Molecular Diversity Of Fungal And Bacterial Communities In The Marine Sponge Dragmacidon Reticulatum

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.552207220Sfanos, K., Harmody, D., Dang, P., Ledger, A., Pomponi, S., A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates (2005) Syst. Appl. Microbiol., 28, pp. 242-264Gao, Z., Li, B., Zheng, C., Wang, G., Molecular detection of fungal communities in the hawaiian marine sponges Suberites zeteki and Mycale armata (2008) Appl. Environ. Microbiol., 74, pp. 6091-6101Li, Q., Wang, G., Diversity of fungal isolates from three Hawaiian marine sponges (2009) Microbiol. Res., 164, pp. 233-241Menezes, C.B.A., Bonugli-Santos, R.C., Miqueletto, P.B., Passarini, M.R.Z., Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil (2010) Microbiol. Res., 165, pp. 466-482Passarini, M.R.Z.P., Santos, C., Lima, N., Berlinck, R.G.S., Filamentous fungi from the Atlantic marine sponge Dragmacidon reticulatum (2013) Arch. Microbiol., 195, pp. 99-111Thacker, R.W., Freeman, C.J., Sponge-microbe symbioses: recent advances and new directions (2012) Adv. Mar. Biol., 62, pp. 57-112Kim, S.K., Dewapriya, P., Bioactive compounds from marine sponges and their symbiotic microbes: a potential source of nutraceuticals (2012) Adv. Food. Nutr. Res., 65, pp. 137-151Hentschel, U., Usher, K.M., Taylor, M.W., Marine sponges as microbial fermenters (2006) FEMS Microbiol. 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Fungal Communities In The Garden Chamber Soils Of Leaf-cutting Ants

Leaf-cutting ants modify the properties of the soil adjacent to their nests. Here, we examined whether such an ant-altered environment impacts the belowground fungal communities. Fungal diversity and community structure of soil from the fungus garden chambers of Atta sexdens rubropilosa and Atta bisphaerica, two widespread leaf-cutting ants in Brazil, were determined and compared with non-nest soils. Culture-dependent methods revealed similar species richness but different community compositions between both types of soils. Penicillium janthinellum and Trichoderma spirale were the prevalent isolates in fungus chamber soils and non-nest soils, respectively. In contrast to cultivation methods, analyses of clone libraries based on the internal transcribed spacer (ITS) region indicated that richness of operational taxonomic units significantly differed between soils of the fungus chamber and non-nest soils. FastUnifrac analyses based on ITS sequences further revealed a clear distinction in the community structure between both types of soils. Plectania milleri and an uncultured Clavariaceae fungus were prevalent in fungus chamber soils and non-nest soils, respectively. FastUnifrac analyses also revealed that fungal community structures of soil from the garden chambers markedly differed among ant species. Our findings suggest that leaf-cutting ants affect fungal communities in the soil from the fungus chamber in comparison to non-nest soils.541111861196Schultz, T.R., Brady, S.G., Major evolutionary transitions in ant agriculture (2008) Proc. Natl. Acad. Sci. USA, 105, pp. 5435-5440Weber, N.A., (1972) Gardening Ants: The Attines, , Memoirs of the American Philosophical Society, PhiladelphiaCaldera, E.J., Poulsen, M., Suen, G., Currie, C.R., Insect symbioses: a case study of past, present, and future fungus-growing ant research (2009) Environ. Entomol., 38, pp. 78-92Currie, C.R., Mueller, U.G., Malloch, D., The agricultural pathology of ant fungus gardens (1999) Proc. Natl. Acad. Sci. USA, 96, pp. 7998-8002Currie, C.R., Prevalence and impact of a virulent parasite on a tripartite mutualism (2001) Oecologia, 128, pp. 99-106Mueller, U.G., Symbiont recruitment versus ant-symbiont co-evolution in the attine ant-microbe symbiosys (2012) Curr. Opin. Microbiol., 15, pp. 269-277Little, A.E.F., Currie, C.R., Symbiotic complexity: discovery of a fifth symbiont in the attine ant-microbe symbiosis (2007) Biol. Lett., 3, pp. 501-504Little, A.E.F., Currie, C.R., Black yeasts symbionts compromise the efficiency of antibiotic defenses in fungus-growing ants (2008) Ecology, 89, pp. 1216-1222Bacci, M., Jr., Ribeiro, S.B., Casarotto, M.E.F., Pagnocca, F.C., Biopolymer-degrading bacteria from nests of the leaf-cutting ant Atta sexdens rubropilosa (1995) Braz. J. Med. Biol. Res., 28, pp. 79-82Scott, J.J., Budsberg, K.J., Suen, G., Wixon, D.L., Microbial community structure of leaf-cutter ant fungus-gardens and refuse dumps (2010) PLoS ONE, 5, p. e9992Rodrigues, A., Bacci, M., Jr., Mueller, U.G., Ortiz, A., Microfungal "weeds" in the leafcutter ant symbiosis (2008) Microb. Ecol., 56, pp. 604-614Rodrigues, A., Mueller, U.G., Ishak, H.D., Bacci, M., Jr., Ecology of microfungal communities in gardens of fungus-growing ants (Hymenoptera: Formicidae): a year-long survey of three species in Central Texas (2011) FEMS Microbiol. Ecol., 78, pp. 244-255Pinto-Tomás, A.A., Anderson, M.A., Suen, G., Stevenson, D.M., Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants (2009) Science, 326, pp. 1120-1123Currie, C.R., Stuart, A.E., Weeding and grooming of pathogens in agriculture by ants (2001) Proc. R. Soc. B., 268, pp. 1033-1039Cremer, S., Armitage, S.A.O., Schmid-Hempel, P., Social immunity (2007) Curr. Biol., 17, pp. 693-702Vander Meer, R., Ant interactions with soil organisms and associated semiochemicals (2012) J. Chem. Ecol., 38, pp. 728-745Schoenian, I., Spiteller, M., Ghaste, M., Wirth, R., Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants (2011) Proc. Natl. Acad. Sci. USA, 108, pp. 1955-1960Fernández-Marín, H., Zimmerman, J.K., Rehner, S.A., Wcislo, W.T., Active use of the metapleural glands by ants in controlling fungal infection (2006) Proc. R. Soc. B, 273, pp. 1689-1695Fernández-Marín, H., Zimmerman, J.K., Nash, D., Boomsma, J.J., Reduced biological control and enhanced chemical pest management in the evolution of fungus farming ants (2009) Proc. R. Soc. B, 276, pp. 2263-2269Farji-Brener, A.G., Leaf-cutting ant nests and soil biota abundance in a semi-arid steppe of northwestern Patagonia (2010) Sociobiology, 56, pp. 549-557Mora, P., Miambi, E., Jiménez, J.J., Decaëns, T., Functional complement of biogenic structures produced by earthworms, termites and ants in the neotropical savannas (2005) Soil Biol. Biochem., 37, pp. 1043-1048Holec, M., Frouz, J., The effect of two ant species Lasius niger and Lasius flavus on soil properties in two contrasting habitats (2006) Eur. J. Soil Biol., 42, pp. S213-S217Ba, A.S., Phillips, S.A., Anderson, J.T., Yeasts in mound soil of the red imported fire ant (2000) Mycol. Res., 104, pp. 969-973Baird, R., Woolfolk, S., Watson, C.E., Survey of bacterial associates of black/hybrid imported fire ants from mounds in Mississippi (2007) Southeast Natl., 6, pp. 615-632Zettler, J.A., McInnis, T.M., Allen, C.R., Spira, T.P., Biodiversity of fungi in red imported fire ant (Hymenoptera: Formicidae) mounds (2002) Ann. Entomol. Soc. Am., 95, pp. 487-491Folgarait, P., Ant biodiversity and its relationship to ecosystem functioning: a review (1998) Biodivers. Conserv., 7, pp. 1221-1244Hudson, T.M., Turner, B.L., Herz, H., Robinson, J.S., Temporal patterns of nutrient availability around nests of leaf-cutting ants (Atta colombica) in secondary moist tropical forest (2009) Soil Biol. Biochem., 41, pp. 1088-1093Jones, C.G., Lawton, J.H., Shachak, M., Organisms as ecosystem engineers (1994) Oikos, 69, pp. 373-386Jiménez, J.J., Decaëns, T., Chemical variations in the biostructures produced by soil ecosystem engineers. Examples from the neotropical savannas (2006) Eur. J. Soil Biol., 42, pp. S92-S102Jiménez, J.J., Decaëns, T., Lavelle, P., C and N concentrations in biogenic structures of a soil-feeding termite and a fungus-growing ant in the Colombian savannas (2008) Appl. Soil Ecol., 40, pp. 120-128Moutinho, P., Nepstad, D.C., Davidson, E.A., Influence of leaf-cutting ant nests on secondary forest growth and soil properties in Amazonia (2003) Ecology, 84, pp. 1265-1276Boulton, A.M., Jaffee, B.A., Scow, K.M., Effects of a common harvester ant (Messor andrei) on richness and abundance of soil biota (2003) Appl. Soil Ecol., 23, pp. 257-265Boulton, A.M., Amberman, K.D., How ants increase soil biota richness and abundance: a field experiment (2006) Biodivers. Conserv., 15, pp. 69-82Dauber, J., Niechoj, R., Baltruschat, H., Wolters, V., Soil engineering ants increase grass root arbuscular mycorrhizal colonization (2008) Biol. Fertil. Soils, 44, pp. 791-796Ginzburg, O., Whitford, W.G., Steinberger, Y., Effects of harvester ant (Messor spp.) activity on soil properties and microbial communities in a Negev Desert ecosystem (2008) Biol. Fertil. Soils, 45, pp. 165-173Ishak, H.D., Plowes, R., Sen, R., Kellner, K., Bacterial diversity in Solenopsis invicta and Solenopsis geminata ant colonies characterized by 16S amplicon 454 pyrosequencing (2011) Env. Microbiol., 61, pp. 821-831Dauber, J., Wolters, V., Microbial activity and functional diversity in the mounds of the three different ant species (2000) Soil. Biol. Biochem., 32, pp. 93-99Moreira, A.A., Forti, L.C., Boaretto, M.A.C., Andrade, A.P.P., External and internal structure of Atta bisphaerica Forel (Hymenoptera: Formicidae) nests (2004) J. Appl. Entomol., 128, pp. 204-211Rodrigues, A., Cable, R.N., Mueller, U.G., Bacci, M., Jr., Antagonistic interaction between garden yeasts and microfungal garden pathogens of leaf-cutting ants (2009) Anton. van Leeuwen., 96, pp. 331-342Domsch, K.H., Gams, W., Anderson, T., (1980) Compendium of Soil Fungi, , Academic Press, LondonSamson, R.A., Hoekstra, E.S., Frisvad, J.C., (2000) Introduction to Food-Airborne Fungi, , 6th edn., Centraalbureau voor Schimmelcultures, BaarnKlich, M.A., (2002) Identification of common Aspergillus species, , Centraalbureau voor Schimmelcultures, BaarnPitt, J.I., (2000) A Laboratory Guide to Common Penicillium Species, , 3rd edn., Commonwealth Scientific and Industrial Research Organization, North RydeSampaio, J.P., Gadanho, M., Santos, S., Duarte, F.L., Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: Rhodosporidium kratochvilovae and related anamorphic species (2001) Int. J. Syst. Evol. Microbiol., 51, pp. 687-697Pagnocca, F.C., Rodrigues, A., Nagamoto, N.S., Bacci, M., Jr., Yeasts and filamentous fungi carried by the gynes of leaf-cutting ants (2008) Anton. van Leeuwen., 94, pp. 517-526Kurtzman, C.P., Robnett, C.J., Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequence (1998) Anton. van Leeuwen., 73, pp. 331-371White, T.J., Bruns, T., Lee, S., Taylor, J.W., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics (1990) PCR Protocols: A Guide to Methods and Applications, pp. 315-322. , in: Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J., Eds.), Academic Press, New YorkHall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT (1999) Nucl. Acids Symp. Ser., 41, pp. 95-98Unterseher, M., Schnittler, M., Species richness analysis and ITS rDNA phylogeny revealed the majority of cultivable foliar endophytes from beech (Fagus sylvatica) (2010) Fungal Ecol., 3, pp. 366-378Durham, A.M., Kashiwabara, A.Y., Matsunaga, F.T., Ahagon, P.H., EGene: a configurable pipeline generation system for automated sequence analysis (2005) Bioinformatics, 21, pp. 2812-2813Nilsson, R.H., Abarenkov, K., Veldre, V., Nylinder, S., An open source chimera checker for the fungal ITS region (2010) Mol. Ecol. Res., 10, pp. 1076-1081Götz, S., García-Gómez, J.M., Terol, J., Williams, T.D., A high-throughput functional annotation and data mining with the Blast2GO suite (2008) Nucl. Acids Res., 36, pp. 3420-3435Colwell, R.K., (2009), http://purl.oclc.org/estimates, EstimateS: Statistical estimation of species richness and shared species from samples. Version 8.2. User's Guide and application published at:Edgar, R.C., Search and clustering orders of magnitude faster than BLAST (2010) Bioinformatics, 26, pp. 2460-2461Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities (2009) Appl. Env. Microbiol., 75, pp. 7537-7541Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput (2004) Nucl. Acids Res., 32, pp. 1792-1797Tamura, K., Peterson, D., Peterson, N., Stecher, G., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods (2011) Mol. Biol. Evol., 28, pp. 2731-2739Hamady, M., Lozupone, C., Knight, R., Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data (2010) ISME J., 4, pp. 17-27Price, M.N., Dehal, P.S., Arkin, A.P., FastTree: computing large minimum-evolution trees with profiles instead of a distance matrix (2009) Mol. Biol. Evol., 26, pp. 1641-1650Pagnocca, F.C., Masiulionis, V.E., Rodrigues, A., Specialized fungal parasites and opportunistic fungi in gardens of attine ants (2012) Psyche, 12, p. 9. , Article ID 905109Rodrigues, A., Pagnocca, F.C., Bacci, M., Jr., Hebling, M.J.A., Variability of non-mutualistic fungi associated with Atta sexdens rubropilosa nests (2005) Folia Microbiol., 50, pp. 421-425Bento, J.M.S., Della Lucia, T.M.C., Muchovej, R.M.C., Vilela, E.F., Influência da composição química e da população microbiana de diferentes horizontes do solo no estabelecimento de sauveiros iniciais de Atta laevigata (Hymenoptera: Formicidae) em laboratório (1991) An. Soc. Entomol. Bras., 20, pp. 307-317Rodrigues, O.D., (2007), Influência da comunidade microbiana do solo no estabelecimento de sauveiros iniciais de Atta sexdens rubropilosa Forel, 1908 (Hymenoptera: Formicidae). 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Microbial Diversity Associated With Algae, Ascidians And Sponges From The North Coast Of São Paulo State, Brazil

Little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. The aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. Data derived from ARDRA and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. Microbial strains identified up to the genus level revealed 144 distinct ribotypes out of 256 fungal strains and 158 distinct ribotypes out of 181 bacterial strains. Filamentous fungi were distributed among 24 different genera belonging to Ascomycota, Zygomycota and Basidiomycota, some of which had never been reported in the literature as marine invertebrate-inhabiting fungi (Pestalotiopsis, Xylaria, Botrysphaeria and Cunnninghamella). Bacterial isolates were affiliated to 41 different genera, being Bacillus, Ruegeria, Micrococcus, Pseudovibrio and Staphylococcus the most abundant ones. Results revealed an unexpected high microbial diversity associated to the macroorganisms which have been collected and suggested the selection of certain microbial taxonomic groups according to the host. The combined data gathered from this investigation contribute to broaden the knowledge of microbial diversity associated to marine macroorganisms, including as a promising source for the discovery of new natural products. © 2009 Elsevier GmbH.1656466482Alves, A., Phillips, A.J.L., Henriques, I., Correia, A., Rapid differentiation of species of Botryosphaeriaceae by PCR fingerprinting (2007) Res Microbiol, 158, pp. 112-121Anand, T.P., Bhat, A.W., Shouche, Y.S., Roy, U., Siddharth, J., Sarma, S.P., Antimicrobial activity of marine bacteria associated with sponges from the waters off the coast of South East India (2006) Microbiol Res, 161 (3), pp. 252-262Baker, P.W., Kennedy, J., Dobson, A.D.W., Marchesi, J.R., Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters Mar Biotechnol, , 200810.1007/s10126-008-9169-7Blunt, J.W., Copp, B.R., Hu, W.P., Munro, M.H.G., Northcote, P.T., Prinsep, M.R., Marine natural 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