limitation.

  14. Effects of UV-accelerated weathering and natural weathering conditions on anti-fungal efficacy of wood/PVC composites doped with propylene glycol-based HPQM

    Directory of Open Access Journals (Sweden)

    P. Srimalanon

    2016-04-01

    Full Text Available This work studied the mechanical, physical and weathering properties and anti-fungal efficacy of polyvinyl chloride(PVC and wood flour/polyvinyl chloride composites(WPVC. 2-hydroxypropyl-3-piperazinyl-quinoline carboxylic acid methacrylate (HPQM in propylene glycol was used as an anti-fungal agent. Propylene glycol-based HPQM was doped in neat PVC and in WPVC containing 50 and 100 pph wood (WPVC-50 and WPVC-100. The flexural properties of PVC decreased when propylene glycol-based HPQM was added. However, adding this component did not affect the flexural properties of WPVC. Fungal growth inhibition test and dry weight technique were used for evaluation of anti-fungal effectiveness. Aspergillus niger was used as a testing fungus. Adding propylene glycol-based HPQM to WPVC-100 led to the most effective anti-fungal performance. Wood flour acted as an anti-fungal promoter for the WPVC composites. The optimal dosages of propylene glycol-based HPQM in PVC, WPVC-50, and WPVC-100 were 50000, 15000, and 10000 ppm, respectively. UV-accelerated weathering aging and natural weathering conditions were found to affect the flexural properties of PVC and WPVC. The change in the anti-microbial performance of WPVC under natural weathering were slower than those under UV-accelerated weathering aging. The anti-microbial evaluation indicated that the samples doped with less than 20000 ppm propylene glycol-based HPQM had a more pronounced effect than the ones doped with higher dosages.

  15. variabilty in parasites' community structure and composition in cat ...

    African Journals Online (AJOL)

    Mgina

    ABSTRACT. This study investigated the composition and structure of the parasite communities in Cat fish ... The western shore is mainly sandy ... part of which is sandy and rocky and along the shores ..... Sediment And Microalgae From Lake ...

  16. How microbial community composition regulates coral disease development

    National Research Council Canada - National Science Library

    Mao-Jones, Justin; Ritchie, Kim B; Jones, Laura E; Ellner, Stephen P

    2010-01-01

    ...) and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral...

  17. Co-existing ericaceous plant species in a subarctic mire community share fungal root endophytes

    DEFF Research Database (Denmark)

    Kjøller, Rasmus; Olsrud, Maria; Michelsen, Anders

    2010-01-01

    During the last decade, culture-independent identification tools have widened our knowledge of fungi colonizing ericaceous roots including ericoid mycorrhizal fungi. One focal interest has been to identify fungi, which simultaneously can establish ericoid and ectomycorrhiza, while knowledge about......, was studied. From each of these plants, in each of five plots, clone libraries were established using fungal specific ITS-PCR followed by cloning, PCR–RFLP and sequencing. The clone libraries were dominated by potential ericoid mycorrhizal fungi, particularly Rhizoscyphus ericae, fungi belonging...

  18. Response of soil microbial community composition to afforestation with pure and mixed tree species

    Science.gov (United States)

    Gunina, Anna; Smith, Andrew; Godbold, Douglas; Kuzyakov, Yakov; Jones, Davey

    2016-04-01

    Afforestation of agricultural land affects soil ecosystem functions by inducing carbon (C) and nitrogen (N) sequestration and promoting shifts in microbial community structure. Soil C and N stocks undergo progressive changes over several decades after forest establishment, particularly in successional forests. In contrast, microbial community structure can be shifted already in the first decade and thus, direct effect of tree species can be revealed. Thus, the aim of this study was to determine how soil microbial community composition is altered by afforestation with either one, two or three species mixtures of trees, which possess strongly contrasting functional traits. The study was conducted at the BangorDIVERSE temperate forest experiment established in 2004 on a former arable soil. Soil samples were collected under single, two and three species mixtures of alder, birch, beech and oak, while contiguous field was chosen as a control. Soil samples were analysed for key quality indicators (total C and N, pH, nitrate and ammonium), and microbial community structure was determined by phospholipid fatty acids (PLFAs) analysis. Ten years after afforestation, total soil C, N and C/N ratios were not strongly affected, with the highest positive changes (up to 20%) for the birch, alder+oak and birch+beech plots. Decrease of C and N contents were observed for the pure beech plot. pH decreased by 1-1.2 units for all forest plots compare to the control soil. Total PLFAs content (370-630 nmol g-1 soil) increased in comparison to the control (315 nmol g-1 soil), resulting in the changes in total PLFAs content from 20 to 100%. Thus, changes of chemical properties (C, N) occur slower than changes of microbial biomarkers at the early stage of afforestation. Bacterial PLFA content was shifted by 20-120%, whereas fungal PLFAs were changed by 50-300%, reflecting stronger impact of afforestation on the recovery of fungal communities than on bacterial. Principal component analysis of

  19. The role of endophytic fungal individuals and communities in the decomposition of Pinus massoniana needle litter.

    Directory of Open Access Journals (Sweden)

    Zhilin Yuan

    Full Text Available The role of fungal endophytes (FEs as "pioneer" decomposers has recently been recognized; however, the extent to which FEs contribute to litter loss is less well understood. The genetic and enzymatic bases of FE-mediated decomposition have also rarely been addressed. The effects of populations and individuals (with an emphasis on two dominant Lophodermium taxa of FEs on needle-litter decomposition were assessed for Pinus massoniana, a ubiquitous pine in southern China. Data from in vivo (microcosm experiments indicated that the percentage of litter-mass loss triggered by FEs was linearly correlated with incubation time and approached 60% after seven months. In vitro decomposition tests also confirmed that endophytic Lophodermium isolates caused 14-22% mass loss within two months. Qualitative analysis of exoenzymes (cellulase and laccase, important for lignocellulose degradation revealed that almost all of the Lophodermium isolates showed moderate or strong positive reactions. Furthermore, partial sequences of β-glucosidase (glycoside hydrolase family 3, GH3, laccase, and cellobiohydrolase (GH7 genes were amplified from Lophodermium isolates as "functional markers" to evaluate their potential for lignocellulolytic activity. Three different genes were detected, suggesting a flexible and delicate decomposition system rich in FEs. Our work highlights the possibility that the saprophytism and endophytism of FEs may be prerequisites to initiating rapid decomposition and thus may be key in Fes' contribution to litter decomposition, at least in the early stage. Potential indicators of the presence of core fungal decomposers are also briefly discussed.

  20. Response of fungal community in the unpolluted and polluted (textile and distillery wastes) habitats.

    Science.gov (United States)

    Grover, Ruby; Sharma, K P; Kumar, Pawan; Kumar, Suresh

    2007-04-01

    37 fungal species were recorded, maximum found in textile wastewater polluted habitats (35) followed by unpolluted (15) and distillery polluted (6) habitats. Fungal diversity in sediment samples of textile wastewater polluted habitats (25) was a little lower than wastewater samples (32), whereas it varied little both in the samples of unpolluted habitats (Sambhar wetlands: 5-6; Garden tanks: 9-10) and distillery waste (3-5). Seasonal variation in species diversity was more pronounced in the textile wastewater polluted habitats. Their minimum number was often found during the rainy season while maximum in the winter season, in the polluted habitats but during summer in the unpolluted habitats. Aspergillus was the most diverse genus represented by 7 species, followed by Cladosporium and Fusarium (3 species each) while Drechslera, Rhizopus and Trichoderma had 2 species each. The remaining genera (18) were monotypic. Colony Forming Units (CFUs) were also maximum in the textile wastewater polluted habitats (5.6-1898.9 x 10(3)/L), followed by unpolluted (6.7-560.0 x 10(3)/L) and distillery waste polluted habitats (3.1-53.3 x 10(3)/L), being usually higher in the sediment samples. Their number also varied seasonally, being maximum during winter season in the water samples, whereas in summer in the sediment samples. Aspergillus fumigatus, A. niger, Cladosporium cladosporioides, C. sphaerospermum and Penicillium chrysogenum usually contributed maximum to the CFU values in the polluted as well as in unpolluted habitats.

  1. Effect of Soil Ameliorators on Ectomycorrhizal Fungal Communities that Colonize Seedlings of Pinus densiflora in Abandoned Coal Mine Spoils.

    Science.gov (United States)

    Lee, Eun-Hwa; Eo, Ju-Kyeong; Lee, Chang-Seok; Eom, Ahn-Heum

    2012-09-01

    In this study, the effect of soil ameliorators on ectomycorrhizal (ECM) fungal communities in coal mine spoils was investigated. Organic fertilizers and slaked lime were applied as soil ameliorators in 3 abandoned coal mine spoils. One year after the initial treatment, roots of Pinus densiflora seedlings were collected and the number of ECM species, colonization rate, and species diversity were assessed. The results showed that the soil ameliorators significantly increased ECM colonization on the roots of P. densiflora. The results suggest that soil ameliorators can have a positive effect on ECM fungi in terms of growth of host plants and show the potential use of soil ameliorator treatment for revegetation with ECM-colonized pine seedlings in the coal mine spoils.

  2. Arbuscular Mycorrhizal Fungal Communities in the Roots of Maize Lines Contrasting for Al Tolerance Grown in Limed and Non-Limed Brazilian Oxisoil.

    Science.gov (United States)

    Gomes, Eliane A; Oliveira, Christiane A; Lana, Ubiraci G P; Noda, Roberto W; Marriel, Ivanildo E; de Souza, Francisco A

    2015-07-01

    Aluminum (Al) toxicity is one of the greatest limitations to agriculture in acid soils, particularly in tropical regions. Arbuscular mycorrhizal fungi (AMF) can supply plants with nutrients and give protection against Al toxicity. The aim of this work was to evaluate the effects of soil liming (i.e., reducing Al saturation) on the AMF community composition and structure in the roots of maize lines contrasting for Al tolerance. To this end, we constructed four 18S rDNA cloning libraries from L3 (Al tolerant) and L22 (Al sensitive) maize lines grown in limed and non-limed soils. A total of 790 clones were sequenced, 69% belonging to the Glomeromycota phylum. The remaining sequences were from Ascomycota, which were more prominent in the limed soil, mainly in the L3 line. The most abundant AM fungal clones were related to the family Glomeraceae represented by the genera uncultured Glomus followed by Rhizophagus and Funneliformis. However, the most abundant operational taxonomic units with 27% of the Glomeromycota clones was affiliated to genus Racocetra. This genus was present in all the four libraries, but it was predominant in the non-limed soils, suggesting that Racocetra is tolerant to Al toxicity. Similarly, Acaulospora and Rhizophagus were also present mostly in both lines in non-limed soils. The community richness of AMF in the non-limed soils was higher than the limed soil for both lines. The results suggest that the soil Al saturation was the parameter that mostly influences the AMF species composition in the soils in this study.

  3. Laboratory study of fungal bioreceptivity of different fractions of composite flooring tiles showing efflorescence.

    Science.gov (United States)

    Masaphy, Segula; Lavi, Ido; Sultz, Stephan; Zabari, Limor

    2014-06-01

    Fungi can grow in extreme habitats, such as natural stone and mineral building materials, sometimes causing deterioration. Efflorescence-concentrated salt deposits-results from water movement through building material; it can damage masonry materials and other bricks. Fungal isolate KUR1, capable of growth on, and dissolution of stone chips composing terrazzo-type floor tiles, was isolated from such tiles showing fiber-like crystalline efflorescence. The isolate's ribosomal DNA sequences were 100 % identical to those of Nigrospora sphaerica. The ability of KUR1 to colonize and degrade the different stone chips composing the tiles was studied in axenic culture experiments. When exposed to each of the different mineral chip types composed of dolomite, calcite, or calcite-apatite mineral in low-nutrition medium, the fungus showed selective nutrient consumption, and different growth and stone mineral dissolution rates. Micromorphological examination of the fungus-colonized chips by electron microscopy showed the production of a fungal biofilm with thin films around the hyphae on the surface of the examined chips and disintegration of the calcite-apatite fraction. More than 70 % dissolution of the introduced powdered (mineral was obtained within 10 days of incubation for the soft calcite-apatite fraction.

  4. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.

    Science.gov (United States)

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2014-04-01

    Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date.

  5. A 3-year study reveals that plant growth stage, season and field site affect soil fungal communities while cultivar and GM-trait have minor effects

    NARCIS (Netherlands)

    Hannula, S.E.; De Boer, W.; Van Veen, J.A.

    2012-01-01

    In this three year field study the impact of different potato (Solanum tuberosum L.) cultivars including a genetically modified (GM) amylopectin-accumulating potato line on rhizosphere fungal communities are investigated using molecular microbiological methods. The effects of growth stage of a plant

  6. Fungal community analysis in the deep-sea sediments of the central Indian Basin by culture-independent approach

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, P.; Raghukumar, C.; Verma, P.; Shouche, Y.

    of 39 fungal operational taxonomic units, with 32 distinct fungal taxa were recovered from 768 clones generated from 16 environmental clone libraries. The application of multiple primers enabled the recovery of eight sequences that appeared to be new...

  7. [Characteristics of soil microbial biomass and community composition in three types of plantations in southern subtropical area of China].

    Science.gov (United States)

    Wang, Wei-Xia; Shi, Zuo-Min; Luo, Da; Liu, Shi-Rong; Lu, Li-Hua

    2013-07-01

    By using fumigation-extraction method and phospholipid fatty acids (PLFAs) analysis, this paper studied the characteristics of soil microbial biomass and community composition in the Erythrophleum fordii, Castanopsis hystrix, and Pinus massoniana plantations in south subtropical China. The soil microbial biomass, total PLFAs, bacterial PLFAs, and fungal PLFAs in the plantations were significantly affected by the plantation type and season, and the soil microbial biomass, total PLFAs, and individual PLFA signatures were higher in dry season than in rainy season. The C. hystrix plantation had the highest soil microbial biomass carbon and total PLFAs, while the E. fordii plantation had the highest soil microbial biomass nitrogen. There was a significant positive correlation between the soil pH and arbuscular mycorrhizal fungal (AMF) PLFA (16:1omega5c). The soil total PLFAs, gram-positive bacterial PLFAs, saprophytic fungal PLFA (18:2omega6,9c), and the ratio of gram-positive to gram-negative bacterial PLFAs were significantly positively correlated with soil organic carbon, total nitrogen, and total phosphorus, suggesting that the soil organic carbon, total nitrogen, and total phosphorus contents were the most important nutrient factors affecting the numbers and types of the soil microorganisms. In addition, the ectomycorrhizae fungal PLFA (18:1omega9c) and AMF PLFA were significantly correlated with the soil C/N ratio.

  8. Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland.

    Science.gov (United States)

    Klabi, Rim; Bell, Terrence H; Hamel, Chantal; Iwaasa, Alan; Schellenberg, Mike; Raies, Aly; St-Arnaud, Marc

    2015-01-01

    Adding inorganic P- and N-fixing legumes to semi-arid grasslands can increase forage yield, but soil nutrient concentrations and plant cover may also interact to modify soil fungal populations, impacting short- and long-term forage production. We tested the effect of plant assemblage (seven native grasses, seven native grasses + the domesticated N-fixing legume Medicago sativa, seven native grasses + the native N-fixing legume Dalea purpurea or the introduced grass Bromus biebersteinii + M. sativa) and soil P concentration (addition of 0 or 200 P2O5 kg ha(-1) at sowing) on the diversity and community structure of arbuscular mycorrhizal (AM) fungi and total fungi over two consecutive years, using 454-pyrosequencing of 18S rDNA and ITS amplicons. Treatment effects were stronger in the wet year (2008) than the dry year (2009). The presence of an N-fixing legume with native grasses generally increased AM fungal diversity, while the interaction between soil P concentration and plant assemblage modified total fungal community structure in 2008. Excluding interannual variations, which are likely driven by moisture and plant productivity, AM fungal communities in semi-arid grasslands appear to be primarily affected by plant assemblage composition, while the composition of other fungi is more closely linked to soil P.

  9. Enhancement of the Knowledge on Fungal Communities in Directly Brined Aloreña de Málaga Green Olive Fermentations by Metabarcoding Analysis

    Science.gov (United States)

    Arroyo-López, Francisco Noé; Medina, Eduardo; Ruiz-Bellido, Miguel Ángel; Romero-Gil, Verónica; Montes-Borrego, Miguel

    2016-01-01

    Nowadays, our knowledge of the fungal biodiversity in fermented vegetables is limited although these microorganisms could have a great influence on the quality and safety of this kind of food. This work uses a metagenetic approach to obtain basic knowledge of the fungal community ecology during the course of fermentation of natural Aloreña de Málaga table olives, from reception of raw material to edible fruits. For this purpose, samples of brines and fruits were collected from two industries in Guadalhorce Valley (Málaga, Spain) at different moments of fermentation (0, 7, 30 and 120 days). The physicochemical and microbial counts performed during fermentation showed the typical evolution of this type of processes, mainly dominated by yeasts in apparent absence of Enterobacteriaceae and Lactobacillaceae. High-throughput barcoded pyrosequencing analysis of ITS1-5.8S-ITS2 region showed a low biodiversity of the fungal community, with the presence at 97% identity of 29 different fungal genera included in 105 operational taxonomic units (OTUs). The most important genera in the raw material at the moment of reception in the industry were Penicillium, Cladosporium, Malassezia, and Candida, whilst after 4 months of fermentation in brines Zygotorulaspora and Pichia were predominant, whereas in fruits were Candida, Penicillium, Debaryomyces and Saccharomyces. The fungal genera Penicillium, Pichia, and Zygotorulaspora were shared among the three types of substrates during all the course of fermentation, representing the core fungal population for this table olive specialty. A phylogenetic analysis of the ITS sequences allowed a more accurate assignment of diverse OTUs to Pichia manshurica, Candida parapsilosis/C. tropicalis, Candida diddensiae, and Citeromyces nyonensis clades. This study highlights the existence of a complex fungal consortium in olive fermentations including phytopathogenic, saprofitic, spoilage and fermentative genera. Insights into the ecology

  10. Cohort Study of Airway Mycobiome in Adult Cystic Fibrosis Patients: Differences in Community Structure between Fungi and Bacteria Reveal Predominance of Transient Fungal Elements

    Science.gov (United States)

    Sauer-Heilborn, Annette; Welte, Tobias; Guzman, Carlos A.; Abraham, Wolf-Rainer; Höfle, Manfred G.

    2015-01-01

    The respiratory mycobiome is an important but understudied component of the human microbiota. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. This study compared the bacterial and fungal communities of sputum samples from a large cohort of 56 adult patients with cystic fibrosis (CF) during nonexacerbation periods and under continuous antibiotic treatment. Molecular fingerprinting based on single-strand conformation polymorphism (SSCP) analysis revealed fundamental differences between bacterial and fungal communities. Both groups of microorganisms were taxonomically classified by identification of gene sequences (16S rRNA and internal transcript spacer), and prevalences of single taxa were determined for the entire cohort. Major bacterial pathogens were frequently observed, whereas fungi of known pathogenicity in CF were detected only in low numbers. Fungal species richness increased without reaching a constant level (saturation), whereas bacterial richness showed saturation after 50 patients were analyzed. In contrast to bacteria, a large number of fungal species were observed together with high fluctuations over time and among patients. These findings demonstrated that the mycobiome was dominated by transient species, which strongly suggested that the main driving force was their presence in inhaled air rather than colonization. Considering the high exposure of human airways to fungal spores, we concluded that fungi have low colonization abilities in CF, and colonization by pathogenic fungal species may be considered a rare event. A comprehensive understanding of the conditions promoting fungal colonization may offer the opportunity to prevent colonization and substantially reduce or even eliminate fungus-related disease progression in CF. PMID:26135861

  11. Enhancement of the Knowledge on Fungal Communities in Directly Brined Aloreña de Málaga Green Olive Fermentations by Metabarcoding Analysis.

    Science.gov (United States)

    Arroyo-López, Francisco Noé; Medina, Eduardo; Ruiz-Bellido, Miguel Ángel; Romero-Gil, Verónica; Montes-Borrego, Miguel; Landa, Blanca B

    2016-01-01

    Nowadays, our knowledge of the fungal biodiversity in fermented vegetables is limited although these microorganisms could have a great influence on the quality and safety of this kind of food. This work uses a metagenetic approach to obtain basic knowledge of the fungal community ecology during the course of fermentation of natural Aloreña de Málaga table olives, from reception of raw material to edible fruits. For this purpose, samples of brines and fruits were collected from two industries in Guadalhorce Valley (Málaga, Spain) at different moments of fermentation (0, 7, 30 and 120 days). The physicochemical and microbial counts performed during fermentation showed the typical evolution of this type of processes, mainly dominated by yeasts in apparent absence of Enterobacteriaceae and Lactobacillaceae. High-throughput barcoded pyrosequencing analysis of ITS1-5.8S-ITS2 region showed a low biodiversity of the fungal community, with the presence at 97% identity of 29 different fungal genera included in 105 operational taxonomic units (OTUs). The most important genera in the raw material at the moment of reception in the industry were Penicillium, Cladosporium, Malassezia, and Candida, whilst after 4 months of fermentation in brines Zygotorulaspora and Pichia were predominant, whereas in fruits were Candida, Penicillium, Debaryomyces and Saccharomyces. The fungal genera Penicillium, Pichia, and Zygotorulaspora were shared among the three types of substrates during all the course of fermentation, representing the core fungal population for this table olive specialty. A phylogenetic analysis of the ITS sequences allowed a more accurate assignment of diverse OTUs to Pichia manshurica, Candida parapsilosis/C. tropicalis, Candida diddensiae, and Citeromyces nyonensis clades. This study highlights the existence of a complex fungal consortium in olive fermentations including phytopathogenic, saprofitic, spoilage and fermentative genera. Insights into the ecology

  12. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR.

    Directory of Open Access Journals (Sweden)

    Nicolas Chemidlin Prévost-Bouré

    Full Text Available Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR. The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning--sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.

  13. Community composition has greater impact on the functioning of marine phytoplankton communities than ocean acidification.

    Science.gov (United States)

    Eggers, Sarah L; Lewandowska, Aleksandra M; Barcelos E Ramos, Joana; Blanco-Ameijeiras, Sonia; Gallo, Francesca; Matthiessen, Birte

    2014-03-01

    Ecosystem functioning is simultaneously affected by changes in community composition and environmental change such as increasing atmospheric carbon dioxide (CO2 ) and subsequent ocean acidification. However, it largely remains uncertain how the effects of these factors compare to each other. Addressing this question, we experimentally tested the hypothesis that initial community composition and elevated CO2 are equally important to the regulation of phytoplankton biomass. We full-factorially exposed three compositionally different marine phytoplankton communities to two different CO2 levels and examined the effects and relative importance (ω(2) ) of the two factors and their interaction on phytoplankton biomass at bloom peak. The results showed that initial community composition had a significantly greater impact than elevated CO2 on phytoplankton biomass, which varied largely among communities. We suggest that the different initial ratios between cyanobacteria, diatoms, and dinoflagellates might be the key for the varying competitive and thus functional outcome among communities. Furthermore, the results showed that depending on initial community composition elevated CO2 selected for larger sized diatoms, which led to increased total phytoplankton biomass. This study highlights the relevance of initial community composition, which strongly drives the functional outcome, when assessing impacts of climate change on ecosystem functioning. In particular, the increase in phytoplankton biomass driven by the gain of larger sized diatoms in response to elevated CO2 potentially has strong implications for nutrient cycling and carbon export in future oceans.

  14. Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

    NARCIS (Netherlands)

    Pereira e Silva, Michele C.; Franco Dias, Armando Cavalcante; van Elsas, Jan Dirk; Salles, Joana Falcao

    2012-01-01

    Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this st

  15. Fungal growth and biomass development is boosted by plants in snow-covered soil.

    Science.gov (United States)

    Kuhnert, Regina; Oberkofler, Irmgard; Peintner, Ursula

    2012-07-01

    Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We found distinct seasonal patterns for all biomass parameters, with highest biomass concentrations during winter in snow-covered soil. The presence of plant cover had a significant positive effect on the amount of biomass in the soil, but the type of plant cover (plant species) was not a significant factor. A mean hyphal ingrowth of 5.6 m g(-1) soil was detected in snow-covered soil during winter, thus clearly proving fungal growth during winter in snow-covered soil. Winter fungal communities had a typical species composition: saprobial fungi were dominating, among them many basidiomycete yeasts. Plant cover had no influence on the composition of winter fungal communities.

  16. UTILIZATION OF T-RFLP (TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM) TO CHARACTERIZE MIXED ECTOMYCORRHIZAL FUNGAL COMMUNITIES

    Science.gov (United States)

    Studies of ectomycorrhizal community structure have used a variety of analytical regimens including sole or partial reliance on gross morphological characterization of colonized root tips. Depending on the rigor of the classification protocol, this technique can incorrectly assig...

  17. Shifting fungal endophyte communities colonize Bouteloua gracilis: effect of host tissue and geographical distribution.

    Science.gov (United States)

    Herrera, José; Khidir, Hana H; Eudy, Douglas M; Porras-Alfaro, Andrea; Natvig, Donald O; Sinsabaugh, Robert L

    2010-01-01

    Communities of root-associated fungi (RAF) commonly have been studied under the auspices of arbuscular mycorrhizal fungi (AMF) or ectomycorrhizal fungi. However many studies now indicate that other groups of endophytic RAF, including dark septate endophytes (DSE) are more abundant in some plants and environments. The common forage grass, Bouteloua gracilis, was used as a model to examine whether RAF also colonize different organs within the same plant and to compare RAF communities from sites across North America, spanning the latitudinal range of B. gracilis (from Canada to Mexico). We compared the RAF communities of organs within individual plants at one site and within plant roots among six sites. With the possible exception of one group related to genus Paraphaeosphaeria there was little evidence that RAF colonized vertically beyond the crowns. Furthermore, although there was some variation in the constitution of rare members of the RAF communities, several taxonomically related groups dominated the RAF community at all sites. These dominant taxa included members in the Pleosporales (related to the DSE, Paraphaeosphaeria spp.), Agaricales (related to Moniliophthora spp., or Campanella spp.) and Hypocreales (related to Fusarium spp.). AMF were notable by their near absence. Similar phylotypes from the dominant groups clustered around adjacent sites so that similarity of the RAF communities was negatively correlated to site inter-distance and the RAF communities appeared to group by country. These results increase the possibility that at least some of these common and widely distributed core members of the RAF community form important, intimate and long lasting relationships with grasses.

  18. Long-term in situ dynamics of the fungal communities in a multi-contaminated soil are mainly driven by plants.

    Science.gov (United States)

    Thion, Cécile; Cébron, Aurélie; Beguiristain, Thierry; Leyval, Corinne

    2012-10-01

    The fungal communities of a multi-contaminated soil polluted by polycyclic aromatic hydrocarbons and heavy metals (NM) were studied within a long-term in situ experiment of natural attenuation assisted by plants. Three treatments were monitored: bare soil (NM-BS), soil planted with alfalfa and inoculated with mycorrhizal fungi (NM-Msm), and soil with spontaneous vegetation (NM-SV). The same soil after thermal desorption (TD) was planted with alfalfa and inoculated with mycorrhizal fungi (TD-Msm). Twice a year for 5 years, the fungal abundance and the community structure were evaluated by real-time PCR and temporal temperature gradient gel electrophoresis targeting 18S rRNA genes. The fungal abundance increased over time and was higher in planted than in bare NM soil and in TD than in NM soil. The Shannon diversity index (H') increased during the first 2 years with the emergence of more than 30 ribotypes, but decreased after 3 years with the selection of a few competitive species, mostly Ascomycetes. H' was higher under complex plant assemblage (NM-SV) than in the NM-BS plots but did not differ between NM and TD soils planted with alfalfa. These results indicated that even in a highly polluted soil, the plant cover was the main driver of the fungal community structure. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  19. Bacterial and fungal communities of wilted Italian ryegrass silage inoculated with and without Lactobacillus rhamnosus or Lactobacillus buchneri.

    Science.gov (United States)

    Li, Y; Nishino, N

    2011-04-01

    To understand the effects of lactic acid bacteria (LAB) inoculation on fermentation products, aerobic stability and microbial communities of silage. Wilted Italian ryegrass was stored in laboratory silos with and without inoculation of Lactobacillus rhamnosus and Lactobacillus buchneri. The silos were opened after 14, 56 and 120 days and then subjected to aerobic deterioration for 7 days. Intensive alcoholic fermentation was found in untreated silage; the sum of ethanol and 2,3-butanediol content at day 14 was about 7 times higher than that of lactic and volatile fatty acids. Alcoholic fermentation was suppressed by L. rhamnosus and L. buchneri inoculation and lactic acid and acetic acid became the dominant fermentation products, respectively. Silages were deteriorated in untreated and L. rhamnosus-inoculated silages, whereas no spoilage was found in L. buchneri-inoculated silage. Enterobacteria such as Erwinia persicina, Pantoea agglomerans and Rahnella aquatilis were detected in untreated silage, whereas some of these bacteria disappeared or became faint with L. rhamnosus treatment. When silage was deteriorated, Lactobacillus brevis and Bacillus pumilus were observed in untreated and L. rhamnosus-inoculated communities, respectively. The inoculated LAB species was detectable in addition to untreated bacterial communities. Saccharomyces cerevisiae and Pichia anomala were the main fungi in untreated and L. rhamnosus-inoculated silages; however, P. anomala was not visibly seen in L. buchneri-inoculated silage either at silo opening or after exposure to air. Inoculation with L. rhamnosus can suppress alcoholic fermentation of wilted grass silage with elimination of enterobacteria at the beginning of fermentation. Addition of L. buchneri may improve aerobic stability, with distinct inhibitory effect observed on P. anomala after silo opening. Bacterial and fungal community analyses help us to understand how inoculated LAB can function to improve the fermentation and

  20. A Community-oriented CEOS Atmospheric Composition Portal (ACP)

    Science.gov (United States)

    Bernonville, S.; Goussev, O.; Falke, S.; Lindsay, F.; Lynnes, C. S.; Yang, W.; Zhao, P.; Johnson, J.

    2012-04-01

    The Atmospheric Composition Constellation (ACC) and the Workgroup for Information Systems and Services (WGISS) within the Committee on Earth Observation Satellites (CEOS) is developing a portal to support interoperability among the atmospheric composition research and applications communities. The CEOS Atmospheric Composition Portal (ACP) is defining approaches for providing data access, tools and contextual guidance for an international suite of remote sensing datasets. An initial prototype provides access to data services and analysis tools hosted by the World Data Center for Remote Sensing of the Atmosphere (WDC-RSAT), NASA's Goddard Earth Sciences Data and Information Services Center (GES DISC) and DataFed. Distributed access to data is implemented via interoperability standards, including the Open Geospatial Consortium's (OGC) Web Map Service (WMS) and Web Coverage Service (WCS). A fundamental aspect to the design, implementation and evolution of the ACP is community collaboration. The portal is intended as a community resource that is created through collaboration across remotely sensed atmospheric composition data organizations and used by a variety of groups across the climate, air quality, and stratospheric ozone domains. The implementation of interoperability standards in the ACP has involved coordination on identifying the most applicable standards and the definition of community-specific conventions to ensure consistent adoption of standards. This presentation includes an overview of the ACP, its community oriented approach, and use of community-conventions in achieving standards-based interoperability.

  1. The effect of native and introduced biofuel crops on the composition of soil biota communities

    Science.gov (United States)

    Frouz, Jan; Hedenec, Petr

    2016-04-01

    Biofuel crops are an accepted alternative to fossil fuels, but little is known about the ecological impact of their production. The aim of this contribution is to study the effect of native (Salix viminalis and Phalaris arundinacea) and introduced (Helianthus tuberosus, Reynoutria sachalinensis and Silphium perfoliatum) biofuel crop plantations on the soil biota in comparison with cultural meadow vegetation used as control. The study was performed as part of a split plot field experiment of the Crop Research Institute in the city of Chomutov (Czech Republic). The composition of the soil meso- and macrofauna community, composition of the cultivable fraction of the soil fungal community, cellulose decomposition (using litter bags), microbial biomass, basal soil respiration and PLFA composition (incl. F/B ratio) were studied in each site. The C:N ratio and content of polyphenols differed among plant species, but these results could not be considered significant between introduced and native plant species. Abundance of the soil meso- and macrofauna was higher in field sites planted with S. viminalis and P. arundinacea than those planted with S. perfoliatum, H. tuberosus and R. sachalinensis. RDA and Monte Carlo Permutation Test showed that the composition of the faunal community differed significantly between various native and introduced plants. Significantly different basal soil respiration was found in sites planted with various energy crops; however, this difference was not significant between native and introduced species. Microbial biomass carbon and cellulose decomposition did not exhibit any statistical differences among the biofuel crops. The largest statistically significant difference we found was in the content of actinobacterial and bacterial (bacteria, G+ bacteria and G- bacteria) PLFA in sites overgrown by P. arundinacea compared to introduced as well as native biofuel crops. In conclusion, certain parameters significantly differ between various native

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

    Science.gov (United States)

    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.

  3. Evidence that chytrids dominate fungal communities in high-elevation soils.

    Science.gov (United States)

    Freeman, K R; Martin, A P; Karki, D; Lynch, R C; Mitter, M S; Meyer, A F; Longcore, J E; Simmons, D R; Schmidt, S K

    2009-10-27

    Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread and are increasing in area due to retreat of glaciers worldwide. Soils in these environments are cold and during the brief summer are exposed to high levels of UV radiation and dramatic fluctuations in moisture and temperature. Recent research suggests that these environments harbor immense microbial diversity. Here we use sequencing of environmental DNA, culturing of isolates, and analysis of environmental variables to show that members of the Chytridiomycota (chytrids) dominate fungal biodiversity and perhaps decomposition processes in plant-free, high-elevation soils from the highest mountain ranges on Earth. The zoosporic reproduction of chytrids requires free water, yet we found that chytrids constituted over 70% of the ribosomal gene sequences of clone libraries from barren soils of the Himalayas and Rockies; by contrast, they are rare in other soil environments. Very few chytrids have been cultured, although we were successful at culturing chytrids from high-elevation sites throughout the world. In a more focused study of our sites in Colorado, we show that carbon sources that support chytrid growth (eolian deposited pollen and microbial phototrophs) are abundant and that soils are saturated with water for several months under the snow, thus creating ideal conditions for the development of a chytrid-dominated ecosystem. Our work broadens the known biodiversity of the Chytridomycota, and describes previously unsuspected links between aquatic and terrestrial ecosystems in alpine regions.

  4. Soil biodiversity and soil community composition determine ecosystem multifunctionality.

    Science.gov (United States)

    Wagg, Cameron; Bender, S Franz; Widmer, Franco; van der Heijden, Marcel G A

    2014-04-08

    Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth's biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.

  5. Arbuscular mycorrhizal fungal communities along a pedo-hydrological gradient in a Central Amazonian terra firme forest.

    Science.gov (United States)

    de Oliveira Freitas, Rejane; Buscardo, Erika; Nagy, Laszlo; dos Santos Maciel, Alex Bruno; Carrenho, Rosilaine; Luizão, Regina C C

    2014-01-01

    Little attention has been paid to plant mutualistic interactions in the Amazon rainforest, and the general pattern of occurrence and diversity of arbuscular mycorrhizal fungi (AMF) in these ecosystems is largely unknown. This study investigated AMF communities through their spores in soil in a 'terra firme forest' in Central Amazonia. The contribution played by abiotic factors and plant host species identity in regulating the composition, abundance and diversity of such communities along a topographic gradient with different soils and hydrology was also evaluated. Forty-one spore morphotypes were observed with species belonging to the genera Glomus and Acaulospora, representing 44 % of the total taxa. Soil texture and moisture, together with host identity, were predominant factors responsible for shaping AMF communities along the pedo-hydrological gradient. However, the variability within AMF communities was largely associated with shifts in the relative abundance of spores rather than changes in species composition, confirming that common AMF species are widely distributed in plant communities and all plants recruited into the forest are likely to be exposed to the dominant sporulating AMF species.

  6. Influence of shredder feeding and nutrients on fungal activity and community structure in headwater streams

    Science.gov (United States)

    Namil Chung; Keller. Suberkropp

    2008-01-01

    In stream detrital food webs, interactions occur between aquatic hyphomycetes associated with decomposing leaves and shredders consuming those leaves. However, few studies have examined how the feeding activity of shredders affects aquatic hyphomycetes. We examined the effect of shredder feeding on aquatic hyphomycete communities associated with submerged leaves in two...

  7. Fertility-dependent effects of ectomycorrhizal fungal communities on white spruce seedling nutrition

    Science.gov (United States)

    Alistair J. H. Smith; Lynette R. Potvin; Erik A. Lilleskov

    2015-01-01

    Ectomycorrhizal fungi (EcMF) typically colonize nursery seedlings, but nutritional and growth effects of these communities are only partly understood. To examine these effects, Picea glauca seedlings collected from a tree nursery naturally colonized by three dominant EcMF were divided between fertilized and unfertilized treatments. After one...

  8. Dynamics of bacterial and fungal communities associated with eggshells during incubation

    NARCIS (Netherlands)

    Grizard, Stephanie; Dini Andreote, Francisco; Tieleman, B. Irene; Falcao Salles, Joana

    Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and

  9. Resilience of arctic mycorrhizal fungal communities after wildfire facilitated by resprouting shrubs

    Science.gov (United States)

    Rebecca E. Hewitt; Elizabeth Bent; Teresa N. Hollingsworth; F. Stuart Chapin; D. Lee. Taylor

    2013-01-01

    Climate-induced changes in the tundra fire regime are expected to alter shrub abundance and distribution across the Arctic. However, little is known about how fire may indirectly impact shrub performance by altering mycorrhizal symbionts. We used molecular tools, including ARISA and ITS sequencing, to characterize the mycorrhizal communities on resprouting ...

  10. Fertility-dependent effects of ectomycorrhizal fungal communities on white spruce seedling nutrition.

    Science.gov (United States)

    Smith, Alistair J H; Potvin, Lynette R; Lilleskov, Erik A

    2015-11-01

    Ectomycorrhizal fungi (EcMF) typically colonize nursery seedlings, but nutritional and growth effects of these communities are only partly understood. To examine these effects, Picea glauca seedlings collected from a tree nursery naturally colonized by three dominant EcMF were divided between fertilized and unfertilized treatments. After one growing season seedlings were harvested, ectomycorrhizas identified using DNA sequencing, and seedlings analyzed for leaf nutrient concentration and content, and biomass parameters. EcMF community structure-nutrient interactions were tested using nonmetric multidimensional scaling (NMDS) combined with vector analysis of foliar nutrients and biomass. We identified three dominant species: Amphinema sp., Atheliaceae sp., and Thelephora terrestris. NMDS + envfit revealed significant community effects on seedling nutrition that differed with fertilization treatment. PERMANOVA and regression analyses uncovered significant species effects on host nutrient concentration, content, and stoichiometry. Amphinema sp. had a significant positive effect on phosphorus (P), calcium and zinc concentration, and P content; in contrast, T. terrestris had a negative effect on P concentration. In the unfertilized treatment, percent abundance of the Amphinema sp. negatively affected foliar nitrogen (N) concentration but not content, and reduced foliar N/P. In fertilized seedlings, Amphinema sp. was positively related to foliar concentrations of N, magnesium, and boron, and both concentration and content of manganese, and Atheliaceae sp. had a negative relationship with P content. Findings shed light on the community and species effects on seedling condition, revealing clear functional differences among dominants. The approach used should be scalable to explore function in more complex communities composed of unculturable EcMF.

  11. Microbial community composition of transiently wetted Antarctic Dry Valley soils

    Directory of Open Access Journals (Sweden)

    Thomas D. Neiderberger

    2015-01-01

    Full Text Available During the summer months, wet (hyporheic soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DV become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and to compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~ 5 µg/cm3 for chlorophyll a, respectively. Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

  12. Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity.

    Directory of Open Access Journals (Sweden)

    Martin Kemler

    Full Text Available The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1 nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM. We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters. Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.

  13. Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity.

    Science.gov (United States)

    Kemler, Martin; Garnas, Jeff; Wingfield, Michael J; Gryzenhout, Marieka; Pillay, Kerry-Anne; Slippers, Bernard

    2013-01-01

    The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters). Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.

  14. The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

    Directory of Open Access Journals (Sweden)

    Sandra Granzow

    2017-05-01

    Full Text Available Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating

  15. The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

    Science.gov (United States)

    Granzow, Sandra; Kaiser, Kristin; Wemheuer, Bernd; Pfeiffer, Birgit; Daniel, Rolf; Vidal, Stefan; Wemheuer, Franziska

    2017-01-01

    Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in

  16. Effect of fungal infection on the composition of acyl lipids in wheat seedlings.

    Science.gov (United States)

    Vereshchagin, A G; Zhukov, A V

    2000-12-01

    Infection of etiolated wheat seedlings with a root rot fungus Bipolaris sorokiniana caused a strong deviation in the fatty acid composition of their total lipids from the control. The deviation occurred at the expense of that lipid group, which predominates in a given plant organ (shoots or roots), and peak deviation coincided with the onset of a severe inhibition of growth.

  17. Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols.

    Science.gov (United States)

    Prussin, Aaron J; Marr, Linsey C; Bibby, Kyle J

    2014-08-01

    Despite the obvious importance of viral transmission and ecology to medicine, epidemiology, ecology, agriculture, and microbiology, the study of viral bioaerosols and community structure has remained a vastly underexplored area, due to both unresolved technical challenges and unrecognized importance. High-throughput, culture-independent techniques such as viral metagenomics are beginning to revolutionize the study of viral ecology. With recent developments in viral metagenomics, characterization of viral bioaerosol communities provides an opportunity for high-impact future research. However, there remain significant challenges for the study of viral bioaerosols compared with viruses in other matrices, such as water, the human gut, and soil. Collecting enough biomass is essential for successful metagenomic analysis, but this is a challenge with viral bioaerosols. Herein, we provide a perspective on the importance of studying viral bioaerosols, the challenges of studying viral community structure, and the potential opportunities for improvements in methods to study viruses in indoor and outdoor air. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  18. Synthesis and anti-fungal effect of silver nanoparticles–chitosan composite particles

    Science.gov (United States)

    Wang, Lung-Shuo; Wang, Chih-Yu; Yang, Chih-Hui; Hsieh, Chen-Ling; Chen, Szu-Yu; Shen, Chi-Yen; Wang, Jia-Jung; Huang, Keng-Shiang

    2015-01-01

    Silver nanoparticles have been used in various fields, and several synthesis processes have been developed. The stability and dispersion of the synthesized nanoparticles is vital. The present article describes a novel approach for one-step synthesis of silver nanoparticles–embedded chitosan particles. The proposed approach was applied to simultaneously obtain and stabilize silver nanoparticles in a chitosan polymer matrix in-situ. The diameter of the synthesized chitosan composite particles ranged from 1.7 mm to 2.5 mm, and the embedded silver nanoparticles were measured to be 15±3.3 nm. Further, the analyses of ultraviolet-visible spectroscopy, energy dispersive spectroscopy, and X-ray diffraction were employed to characterize the prepared composites. The results show that the silver nanoparticles were distributed over the surface and interior of the chitosan spheres. The fabricated spheres had macroporous property, and could be used for many applications such as fungicidal agents in the future. PMID:25878501

  19. Sponge diversity and community composition in Irish bathyal coral reefs

    NARCIS (Netherlands)

    Soest, van R.W.M; Cleary, D.F.R.; Kluijver, de M.J.; Lavaleye, M.S.S.; Maier, C.; Duy, van F.C.

    2007-01-01

    Sponge diversity and community composition in bathyal cold water coral reefs (CWRs) were examined at 500-900 m depth on the southeastern slopes of Rockall Bank and the northwestern slope of Porcupine Bank, to the west of Ireland in 2004 and 2005 with boxcores. A total of 104 boxcore samples, supplem

  20. Do shifts in ectomycorrhizal fungal communities change the sources of N and S for Bishop pine trees?

    Science.gov (United States)

    Willing, C.; Roddy, A. B.; Glassman, S. I.; Dawson, T. E.

    2016-12-01

    Estimates predict that more than 90% percent of land plants are hosts to mycorrhizal fungi. As these ubiquitous symbionts interact with their plant hosts along a spectrum from parasitism to mutualism, it is important to determine how different communities of these fungi might function along this continuum. In this study, we investigated the consequences of Pinus muricata association with ectomycorrhizal fungi (EcM) sampled from different environments throughout North America. Pines are rarely, if ever, found in nature without their EcM associates. As such, it is important to consider the potential consequences of shifts in EcM communities on the trees themselves and how this may also change across different geographical areas occupied by the trees. Our focus was on quantifying how mycorrhizal (M) and non-mycorhizal (NM) trees may differ in their acquisition of the nutrient resources, N and S. N is essential to life, yet it is typically the most limiting nutrient in temperate terrestrial ecosystems. Though C:N ratios did not vary between our treatments, the stable N isotope ratio between M and NM treatments did differ. This result suggests plants could be using different sources (organic versus inorganic) of N. In addition, the relative dependence on organic N pools also appears to vary with latitude of M origin. S is required for the production of many amino-acids, vitamins, chlorophyll, and important antioxidants such as glutathionine, which has been shown to mitigate reactive oxygen species (ROS). In spite of its potential nutritional and ecological importance, sulfur dynamics and the influence of EcM on sulfur uptake is poorly understood. We found that all M treatments demonstrated S isotope enrichment of approximately 6‰ compared to NM treatments. We hypothesize that this apparent enrichment is due to the EcM reduction of soil-borne sulfate to sulfite and the subsequent transport of sulfite from the fungal associate into the tree's roots.

  1. Stable microbial community composition on the Greenland Ice Sheet

    Directory of Open Access Journals (Sweden)

    Michaela eMusilova

    2015-03-01

    Full Text Available The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS. Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite into the surface ice forms cryoconite holes, which are considered ‘hot spots’ for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria and Actinobacteria. However, the dominant bacterial taxa in the aeolian samples (Firmicutes did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ13C values (-28.0 to -27.0‰ from the glacier surface values (-25.7 to -23.6‰, indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers.

  2. Stable microbial community composition on the Greenland Ice Sheet.

    Science.gov (United States)

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A; Wadham, Jemma; Anesio, Alexandre M

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered 'hot spots' for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ(13)C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers.

  3. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes

    DEFF Research Database (Denmark)

    Barnes, Christopher James; Maldonado Goyzueta, Carla Brenda; Frøslev, Tobias Guldberg;

    2016-01-01

    variation respectively. Surprisingly, altitude does not influence community formation, and there is limited evidence that climate (precipitation and temperature) play a role. Our results suggest that sampling should be performed over a wide geographical and environmental range in order to capture the full......Bolivia is one of the most biologically diverse countries on the planet. Between the Andes and the Amazon drainage basin spans the Yungas, a vast forested region shown to be extremely species rich in macro-organisms. However, it remains unclear whether this high diversity is also reflected...... in microbial diversity. Here we assess the genetic, taxonomic and functional diversity of root-associated fungi surrounding Cinchona calisaya calisaya trees, a typical element of the intermediate altitudes of the Bolivian Yungas. We determine the relative effects of edaphic properties, climate, and geography...

  4. Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity in Tuber melanosporum brûlés developed in multi-host Mediterranean plant communities.

    Science.gov (United States)

    Taschen, Elisa; Sauve, Mathieu; Taudiere, Adrien; Parlade, Javier; Selosse, Marc-André; Richard, Franck

    2015-08-01

    In the Mediterranean region, patches of vegetation recovering from disturbance and transiently dominated by shrubs produce one of the world's most prized fungi, the black truffle (Tuber melanosporum). In these successional plant communities, we have fragmentary knowledge of the distribution of T. melanosporum in space among ectomycorrhizal (ECM) host species and in time. Molecular identification of hosts (Restriction Fragment Length Polymorphism) and fungi (Internal Transcribed Spacer sequencing) and quantification of T. melanosporum mycelium (quantitative Polymerase Chain Reaction) were employed to evaluate the presence of T. melanosporum on four dominant ECM host species (Quercus ilex, Quercus  coccifera, Arbutus unedo, Cistus albidus) and the extent to which their respective ECM communities shared fungal diversity, over the course of development of truffle grounds, from recent unproductive brûlés to senescent ones where production has stopped. We found that truffle grounds host rich communities in which multi-host fungal species dominate in frequency. When considering both ECM tips and soil mycelia, we documented a dynamic and spatially heterogeneous pattern of T. melanosporum distribution in soils and a presence of ECM tips restricted to Q. ilex roots. This study advances our knowledge of the ecology of T. melanosporum, and provides insight into the extent of ECM fungal sharing among plant species that dominate Mediterranean landscapes. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Microbial community structure affects marine dissolved organic matter composition

    Directory of Open Access Journals (Sweden)

    Elizabeth B Kujawinski

    2016-04-01

    Full Text Available Marine microbes are critical players in the global carbon cycle, affecting both the reduction of inorganic carbon and the remineralization of reduced organic compounds back to carbon dioxide. Members of microbial consortia all depend on marine dissolved organic matter (DOM and in turn, affect the molecules present in this heterogeneous pool. Our understanding of DOM produced by marine microbes is biased towards single species laboratory cultures or simplified field incubations, which exclude large phototrophs and protozoan grazers. Here we explore the interdependence of DOM composition and bacterial diversity in two mixed microbial consortia from coastal seawater: a whole water community and a <1.0-μm community dominated by heterotrophic bacteria. Each consortium was incubated with isotopically-labeled glucose for 9 days. Using stable-isotope probing techniques and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry, we show that the presence of organisms larger than 1.0-μm is the dominant factor affecting bacterial diversity and low-molecular-weight (<1000 Da DOM composition over this experiment. In the <1.0-μm community, DOM composition was dominated by compounds with lipid and peptide character at all time points, confirmed by fragmentation spectra with peptide-containing neutral losses. In contrast, DOM composition in the whole water community was nearly identical to that in the initial coastal seawater. These differences in DOM composition persisted throughout the experiment despite shifts in bacterial diversity, underscoring an unappreciated role for larger microorganisms in constraining DOM composition in the marine environment.

  6. Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

    Science.gov (United States)

    Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2013-10-01

    Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike.

  7. Effects of meteorological factors on the composition of selected fungal spores in the air.

    Science.gov (United States)

    Grinn-Gofroń, Agnieszka; Bosiacka, Beata

    The aim of the study was to determine functional relationships between composition of air spora and meteorological factors, using multivariate statistical technique: canonical correspondence analysis (CCA). Analyses were conducted for the data collected during the 4 year (2007-2010) and, in order to show the dynamics of such relationships, for each year separately. The CCA results indicated that all statistically significant variables accounted for 15.3 % of the total variance in the spore data in the 4 years. The largest amount of the total variance was explained in this period by the mean air temperature (9.2 %). The meteorological factors impacted spore composition differently in different years, when analysis was done for each year separately. The highest values of the total variance in the spore data, explained by the statistically significant variables, were found in 2010 (32.3 %), with the highest contribution of mean air temperature (23.8 %). In that year, the above-mentioned parameter had the lowest value in comparison to other years. Canonical correspondence analysis provides not only a comprehensive assessment of the impact of meteorological factors on specific spore combinations in the air, but also informative graphical presentations of the results, illustrating the correlation between the occurrence of particular spore taxa and meteorological variables.

  8. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  9. Diversity of root-associated arbuscular mycorrhizal fungal communities in a rubber tree plantation chronosequence in Northeast Thailand.

    Science.gov (United States)

    Herrmann, Laetitia; Lesueur, Didier; Bräu, Lambert; Davison, John; Jairus, Teele; Robain, Henri; Robin, Agnès; Vasar, Martti; Wiriyakitnateekul, Wanpen; Öpik, Maarja

    2016-11-01

    Rubber tree (Hevea brasiliensis) is of major economic importance in Southeast Asia and for small land holders in Thailand in particular. Due to the high value of latex, plantations are expanding into unsuitable areas, such as the northeast province of Thailand where soil fertility is very low and therefore appropriate management practices are of primary importance. Arbuscular mycorrhizal fungi (AMF) contribute to plant growth through a range of mechanisms and could play a key role in a more sustainable management of the rubber plantations. We described the diversity of AMF associated with rubber tree roots in Northeast Thailand in relation to tree age and soil parameters along a chronosequence of rubber tree plantations. Cassava fields were included for comparison. Rubber tree and cassava roots harbored high diversity of AMF (111 Virtual Taxa, VT), including 20 novel VT. AMF VT richness per sample was consistently high (per site mean 16 to 21 VT per sample) along the chronosequence and was not related to soil properties. The composition of AMF communities differed between cassava and rubber tree plantations and was influenced by soil texture and nutrient content (sand, K, P, Ca). AMF community composition gradually shifted with the age of the trees. Our results suggest that the high diversity of AMF in this region is potentially significant for maintaining high functionality of AMF communities.

  10. Fungal arthritis

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/000444.htm Fungal arthritis To use the sharing features on this page, please enable JavaScript. Fungal arthritis is swelling and irritation (inflammation) of a joint ...

  11. Fungal Meningitis

    Science.gov (United States)

    ... Schedules Preteen & Teen Vaccines Meningococcal Disease Sepsis Fungal Meningitis Language: English Español (Spanish) Recommend on Facebook Tweet ... the brain or spinal cord. Investigation of Fungal Meningitis, 2012 In September 2012, the Centers for Disease ...

  12. Assessment of genetic diversity and distribution of endophytic fungal communities of Alternaria solani isolates associated with the dominant Karanja plants in Sanganer Region of Rajasthan.

    Science.gov (United States)

    Tiwari, Kartikeya; Chittora, Manish

    2013-12-01

    Higher plants are ubiquitously colonized with fungal endophytes that often lack readily detectable structures. Current study examines the distribution of endophytic fungal communities within Karanja plants and diversity of novel fungal endophyte Alternaria solani isolates collected from different locations of Sanganer region of Rajasthan. Results confirmed that A. solani is a major fungal endophyte consortium associated with Karanja plants. PCR Amplified fragments using random amplified polymorphic DNA (RAPD) primers were subjected to unweighted pair group method analysis (UPGMA), which clearly distinguished twelve ecologically diverse A. solani isolates. A total of 58 RAPD loci were amplified, out of which 35 (60.34%) were polymorphic and 23 were monomorphic (39.66%) in nature. These polymorphic loci were identified with an average of 2.92 bands per primer. The efficacy of RAPD markers proved as an efficient marker system with respect to detection of polymorphism and number of loci scored and can be used for the identification of a particular isolates, thereby defining core collections and strengthening their exploitation in acquiring novel products produced by them.

  13. Dynamics of Bacterial Community Composition in the Malaria Mosquito's Epithelia.

    Science.gov (United States)

    Tchioffo, Majoline T; Boissière, Anne; Abate, Luc; Nsango, Sandrine E; Bayibéki, Albert N; Awono-Ambéné, Parfait H; Christen, Richard; Gimonneau, Geoffrey; Morlais, Isabelle

    2015-01-01

    The Anopheles midgut hosts diverse bacterial communities and represents a complex ecosystem. Several evidences indicate that mosquito midgut microbiota interferes with malaria parasite transmission. However, the bacterial composition of salivary glands and ovaries, two other biologically important tissues, has not been described so far. In this study, we investigated the dynamics of the bacterial communities in the mosquito tissues from emerging mosquitoes until 8 days after a blood meal containing Plasmodium falciparum gametocytes and described the temporal colonization of the mosquito epithelia. Bacterial communities were identified in the midgut, ovaries, and salivary glands of individual mosquitoes using pyrosequencing of the 16S rRNA gene. We found that the mosquito epithelia share a core microbiota, but some bacteria taxa were more associated with one or another tissue at a particular time point. The bacterial composition in the tissues of emerging mosquitoes varied according to the breeding site, indicating that some bacteria are acquired from the environment. Our results revealed temporal variations in the bacterial community structure, possibly as a result of the mosquito physiological changes. The abundance of Serratia significantly correlated with P. falciparum infection both in the midgut and salivary glands of malaria challenged mosquitoes, which suggests that interactions occur between microbes and parasites. These bacteria may represent promising targets for vector control strategies. Overall, this study points out the importance of characterizing bacterial communities in malaria mosquito vectors.

  14. Herbivores cause a rapid increase in hereditary symbiosis and alter plant community composition.

    Science.gov (United States)

    Clay, Keith; Holah, Jenny; Rudgers, Jennifer A

    2005-08-30

    Microbial symbioses are ubiquitous in nature. Hereditary symbionts warrant particular attention because of their direct effects on the evolutionary potential of their hosts. In plants, hereditary fungal endophytes can increase the competitive ability, drought tolerance, and herbivore resistance of their host, although it is unclear whether or how these ecological benefits may alter the dynamics of the endophyte symbiosis over time. Here, we demonstrate that herbivores alter the dynamics of a hereditary symbiont under field conditions. Also, we show that changes in symbiont frequency were accompanied by shifts in the overall structure of the plant community. Replicated 25-m2 plots were enriched with seed of the introduced grass, Lolium arundinaceum at an initial frequency of 50% infection by the systemic, seed-transmitted endophyte Neotyphodium coenophialum. Over 54 months, there was a significantly greater increase in endophyte-infection frequency in the presence of herbivores (30% increase) than where mammalian and insect herbivory were experimentally reduced by fencing and insecticide application (12% increase). Under ambient mammalian herbivory, the above-ground biomass of nonhost plant species was reduced compared with the mammal-exclusion treatment, and plant composition shifted toward greater relative biomass of infected, tall fescue grass. These results demonstrate that herbivores can drive plant-microbe dynamics and, in doing so, modify plant community structure directly and indirectly.

  15. Richness and composition of niche-assembled viral pathogen communities.

    Directory of Open Access Journals (Sweden)

    Eric W Seabloom

    Full Text Available The pathogen and parasite community that inhabits every free-living organism can control host vital rates including lifespan and reproductive output. To date, however, there have been few experiments examining pathogen community assembly replicated at large-enough spatial scales to inform our understanding of pathogen dynamics in natural systems. Pathogen community assembly may be driven by neutral stochastic colonization and extinction events or by niche differentiation that constrains pathogen distributions to particular environmental conditions, hosts, or vectors. Here, we present results from a regionally-replicated experiment investigating the community of barley and cereal yellow dwarf viruses (B/CYDV's in over 5000 experimentally planted individuals of six grass species along a 700 km latitudinal gradient along the Pacific coast of North America (USA in response to experimentally manipulated nitrogen and phosphorus supplies. The composition of the virus community varied predictably among hosts and across nutrient-addition treatments, indicating niche differentiation among virus species. There were some concordant responses among the viral species. For example, the prevalence of most viral species increased consistently with perennial grass cover, leading to a 60% increase in the richness of the viral community within individual hosts (i.e., coinfection in perennial-dominated plots. Furthermore, infection rates of the six host species in the field were highly correlated with vector preferences assessed in laboratory trials. Our results reveal the importance of niche differentiation in structuring virus assemblages. Virus species distributions reflected a combination of local host community composition, host species-specific vector preferences, and virus responses to host nutrition. In addition, our results suggest that heterogeneity among host species in their capacity to attract vectors or support pathogens between growing seasons can

  16. Analyses of the temporal dynamics of fungal communities colonizing the healthy wood tissues of esca leaf-symptomatic and asymptomatic vines.

    Directory of Open Access Journals (Sweden)

    Emilie Bruez

    Full Text Available Esca, a Grapevine Trunk Disease (GTD, is of major concern for viticulture worldwide. Our study compares the fungal communities that inhabit the wood tissues of vines that expressed or not foliar esca-symptoms. The trunk and rootstock tissues were apparently healthy, whether the 10 year-old plants were symptomatic or not. The only difference was in the cordon, which contained white rot, a typical form of esca, in 79% of symptomatic plants. Observations over a period of one year using a fingerprint method, Single Strand Conformation Polymorphism (SSCP, and the ITS-DNA sequencing of cultivable fungi, showed that shifts occurred in the fungal communities colonizing the healthy wood tissues. However, whatever the sampling time, spring, summer, autumn or winter, the fungi colonizing the healthy tissues of asymptomatic or symptomatic plants were not significantly different. Forty-eight genera were isolated, with species of Hypocreaceae and Botryosphaeriaceae being the most abundant species. Diverse fungal assemblages, made up of potentially plant-pathogenic and -protective fungi, colonized these non-necrotic tissues. Some fungi, possibly involved in GTD, inhabited the non-necrotic wood of young plants, but no increase in necrosis areas was observed over the one-year period.

  17. Root-associated fungal communities in three Pyroleae species and their mycobiont sharing with surrounding trees in subalpine coniferous forests on Mount Fuji, Japan.

    Science.gov (United States)

    Jia, Shuzheng; Nakano, Takashi; Hattori, Masahira; Nara, Kazuhide

    2017-07-13

    Pyroleae species are perennial understory shrubs, many of which are partial mycoheterotrophs. Most fungi colonizing Pyroleae roots are ectomycorrhizal (ECM) and share common mycobionts with their Pyroleae hosts. However, such mycobiont sharing has neither been examined in depth before nor has the interspecific variation in sharing among Pyroleae species. Here, we examined root-associated fungal communities in three co-existing Pyroleae species, including Pyrola alpina, Pyrola incarnata, and Orthilia secunda, with reference to co-existing ECM fungi on the surrounding trees in the same soil blocks in subalpine coniferous forests. We identified 42, 75, and 18 fungal molecular operational taxonomic units in P. alpina, P. incarnata, and O. secunda roots, respectively. Mycobiont sharing with surrounding trees, which was defined as the occurrence of the same mycobiont between Pyroleae and surrounding trees in each soil block, was most frequent among P. incarnata (31 of 44 plants). In P. alpina, sharing was confirmed in 12 of 37 plants, and the fungal community was similar to that of P. incarnata. Mycobiont sharing was least common in O. secunda, found in only 5 of 32 plants. Root-associated fungi of O. secunda were dominated by Wilcoxina species, which were absent from the surrounding ECM roots in the same soil blocks. These results indicate that mycobiont sharing with surrounding trees does not equally occur among Pyroleae plants, some of which may develop independent mycorrhizal associations with ECM fungi, as suggested in O. secunda at our research sites.

  18. House dust fungal communities' characterization: a double take on the six by sixty by six (6 × 60 × 6) project

    Science.gov (United States)

    Amaro, Raquel; Coelho, Sónia D.; Pastorinho, M. Ramiro; Taborda-Barata, Luís; Vaz-Patto, Maria A.; Monteiro, Marisa; Nepomuceno, Miguel C. S.; Lanzinha, Joăo C. G.; Teixeira, Joăo P.; Pereira, Cristiana C.; Sousa, Ana C. A.

    2016-11-01

    Fungi are a group of microbes that are found with particular incidence in the indoor environment. Their direct toxicity or capability of generating toxic compounds has been associated with a large number of adverse health effects, such as infectious diseases and allergies. Given that in modern society people spend a large part of their time indoors; fungal communities' characterization of this environmental compartment assumes paramount importance in the comprehension of health effects. House dust is an easy to obtain, time-integrative matrix, being its use in epidemiological studies on human exposure to environmental contaminants highly recommended. Furthermore, dust can carry a great variety of fungal content that undergoes a large number of processes that modulate and further complexify human exposure. Our study aims to identify and quantify the fungal community on house dust samples collected using two different methodologies (an approach not often seen in the literature): active (vacuum cleaner bags) and passive sampling (dust settled in petri dishes). Sampling was performed as part of the ongoing 6 × 60 × 6 Project in which six houses from Covilhă (Portugal), with building dates representative of six decades, were studied for a period of sixty days.

  19. Cyanobacteria drive community composition and functionality in rock-soil interface communities.

    Science.gov (United States)

    Valverde, Angel; Makhalanyane, Thulani P; Seely, Mary; Cowan, Don A

    2015-02-01

    Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules), and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.

  20. Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi.

    Science.gov (United States)

    U'Ren, Jana M; Riddle, Jakob M; Monacell, James T; Carbone, Ignazio; Miadlikowska, Jolanta; Arnold, A Elizabeth

    2014-09-01

    Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best-practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15-fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.

  1. Fungal removal of gaseous hexane in biofilters packed with poly(ethylene carbonate) pine sawdust or peat composites.

    Science.gov (United States)

    Hernández-Meléndez, Oscar; Bárzana, Eduardo; Arriaga, Sonia; Hernández-Luna, Martín; Revah, Sergio

    2008-08-01

    The removal of volatile organic compounds (VOC) in biofilters packed with organic filter beds, such as peat moss (PM) and pine sawdust (PS), frequently presents drawbacks associated to the collapse of internal structures affecting the long-term operation. Poly(ethylene ether carbonate) (PEEC) groups grafted to these organic carriers cross linked with 4,4'-methylenebis(phenylisocyanate) (MDI) permitted fiber aggregation into specific shapes and with excellent hexane sorption performance. Modified peat moss (IPM) showed very favorable characteristics for rapid microbial development. Water-holding capacity in addition to hexane adsorption almost equal to the dry samples was obtained. Pilot scale hexane biofiltration experiments were performed with the composites after inoculation with the filamentous fungus Fusarium solani. During the operation of the biofilter under non-aseptic conditions, the addition of bacterial antibiotics did not have a relevant effect on hexane removal, confirming the role of fungi in the uptake of hexane and that bacterial growth was intrinsically limited by an adequate performance of the composites. IPM biofilter had a start-up period of 8-13 days with concurrent CO(2) production of approximately 90 g m(-3) h(-1) at day 11. The final pressure drop after 70 days of operation was 5.3 mmH(2)O m(-1) reactor. For modified pine sawdust (IPS) packed biofilter, 5 days were required to develop an EC of about 100 g m(-3) h(-1) with an inlet hexane load of approximately 190 g m(-3) h(-1). Under similar conditions, 12-17 days were required to observe a significant start-up in the reference perlite biofilter to reach gradually an EC of approximately 100 g m(-3) h(-1) at day 32. Under typical biofiltration conditions, the physical-chemical properties of the modified supports maintained a minimum water activity (a(w)) of 0.925 and a pH between 4 and 5.5, which allowed the preferential fungal development and limited bacterial growth. (c) 2008 Wiley

  2. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  3. Composition of endophytic fungal community associated with leaves of maize cultivated in south Brazilian field.

    Science.gov (United States)

    Szilagyi-Zecchin, Vivian J; Adamoski, Douglas; Gomes, Renata Rodrigues; Hungria, Mariangela; Ikeda, Angela C; Kava-Cordeiro, Vanessa; Glienke, Chirlei; Galli-Terasawa, Lygia V

    2016-12-01

    The objective of this study was to conduct a survey about fungi associated with leaves from two different maize plant lineages and to analyze their microbiota diversity. Isolated fungi were identified by morphological analysis and molecular taxonomy was performed using ITS1-5.8S-ITS2 rDNA. About 27 fungi morphotypes were obtained, 15 of them were from the first maize lineage. About 86.7% of the individuals belonged to the Dothideomycetes class (Phoma sorghina, Epicocum nigrum, Cladosporium sp., Bipolaris zeicola, and Alternaria alternata complex) and 13.3% to the Sordariomycetes class (Diaporthe/Phomopsis sp. and Nigrospora sp.). This ratio was opposite in the other maize lineage with 25.0% of Dothideomycetes (E. nigrum and Pleosporales) and 75.0% of Sordariomycetes (Gibberella fujikuroi complex, Fusarium graminearum complex, Diaporthe/Phomopsis sp., and Nigrospora sp.). By concerning the analyses of morphological characteristics and molecular phylogeny, this study intended to identify the groups of saprophytic, phytopathogenic, and mycotoxin fungi, which differently co-inhabit leaf tissue of maize plants in both tested lineages.

  4. Canada's Composite Learning Index: A path towards learning communities

    Science.gov (United States)

    Cappon, Paul; Laughlin, Jarrett

    2013-09-01

    In the development of learning cities/communities, benchmarking progress is a key element. Not only does it permit cities/communities to assess their current strengths and weaknesses, it also engenders a dialogue within and between cities/communities on the means of enhancing learning conditions. Benchmarking thereby is a potentially motivational tool, energising further progress. In Canada, the Canadian Council on Learning created the world's first Composite Learning Index (CLI), the purpose of which is to measure the conditions of learning nationally, regionally and locally. Cities/communities in Canada have utilised the CLI Simulator, an online tool provided by the Canadian Council on Learning, to gauge the change in overall learning conditions which may be expected depending on which particular indicator is emphasised. In this way, the CLI has proved to be both a dynamic and a locally relevant tool for improvement, moreover a strong motivational factor in the development of learning cities/communities. After presenting the main features of the CLI, the authors of this paper sum up the lessons learned during its first 5 years (2006-2010) of existence, also with a view to its transferability to other regions. Indeed, the CLI model was already adopted in Europe by the German Bertelsmann foundation in 2010 and has the potential to be useful in many other countries as well.

  5. A glimpse into the future composition of marine phytoplankton communities

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    Esteban eAcevedo-Trejos

    2014-07-01

    Full Text Available It is expected that climate change will have significant impacts on ecosystems. Most model projections agree that the ocean will experience stronger stratification and less nutrient supply from deep waters. These changes will likely affect marine phytoplankton communities and will thus impact on the higher trophic levels of the oceanic food web. The potential consequences of future climate change on marine microbial communities can be investigated and predicted only with the help of mathematical models. Here we present the application of a model that describes aggregate properties of marine phytoplankton communities and captures the effects of a changing environment on their composition and adaptive capacity. Specifically, the model describes the phytoplankton community in terms of total biomass, mean cell size, and functional diversity. The model is applied to two contrasting regions of the Atlantic Ocean (tropical and temperate and is tested under two emission scenarios: SRES A2 or ``business as usual'' and SRES B1 or ``local utopia''. We find that all three macroecological properties will decline during the next century in both regions, although this effect will be more pronounced in the temperate region. Being consistent with previous model predictions, our results show that a simple trait-based modelling framework represents a valuable tool for investigating how phytoplankton communities may reorganize under a changing climate.

  6. Do honeybees shape the bacterial community composition in floral nectar?

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    Yana Aizenberg-Gershtein

    Full Text Available Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers. Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

  7. Fungal DNA barcoding.

    Science.gov (United States)

    Xu, Jianping

    2016-11-01

    Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

  8. Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

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    Doreen Babin

    Full Text Available The fate of polycyclic aromatic hydrocarbons (PAHs in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I phenanthrene, (II litter, (III litter + phenanthrene, (IV unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE. DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our

  9. Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

    Science.gov (United States)

    Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2014-01-01

    The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of

  10. [Fungal keratitis].

    Science.gov (United States)

    Bourcier, T; Sauer, A; Letscher-Bru, V; Candolfi, E

    2011-10-01

    Fungal keratitis (keratomycosis) is a rare but severe cause of infectious keratitis. Its incidence is constant, due to steroids or immunosuppressive treatments and contact lenses. Pathogens often invade corneas with chronic diseases of the ocular surface but fungal keratitis is also observed following injuries with plant foreign objects. The poor prognosis of these infections is related both to fungal virulence, decreased host defense, as well as delays in diagnosis. However, new antimycotic treatments allow better management and prognosis.

  11. Fungal diversity associated with Hawaiian Drosophila host plants.

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    Brian S Ort

    Full Text Available Hawaiian Drosophila depend primarily, sometimes exclusively, on specific host plants for oviposition and larval development, and most specialize further on a particular decomposing part of that plant. Differences in fungal community between host plants and substrate types may establish the basis for host specificity in Hawaiian Drosophila. Fungi mediate decomposition, releasing plant micronutrients and volatiles that can indicate high quality substrates and serve as cues to stimulate oviposition. This study addresses major gaps in our knowledge by providing the first culture-free, DNA-based survey of fungal diversity associated with four ecologically important tree genera in the Hawaiian Islands. Three genera, Cheirodendron, Clermontia, and Pisonia, are important host plants for Drosophila. The fourth, Acacia, is not an important drosophilid host but is a dominant forest tree. We sampled fresh and rotting leaves from all four taxa, plus rotting stems from Clermontia and Pisonia. Based on sequences from the D1/D2 domain of the 26S rDNA gene, we identified by BLAST search representatives from 113 genera in 13 fungal classes. A total of 160 operational taxonomic units, defined on the basis of ≥97% genetic similarity, were identified in these samples, but sampling curves show this is an underestimate of the total fungal diversity present on these substrates. Shannon diversity indices ranged from 2.0 to 3.5 among the Hawaiian samples, a slight reduction compared to continental surveys. We detected very little sharing of fungal taxa among the substrates, and tests of community composition confirmed that the structure of the fungal community differed significantly among the substrates and host plants. Based on these results, we hypothesize that fungal community structure plays a central role in the establishment of host preference in the Hawaiian Drosophila radiation.

  12. Effects of landscape anthropization on mosquito community composition and abundance

    Science.gov (United States)

    Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-07-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

  13. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone.

    Science.gov (United States)

    Peay, Kabir G; Kennedy, Peter G; Davies, Stuart J; Tan, Sylvester; Bruns, Thomas D

    2010-01-01

    *Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation.

  14. Bacterial community succession in pine-wood decomposition

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    Anna eKielak

    2016-03-01

    Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

  15. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    Science.gov (United States)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

  16. Tropical Aquatic Archaea Show Environment-Specific Community Composition

    Science.gov (United States)

    Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

    2013-01-01

    The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

  17. Effect of genetic modification of potato starch on decomposition of leaves and tubers and on fungal decomposer communities

    NARCIS (Netherlands)

    Hannula, S.E.; De Boer, W.; Baldrian, P.; Van Veen, J.A.

    2013-01-01

    As part of a risk evaluation of growing genetically modified crops, we investigated the effects of a genetic modification of starch quality (increased level of amylopectin) in potato tubers (Solanum Tuberosum L.) on the decomposition of tissues (tubers and leaves) as well as on the associated fungal

  18. Algal and fungal diversity in Antarctic lichens.

    Science.gov (United States)

    Park, Chae Haeng; Kim, Kyung Mo; Elvebakk, Arve; Kim, Ok-Sun; Jeong, Gajin; Hong, Soon Gyu

    2015-01-01

    The composition of lichen ecosystems except mycobiont and photobiont has not been evaluated intensively. In addition, recent studies to identify algal genotypes have raised questions about the specific relationship between mycobiont and photobiont. In the current study, we analyzed algal and fungal community structures in lichen species from King George Island, Antarctica, by pyrosequencing of eukaryotic large subunit (LSU) and algal internal transcribed spacer (ITS) domains of the nuclear rRNA gene. The sequencing results of LSU and ITS regions indicated that each lichen thallus contained diverse algal species. The major algal operational taxonomic unit (OTU) defined at a 99% similarity cutoff of LSU sequences accounted for 78.7-100% of the total algal community in each sample. In several cases, the major OTUs defined by LSU sequences were represented by two closely related OTUs defined by 98% sequence similarity of ITS domain. The results of LSU sequences indicated that lichen-associated fungi belonged to the Arthoniomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes of the Ascomycota, and Tremellomycetes and Cystobasidiomycetes of the Basidiomycota. The composition of major photobiont species and lichen-associated fungal community were mostly related to the mycobiont species. The contribution of growth forms or substrates on composition of photobiont and lichen-associated fungi was not evident.

  19. How microbial community composition regulates coral disease development.

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    Justin Mao-Jones

    2010-03-01

    Full Text Available Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  20. Leaf litter decomposition of four different deciduous tree species - resource stoichiometry, nutrient release and microbial community composition

    Science.gov (United States)

    Leitner, S.; Keiblinger, K. M.; Zechmeister-Boltenstern, S.

    2012-04-01

    Recently, there has been increasing interest in the role of microbial communities for ecosystem processes like litter decomposition and nutrient cycling. For example, fungi are thought to be key players during litter decomposition in terrestrial ecosystems because they are able to degrade recalcitrant compounds like lignin and also dominate the decomposition of cellulose and hemicellulose, whereas bacteria seem to play an important role for lignin decomposition especially under anaerobic conditions. However, our knowledge about the contribution of bacteria and fungi to decomposition is still scarce. The aim of the present study was to elucidate how the microbial decomposer community is affected by resource stoichiometry and how changes in community composition affect litter decomposition and nutrient cycling. To this end, we collected leaf litter of four deciduous tree species (beech (Fagus), oak (Quercus), alder (Alnus) and ash tree (Fraxinus)) at four different seasons (winter, spring, summer and autumn) in an Austrian forest (Schottenwald, 48°14'N16°15'E; MAT=9°C; soil type: dystric cambiosol; soil C:N=16) in 2010. We determined litter nutrient content (micro- and macronutrients) and extractable nutrients and assessed the microbial community by PFLA analysis to test the following hypotheses: (i) tree species affects microbial community composition, (ii) microbial community composition changes over the course of the year, and (iii) narrow litter C:nutrient ratios favour nutrient release. Our data show that litter of different tree species varied in their stoichiometry, with C:N ratios between 16 (alder) and 46 (beech) and C:P ratios between 309 (ash) and 1234 (alder). Tree species had a significant impact on microbial community composition: highest amounts of actinomycetes and protozoa were observed for alder, while arbuscular mycorrhizae were lowest for oak. Bacteria were favoured by litter with narrow C:N shortly after litterfall. During litter decomposition

  1. COMPOSITION AND ACTIVITY OF BACTERIAL COMMUNITY OF COAL TAILING

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    Blayda I. A.

    2014-10-01

    Full Text Available The aim of this research was to study the composition of aboriginal bacterial community of coal tailing and to evaluate lixiviation activity of different groups of microorganisms belonging to this community. Using standard microbiological techniques we obtained and quantified the saving cultures of microorganisms from different physiological groups — filamentous fungi, heterotrophic microorganisms, mesophilic and thermophilic moderately acidophilic sulfur-oxidizing chemolithotrophic bacteria. Their oxidative activity was also established. The optimal results were achieved for collective leaching of rare and heavy metals into the solution under thermophilic conditions, which are favorable for the growth and activity of Sulfobacillus and under mesophilic conditions with the usage of ferrous iron as an energy substrate. This confirms the leading role of A. ferrooxidans in the processes of bacterial leaching of metals. Comparing our results with the available literature data we made a conclusion that the qualitative composition of acidophilic chemolithotrophic bacteria living in technogenic waste did not differ from the microbiocenose structure of natural sulfide ores.

  2. 社区获得性地方性真菌感染研究进展%Research progress on community-acquired endemic fungal infections

    Institute of Scientific and Technical Information of China (English)

    李建华; 张力燕

    2015-01-01

    Local fungal infection is an important cause of community-acquired pneumonia,has distinct geographical distributions in epidemiology,but often occurs in the region outside epidemic areas.This paper reviews the recent literatures,focuses on the epidemiology,clinical manifestations,imaging features,diagnosis and treatment methods of the three major local fungal diseases currently occurred in North America area causing community-acquired pneumonia,including coccidioidomycosis,histoplasmosis,and blastomycosis,in order to cause clinical attention,prevent misdiagnosis and missed diagnosis.%地方性真菌感染是社区获得性肺炎的重要原因,流行病学有明显的地域分布,但经常发生在流行区以外的地区.本文综述近年相关文献,着重论述目前在北美地区发生的引起社区获得性肺炎的3个主要地方性真菌病,即球孢子菌病、组织胞浆菌病和芽生菌病的流行病学、临床表现、影像学特征、诊断方法和当前的治疗策略.以期引起临床重视,防止误诊、漏诊发生.

  3. Diversity of endophytic fungal community of cacao (Theobroma cacao L. and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease

    Directory of Open Access Journals (Sweden)

    2005-02-01

    Full Text Available The basidiomycete fungus Crinipellis perniciosa (Stahel Singer is the causal agent of Witches' Broom Disease of Cacao (Theobroma cacao L. which is the main factor limiting cacao production in the Americas. Pod losses of up to 90% are experienced in affected areas as evidenced by the 50% drop in production in Bahia province, Brazil following the arrival of the C. perniciosa in the area in 1989. The disease has proven particularly difficult to control and many farmers in affected areas have given up cacao cultivation. In order to evaluate the potential of endophytes as a biological control agent of this phytopathogen, the endophytic fungal community of resistant and susceptible cacao plants as well as affected branches was studied between 2001 and 2002. The fungal community was identified by morphological traits and rDNA sequencing as belonging to the genera Acremonium, Blastomyces, Botryosphaeria, Cladosporium, Colletotrichum, Cordyceps, Diaporthe, Fusarium, Geotrichum, Gibberella, Gliocladium, Lasiodiplodia, Monilochoetes, Nectria, Pestalotiopsis, Phomopsis, Pleurotus, Pseudofusarium, Rhizopycnis, Syncephalastrum, Trichoderma, Verticillium and Xylaria. These fungi were evaluated both in vitro and in vivo by their ability to inhibit C. perniciosa. Among these, some were identified as potential antagonists, but only one fungus (Gliocladium catenulatum reduced the incidence of Witches' Broom Disease in cacao seedlings to 70%.

  4. Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

    Science.gov (United States)

    Blackwood, C.B.; Waldrop, M.P.; Zak, D.R.; Sinsabaugh, R. L.

    2007-01-01

    The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5-10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition. ?? 2007 The Authors; Journal compilation ?? 2007 Society for Applied Microbiology and Blackwell Publishing Ltd.

  5. Fungal rhinosinusitis.

    Science.gov (United States)

    Netkovski, J; Shirgoska, B

    2012-01-01

    Fungi are a major part of the ecosystem. In fact, over 250 fungal species have been reported to produce human infections. More than ever, fungal diseases have emerged as major challenges for physicians and clinical microbiologists. The aim of this study was to summarize the diagnostic procedures and endoscopic surgical treatment of patients with fungal rhinosinusitis. Eleven patients, i.e. 10% of all cases with chronic inflammation of paranasal sinuses, were diagnosed with fungal rhinosinusitis. Ten of them were patients with a noninvasive form, fungus ball, while only one patient was classified in the group of chronic invasive fungal rhinosinusitis which was accompanied with diabetes mellitus. All patients underwent nasal endoscopic examination, skin allergy test and had preoperative computed tomography (CT) scans of the sinuses in axial and coronal plane. Functional endoscopic sinus surgery was performed in 10 patients with fungus ball, while a combined approach, endoscopic and external, was done in the immunocompromised patient with the chronic invasive form of fungal rhinosinusitis. Most cases (9/11) had unilateral infection. In 9 cases infection was restricted to a single sinus, and here the maxillary sinus was most commonly affected (8/9) with infections in other patients being restricted to the sphenoid sinus (1/9). Two patients had infections affecting two or more sinuses. In patients with an invasive form of the fungal disease there was involvement of the periorbital and orbital tissues. In patients with fungus ball the mycelia masses were completely removed from the sinus cavities. Long-term outcome was positive in all the operated patients and no recurrence was detected. The most frequent fungal agent that caused rhinosinusitis was Aspergillus. Mucor was identified in the patient with the invasive form. Endoscopic examination of the nasal cavity and CT scanning of paranasal sinuses followed by endoscopic sinus surgery were represented as valuable

  6. Fungal diversity is not determined by mineral and chemical differences in serpentine substrates.

    Directory of Open Access Journals (Sweden)

    Stefania Daghino

    Full Text Available The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.

  7. Coupled Metagenomic and Chemical Analyses of Degrading Fungal Necromass and Implications for Fungal contributions to Stable Soil Organic Carbon

    Science.gov (United States)

    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

  8. Effects of biochar blends on microbial community composition in two coastal plain soils

    Science.gov (United States)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  9. Community composition and species richness of parasitoids infesting Yponomeuta species in the Netherlands

    NARCIS (Netherlands)

    Cleary, Daniel F.R.

    2004-01-01

    Parasitoid assemblages infesting Yponomeuta species in the Netherlands were investigated. Parasitoid species richness and community composition were related to host species, habitat, temporal and spatial variation. Both community structure and species richness did not differ among habitats. There

  10. Fungal allergens.

    OpenAIRE

    1995-01-01

    Airborne fungal spores occur widely and often in far greater concentrations than pollen grains. Immunoglobulin E-specific antigens (allergens) on airborne fungal spores induce type I hypersensitivity (allergic) respiratory reactions in sensitized atopic subjects, causing rhinitis and/or asthma. The prevalence of respiratory allergy to fungi is imprecisely known but is estimated at 20 to 30% of atopic (allergy-predisposed) individuals or up to 6% of the general population. Diagnosis and immuno...

  11. The effects of biological control on fungal communities colonizing eggplant (Solanum melongena L. organs and the substrate used for eggplant cultivation

    Directory of Open Access Journals (Sweden)

    Bożena Cwalina-Ambroziak

    2012-12-01

    Full Text Available Eggplants, cv. Black Beauty, were grown in the greenhouse of the University of Warmia and Mazury in Olsztyn. During the growing season, the plants were sprayed three times with Asahi SL, Biochikol 020 PC and Bravo 500 SC, they were watered with Polyversum, and a mycorrhizal inoculum was applied to the roots of seedlings. Unprotected plants, treated with distilled water, served as control. After fruit harvest, samples of the substrate used for eggplant cultivation, eggplant stems and roots were collected, and fungi were isolated in the laboratory. The fungal soil community was more abundant and diverse than the communities colonizing the stems and roots of eggplants. The applied biological and chemical control agents effectively reduced the abundance of fungi, including pathogenic species, in the organs of eggplants and the substrate used for eggplant cultivation. Potential pathogens (Alternaria alternata, Botrytis cinerea and Fusarium species were isolated in high numbers from eggplant stems in the control treatment and in the Polyversum treatment (67%. The lowest number of potential pathogenic species were isolated from plants treated with the biostimulator Asahi SL, the fungicide Bravo 500 SC and the mycorrhizal inoculum. The population size of pathogenic fungi (Colletotrichum coccodes and Fusarium isolated from eggplant roots was smaller, compared with stems, particularly in the treatments with the fungicide Bravo 500 SC and the biostimulator Biochikol 020 PC. The soil fungal community was dominated by yeast-like fungi (over 60% of all isolates. Fungi known as potential causal agents of diseases were found in low abundance, and they were not detected in substrate samples collected from under fungicide-treated eggplant plants.

  12. Decay extent evaluation of wood degraded by a fungal community using NIRS: application for ecological engineering structures used for natural hazard mitigation

    Science.gov (United States)

    Baptiste Barré, Jean; Bourrier, Franck; Bertrand, David; Rey, Freddy

    2015-04-01

    Ecological engineering corresponds to the design of efficient solutions for protection against natural hazards such as shallow landslides and soil erosion. In particular, bioengineering structures can be composed of a living part, made of plants, cuttings or seeds, and an inert part, a timber logs structure. As wood is not treated by preservatives, fungal degradation can occur from the start of the construction. It results in wood strength loss, which practitioners try to evaluate with non-destructive tools (NDT). Classical NDT are mainly based on density measurements. However, the fungal activity reduces the mechanical properties (modulus of elasticity - MOE) well before well before a density change could be measured. In this context, it would be useful to provide a tool for assessing the residual mechanical strength at different decay stages due to a fungal community. Near-infrared spectroscopy (NIRS) can be used for that purpose, as it can allow evaluating wood mechanical properties as well as wood chemical changes due to brown and white rots. We monitored 160 silver fir samples (30x30x6000mm) from green state to different levels of decay. The degradation process took place in a greenhouse and samples were inoculated with silver fir decayed debris in order to accelerate the process. For each sample, we calculated the normalized bending modulus of elasticity loss (Dw moe) and defined it as decay extent. Near infrared spectra collected from both green and decayed ground samples were corrected by the subtraction of baseline offset. Spectra of green samples were averaged into one mean spectrum and decayed spectra were subtracted from the mean spectrum to calculate the absorption loss. Partial least square regression (PLSR) has been performed between the normalized MOE loss Dw moe (0 wood decay extent in the context of ecological engineering structures used for natural hazard mitigation.

  13. Analysis on the Soil Fungal Community Structure in Melia azedarach-Triticum aestivum Agroforestry Ecosystem%苦楝-小麦农林复合生态系统土壤真菌群落结构分析

    Institute of Scientific and Technical Information of China (English)

    张敏; 周鹏; 季永华

    2015-01-01

    Objective]To explore the influence of tree species on rhizosphere-associated fungal community in an agroforestry ecosystem, and to provide new insights into agroforestry practice, the fungal community structure in rhizosphere and bulk soil in Melia azedarach-Triticum aestivum agroforestry ecosystem was investigated by 18S rDNA PCR-DGGE.[Method]After the fungal DNA was extracted from extraction of nonrhizosphere and rhizosphere-associated soil, and the targeted fungal 18 S rDNA was amplified using universal primers GC-FR1 and FF390 . And then the amplified DNA fragments were analyzed by density gradient gel electrophoresis ( DGGE) . Similarity among different groups was analyzed using the UPGMA ( unweighted pair group method with arithmetic averages) method,and the fungal diversity was evaluated with species richness ( S ) ,Shannon-Wiener index ( H ) and the equitability index ( E ) . Finally,dominant DGGE bands were excised,sequenced and a phylogenetic tree was constructed. [Result]Results showed that the structure and diversity of rhizosphere-associated fungi community were much more complex than that of the bulk soil,and more dominant bands were observed in DGGE profiles of rhizosphere soil samples. The DGGE profiles were further investigated by cluster analysis using the UPGAMA method,revealing that the similarity among the three replicates of each treatment was more than 70% except for the rhizosphere soil of M. azedarach. In clustering diagram,all the samples were grouped into three clusters with a similarity of 51%. The highest similarity ( 72%) was found between the rhizosphere-associated fungal community from wheat and wheat grown under M. azedarach,which indicated that M. azedarach had minor influence on the rhizosphere-associated fungal community of wheat. In addition,only 51% similarity was noticed between the rhizosphere-associated fungal community of M. azedarach and the other groups. The principal-component analysis ( PCA) also demonstrated that all

  14. Morphotype-based characterization of arbuscular mycorrhizal fungal communities in a restored tropical dry forest, Margarita island-Venezuela.

    Science.gov (United States)

    Fajardo, Laurie; Loveral, Milagros; Arrindell, Pauline; Aguilar, Victor Hugo; Hasmy, Zamira; Cuenca, Gisela

    2015-09-01

    The mycorrhizal component of revegetated areas after ecological restoration or rehabilitation in arid and semiarid tropical areas has been scarcely assessed, particularly those made after mining disturbance. We evaluated and compared the presence of arbuscular mycorrhizal fungi of a small area of restored tropical dry forest destroyed by sand extraction, with a non-restored area of similar age, at the peninsula of Macanao, Margarita Island (Venezuela). Our study was undertaken in 2009, four years after planting, and the mycorrhizal status was evaluated in four restored plots (8 x 12.5 m) (two were previously treated with hydrogel (R2 and R2'), and two were left untreated (R1 and R1'), and four non-restored plots of similar size (NR1 and NR1' with graminoid physiognomy with some scattered shrubs; and NR2 and NR2', with a more species rich plant community). Apparently the restoration management promoted higher arbuscular mycorrhizal fungi (AMF) species richness and diversity, particularly in restored soils where the hydrogel was added (R2 treatment). Soil of the NRI treatment (with a higher herbaceous component) showed the highest spore density, compared to samples of soils under the other treatments. Considering species composition, Claroideoglomus etunicatum and Rhizophagus intraradices were found in all treatments; besides, Diversispora spurca and Funnefformis geosporum were only found in non-restored plots, while members of the Gigasporaceae (a family associated with little disturbed sites) were commonly observed in the plots with restored soils. Mycorrhizal colonization was similar in the restored and non-restored areas, being a less sensitive indicator of the ecosystem recovery. The trend of higher richness and diversity of AMF in the restored plot with hydrogel suggests that this management strategy contributes to accelerate the natural regeneration in those ecosystems where water plays an essential role.

  15. Community structure and composition of the Cambrian Chengjiang biota

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Based on previously published species data(228 species in over 18 phyla) and field sampling(114 species and 18406 individuals) in the Chengjiang-Haikou-Anning area,we analyzed quantitatively the paleocommunity composition and structure of the Cambrian Chengjiang biota(Cambrian Series 2,eastern Yunnan,China).Arthropods dominate the community both in species diversity(species:37%) and in abundance(individuals:51.8%).Priapulids(individuals:22.6%) and brachiopods(individuals:16.3%) follow in abundance rank.The arthropod Kunmingella douvillei(26.2%),the priapulid Cricocosmia jinning-ensis(15.4%),and the brachiopod Diandongia pista(11%) are the three most abundant species.Ecological analyses show that the community was dominated by epifaunal organisms(species:63%,individuals:68.4%) followed by infaunal organisms(species:11.9%,individuals:25.9%),nektobenthic organisms(species:11.5%,individuals:2.6%),and pelagic organisms(species:5.3%,individuals:3.1%).The diverse feeding strategies,dominated by suspension feeders(species:35.6%,individuals:26.1%) and hunter/scavengers(species:31.1%,individuals:40.4%),indicate the former existence of a complex food chain and intense competition.Epifaunal vagrant omnivores(28.2%),infaunal vagrant hunter/scavengers(19.8%),epifaunal sessile suspension feeders(17.7%),and epifaunal vagrant hunter/scavengers(15.3%) were the most abundant ecological groups,represented primarily by arthropods,poriferans,priapulids,and brachiopods.Ecological group analyses reveal that the early Cambrian Chengjiang biota is similar in community patterns and functional relations to modern biotas in shallow marine settings.

  16. Fungal nail infection

    Science.gov (United States)

    Nails - fungal infection; Onychomycosis; Infection - fungal - nails; Tinea unguium ... hair, nails, and outer skin layers. Common fungal infections include: Athlete's foot Jock itch Ringworm on the ...

  17. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

    Science.gov (United States)

    Cébron, Aurélie; Beguiristain, Thierry; Bongoua-Devisme, Jeanne; Denonfoux, Jérémie; Faure, Pierre; Lorgeoux, Catherine; Ouvrard, Stéphanie; Parisot, Nicolas; Peyret, Pierre; Leyval, Corinne

    2015-09-01

    The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the

  18. A composite microbial agent containing bacterial and fungal species: Optimization of the preparation process, analysis of characteristics, and use in the purification for volatile organic compounds.

    Science.gov (United States)

    Cheng, Zhuowei; Lu, Lichao; Kennes, Christian; Ye, Jiexu; Yu, Jianming; Chen, Dongzhi; Chen, Jianmeng

    2016-10-01

    Proper preservation of microbial activity over long periods poses a considerable challenge for pollutant biopurification. A composite microbial agent, mainly composed of bacteria and fungi isolated by the current research team, was constructed in this study and its performance in the removal of mixed waste gases (containing α-pinene, n-butyl acetate and o-xylene) was investigated. According to the removal efficiency in the first 24h and the response to starvation, the optimal ratio of selected carriers (activated carbon, wheat bran and sawdust) was found to be 1:2:1. In some cases of storages, the removal capability of the microbial agent was more than twice that of the suspension. Microbial analysis showed that the inoculated bacterial and fungal strains dominated the agent preparation and utilization. These results indicated that the agent has potential for use in biopurification of mixed waste gas, favoring the reduction of environmental passives and longer retention of microbial activity.

  19. Bacterial community composition and diversity in an ancestral ant fungus symbiosis.

    Science.gov (United States)

    Kellner, Katrin; Ishak, Heather D; Linksvayer, Timothy A; Mueller, Ulrich G

    2015-07-01

    Fungus-farming ants (Hymenoptera: Formicidae, Attini) exhibit some of the most complex microbial symbioses because both macroscopic partners (ants and fungus) are associated with a rich community of microorganisms. The ant and fungal microbiomes are thought to serve important beneficial nutritional and defensive roles in these symbioses. While most recent research has investigated the bacterial communities in the higher attines (e.g. the leaf-cutter ant genera Atta and Acromyrmex), which are often associated with antibiotic-producing Actinobacteria, very little is known about the microbial communities in basal lineages, labeled as 'lower attines', which retain the ancestral traits of smaller and more simple societies. In this study, we used 16S amplicon pyrosequencing to characterize bacterial communities of the lower attine ant Mycocepurus smithii among seven sampling sites in central Panama. We discovered that ant and fungus garden-associated microbiota were distinct from surrounding soil, but unlike the situation in the derived fungus-gardening ants, which show distinct ant and fungal microbiomes, microbial community structure of the ants and their fungi were similar. Another surprising finding was that the abundance of actinomycete bacteria was low and instead, these symbioses were characterized by an abundance of Lactobacillus and Pantoea bacteria. Furthermore, our data indicate that Lactobacillus strains are acquired from the environment rather than acquired vertically.

  20. Climate Controls AM Fungal Distributions from Global to Local Scales

    Science.gov (United States)

    Kivlin, S. N.; Hawkes, C.; Muscarella, R.; Treseder, K. K.; Kazenel, M.; Lynn, J.; Rudgers, J.

    2016-12-01

    Arbuscular mycorrhizal (AM) fungi have key functions in terrestrial biogeochemical processes; thus, determining the relative importance of climate, edaphic factors, and plant community composition on their geographic distributions can improve predictions of their sensitivity to global change. Local adaptation by AM fungi to plant hosts, soil nutrients, and climate suggests that all of these factors may control fungal geographic distributions, but their relative importance is unknown. We created species distribution models for 142 AM fungal taxa at the global scale with data from GenBank. We compared climate variables (BioClim and soil moisture), edaphic variables (phosphorus, carbon, pH, and clay content), and plant variables using model selection on models with (1) all variables, (2) climatic variables only (including soil moisture) and (3) resource-related variables only (all other soil parameters and NPP) using the MaxEnt algorithm evaluated with ENMEval. We also evaluated whether drivers of AM fungal distributions were phylogenetically conserved. To test whether global correlates of AM fungal distributions were reflected at local scales, we then surveyed AM fungi in nine plant hosts along three elevation gradients in the Upper Gunnison Basin, Colorado, USA. At the global scale, the distributions of 55% of AM fungal taxa were affected by both climate and soil resources, whereas 16% were only affected by climate and 29% were only affected by soil resources. Even for AM fungi that were affected by both climate and resources, the effects of climatic variables nearly always outweighed those of resources. Soil moisture and isothermality were the main climatic and NPP and soil carbon the main resource related factors influencing AM fungal distributions. Distributions of closely related AM fungal taxa were similarly affected by climate, but not by resources. Local scale surveys of AM fungi across elevations confirmed that climate was a key driver of AM fungal