10 research outputs found
Proceedings of the 3rd international conference on numerical methods in fracture mechanics
Using the Gaussian function to simulate constant potential anodes in multiobjective optimization of cathodic protection systems
Metagenomic Analysis Of A Tropical Composting Operation At The São Paulo Zoo Park Reveals Diversity Of Biomass Degradation Functions And Organisms
Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders. © 2013 Martins et al.84Ryckeboer, J., Mergaert, J., Vaes, K., Klammer, S., De Clercq, D., A survey of bacteria and fungi occurring during composting and self-heating processes (2003) Annals of Microbiology, 53, pp. 349-410Ishii, K., Takii, S., Comparison of microbial communities in four different composting processes as evaluated by denaturing gradient gel electrophoresis analysis (2003) Journal of Applied Microbiology, 95, pp. 109-119Steger, K., Eklind, Y., Olsson, J., Sundh, I., Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels (2005) Microbial Ecology, 50, pp. 163-171Takebayashi, S., Narihiro, T., Fujii, Y., Hiraishi, A., Water availability is a critical determinant of a population shift from Proteobacteria to Actinobacteria during start-up operation of mesophilic fed-batch composting (2007) Microbes and Environments, 22, pp. 279-289Vargas-Garcia, M.C., Suarez-Estrella, F., Lopez, M.J., Moreno, J., Microbial population dynamics and enzyme activities in composting processes with different starting materials (2010) Waste Management, 30, pp. 771-778Partanen, P., Hultman, J., Paulin, L., Auvinen, P., Romantschuk, M., Bacterial diversity at different stages of the composting process (2010) BMC Microbiology, 10, p. 94Kumar, S., Composting of municipal solid waste (2011) Critical Reviews in Biotechnology, 31, pp. 112-136Peters, S., Koschinsky, S., Schwieger, F., Tebbe, C.C., Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes (2000) Applied and Environmental Microbiology, 66, pp. 930-936Alfreider, A., Peters, S., Tebbe, C.C., Rangger, A., Insam, H., Microbial community dynamics during composting of organic matter as determined by 16S ribosomal DNA analysis (2002) Compost Science & Utilization, 10, pp. 303-312Steger, K., Sjogren, A.M., Jarvis, A., Jansson, J.K., Sundh, I., Development of compost maturity and Actinobacteria populations during full-scale composting of organic household waste (2007) Journal of Applied Microbiology, 103, pp. 487-498Guo, Y., Zhu, N., Zhu, S., Deng, C., Molecular phylogenetic diversity of bacteria and its spatial distribution in composts (2007) Journal of Applied Microbiology, 103, pp. 1344-1354Franke-Whittle, I.H., Knapp, B.A., Fuchs, J., Kaufmann, R., Insam, H., Application of COMPOCHIP microarray to investigate the bacterial communities of different composts (2009) Microbial Ecology, 57, pp. 510-521Anastasi, A., Varese, G.C., Marchisio, V.F., Isolation and identification of fungal communities in compost and vermicompost (2005) Mycologia, 97, pp. 33-44Hultman, J., Vasara, T., Partanen, P., Kurola, J., Kontro, M.H., Determination of fungal succession during municipal solid waste composting using a cloning-based analysis (2010) Journal of Applied Microbiology, 108, pp. 472-487Bent, S.J., Forney, L.J., The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity (2008) The ISME Journal, 2, pp. 689-695Hong, S.H., Bunge, J., Leslin, C., Jeon, S., Epstein, S.S., Polymerase chain reaction primers miss half of rRNA microbial diversity (2009) The ISME Journal, 3, pp. 1365-1373van Elsas, J.D., Boersma, F.G.H., A review of molecular methods to study the microbiota of soil and the mycosphere (2011) European Journal of Soil Biology, 47, pp. 77-87Gonzalez, J.M., Portillo, M.C., Belda-Ferre, P., Mira, A., Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities (2012) PloS ONE, 7, pp. e29973Lombard, N., Prestat, E., van Elsas, J.D., Simonet, P., Soil-specific limitations for access and analysis of soil microbial communities by metagenomics (2011) FEMS Microbiology Ecology, 78, pp. 31-49Allgaier, M., Reddy, A., Park, J.I., Ivanova, N., D'haeseleer, P., Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community (2010) PloS ONE, 5, pp. e8812Shokralla, S., Spall, J.L., Gibson, J.F., Hajibabaei, M., Next-generation sequencing technologies for environmental DNA research (2012) Molecular Ecology, 21, pp. 1794-1805Thomas, T., Gilbert, J., Meyer, F., Metagenomics - a guide from sampling to data analysis (2012) Microbial Informatics and Experimentation, 2, p. 3Simon, C., Daniel, R., Achievements and new knowledge unraveled by metagenomic approaches (2009) Applied Microbiology and Biotechnology, 85, pp. 265-276Delmont, T.O., Malandain, C., Prestat, E., Larose, C., Monier, J.M., Metagenomic mining for microbiologists (2011) The ISME Journal, 5, pp. 1837-1843Brulc, J.M., Antonopoulos, D.A., Miller, M.E.B., Wilson, M.K., Yannarell, A.C., Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases (2009) Proceedings of the National Academy of Sciences of the United States of America, 106, pp. 1948-1953Hess, M., Sczyrba, A., Egan, R., Kim, T.W., Chokhawala, H., Metagenomic discovery of biomass-degrading genes and genomes from cow rumen (2011) Science, 331, pp. 463-467Dai, X., Zhu, Y.X., Luo, Y.F., Song, L., Liu, D., Metagenomic insights into the fibrolytic microbiome in yak rumen (2012) PloS ONE, 7, pp. e40430Gladden, J.M., Allgaier, M., Miller, C.S., Hazen, T.C., VanderGheynst, J.S., Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass (2011) Applied and Environmental Microbiology, 77, pp. 5804-5812Dougherty, M.J., D'Haeseleer, P., Hazen, T.C., Simmons, B.A., Adams, P.D., Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization (2012) BMC Biotechnology, 12, p. 38Curtis, T.P., Sloan, W.T., Scannell, J.W., Estimating prokaryotic diversity and its limits (2002) Proceedings of the National Academy of Sciences of the United States of America, 99, pp. 10494-10499Torsvik, V., Ovreas, L., Thingstad, T.F., Prokaryotic diversity-magnitude, dynamics, and controlling factors (2002) Science, 296, pp. 1064-1066Schloss, P.D., Handelsman, J., Toward a census of bacteria in soil (2006) PLoS Computational Biology, 2, pp. e92Dillon, R.J., Dillon, V.M., The gut bacteria of insects: Nonpathogenic interactions (2004) Annual Review of Entomology, 49, pp. 71-92Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Metagenomic analysis of the human distal gut microbiome (2006) Science, 312, pp. 1355-1359Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Evolution of mammals and their gut microbes (2008) Science, 320, pp. 1647-1651DeAngelis, K.M., Gladden, J.M., Allgaier, M., D'haeseleer, P., Fortney, J.L., Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities (2010) Bioenergy Research, 3, pp. 146-158Warnecke, F., Luginbuhl, P., Ivanova, N., Ghassemian, M., Richardson, T.H., Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite (2007) Nature, 450, pp. 560-565Hollister, E.B., Forrest, A.K., Wilkinson, H.H., Ebbole, D.J., Malfatti, S.A., Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production (2010) Applied Microbiology and Biotechnology, 88, pp. 389-399Ramette, A., Multivariate analyses in microbial ecology (2007) FEMS Microbiology Ecology, 62, pp. 142-160Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes (2008) BMC Bioinformatics, 9, p. 386Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2009) Nucleic Acids Research, 37, pp. D141-D145Steger, K., Jarvis, A., Vasara, T., Romantschuk, M., Sundh, I., Effects of differing temperature management on development of Actinobacteria populations during composting (2007) Research in Microbiology, 158, pp. 617-624Dees, P.M., Ghiorse, W.C., Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA (2001) FEMS Microbiology Ecology, 35, pp. 207-216Klammer, S., Knapp, B., Insam, H., Dell'Abate, M.T., Ros, M., Bacterial community patterns and thermal analyses of composts of various origins (2008) Waste Management & Research, 26, pp. 173-187Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy (2007) Applied and Environmental Microbiology, 73, pp. 5261-5267Schloss, P.D., Hay, A.G., Wilson, D.B., Walker, L.P., Tracking temporal changes of bacterial community fingerprints during the initial stages of composting (2003) FEMS Microbiology Ecology, 46, pp. 1-9Atkinson, C.F., Jones, D.D., Gauthier, J.J., Putative anaerobic activity in aerated composts (1996) Journal of Industrial Microbiology, 16, pp. 182-188Lynd, L.R., Weimer, P.J., van Zyl, W.H., Pretorius, I.S., Microbial cellulose utilization: Fundamentals and biotechnology (2002) Microbiology and Molecular Biology Reviews, 66, pp. 506-577Yi, J., Wu, H.Y., Wu, J., Deng, C.Y., Zheng, R., Molecular phylogenetic diversity of Bacillus community and its temporal-spatial distribution during the swine manure of composting (2012) Applied Microbiology and Biotechnology, 93, pp. 411-421Kato, S., Haruta, S., Cui, Z.J., Ishii, M., Igarashi, Y., Effective cellulose degradation by a mixed-culture system composed of a cellulolytic Clostridium and aerobic non-cellulolytic bacteria (2004) FEMS Microbiology Ecology, 51, pp. 133-142Bugg, T.D.H., Ahmad, M., Hardiman, E.M., Rahmanpour, R., Pathways for degradation of lignin in bacteria and fungi (2011) Natural Product Reports, 28, pp. 1883-1896Tuomela, M., Vikman, M., Hatakka, A., Itavaara, M., Biodegradation of lignin in a compost environment: a review (2000) Bioresource Technology, 72, pp. 169-183Yu, H., Zeng, G.M., Huang, H.L., Xi, X.M., Wang, R.Y., Microbial community succession and lignocellulose degradation during agricultural waste composting (2007) Biodegradation, 18, pp. 793-802Rastogi, G., Bhalla, A., Adhikari, A., Bischoff, K.M., Hughes, S.R., Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains (2010) Bioresource Technology, 101, pp. 8798-8806Gu, Y., Ding, Y., Ren, C., Sun, Z., Rodionov, D.A., Reconstruction of xylose utilization pathway and regulons in Firmicutes (2010) BMC Genomics, 11, p. 255Gihring, T.M., Green, S.J., Schadt, C.W., Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes (2012) Environmental Microbiology, 14, pp. 285-290Aoshima, M., Pedro, M.S., Haruta, S., Ding, L.X., Fukada, T., Analyses of microbial community within a composter operated using household garbage with special reference to the addition of soybean oil (2001) Journal of Bioscience and Bioengineering, 91, pp. 456-461Hemmi, H., Shimoyama, T., Nakayama, T., Hoshi, K., Nishino, T., Molecular biological analysis of microflora in a garbage treatment process under thermoacidophilic conditions (2004) Journal of Bioscience and Bioengineering, 97, pp. 119-126Adams, J.D., Frostick, L.E., Analysis of bacterial activity, biomass and diversity during windrow composting (2009) Waste Management, 29, pp. 598-605Azadnia, P., Zamani, M.H., Ghasemi, S.A., Babaki, A.K., Jashni, M.K., Isolation and identification of thermophilic Lactobacilli from traditional yoghurts of tribes of Kazerun (2011) Journal of Animal and Veterinary Advances, 10, pp. 774-776Dobson, A., Cotter, P.D., Ross, R.P., Hill, C., Bacteriocin production: a probiotic trait? (2012) Applied and Environmental Microbiology, 78, pp. 1-6Singh, S., Goswami, P., Singh, R., Heller, K.J., Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: A review (2009) Lwt-Food Science and Technology, 42, pp. 448-457Lukjancenko, O., Ussery, D.W., Wassenaar, T.M., Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera (2012) Microbial Ecology, 63, pp. 651-673Scheirlinck, I., Van der Meulen, R., Van Schoor, A., Huys, G., Vandamme, P., Lactobacillus crustorum sp nov., isolated from two traditional Belgian wheat sourdoughs (2007) International Journal of Systematic and Evolutionary Microbiology, 57, pp. 1461-1467Tanasupawat, S., Shida, O., Okada, S., Komagata, K., Lactobacillus acidipiscis sp nov and Weissella thailandensis sp nov., isolated from fermented fish in Thailand (2000) International Journal of Systematic and Evolutionary Microbiology, 50, pp. 1479-1485Canchaya, C., Claesson, M.J., Fitzgerald, G.F., van Sinderen, D., O'Toole, P.W., Diversity of the genus Lactobacillus revealed by comparative genomics of five species (2006) Microbiology-SGM, 152, pp. 3185-3196Ventura, M., O'Flaherty, S., Claesson, M.J., Turroni, F., Klaenhammer, T.R., Genome-scale analyses of health-promoting bacteria: probiogenomics (2009) Nature Reviews Microbiology, 7, pp. 61-71Endo, A., Futagawa-Endo, Y., Dicks, L.M.T., Diversity of Lactobacillus and Bifidobacterium in feces of herbivores, omnivores and carnivores (2010) Anaerobe, 16, pp. 590-596Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., The COG database: an updated version includes eukaryotes (2003) BMC Bioinformatics, 4, p. 41Piddock, L.J.V., Multidrug-resistance efflux pumps - not just for resistance (2006) Nature Reviews Microbiology, 4, pp. 629-636Cottrell, M.T., Yu, L.Y., Kirchman, D.L., Sequence and expression analyses of Cytophaga-like hydrolases in a Western arctic metagenomic library and the Sargasso seat (2005) Applied and Environmental Microbiology, 71, pp. 8506-8513Demain, A.L., Newcomb, M., Wu, J.H.D., Cellulase, clostridia, and ethanol (2005) Microbiology and Molecular Biology Reviews, 69, pp. 124-154Fontes, C.M.G.A., Gilbert, H.J., Cellulosomes: Highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates (2010) Annual Review of Biochemistry, 79, pp. 655-681Bugg, T.D.H., Ahmad, M., Hardiman, E.M., Singh, R., The emerging role for bacteria in lignin degradation and bio-product formation (2011) Current Opinion in Biotechnology, 22, pp. 394-400Sanchez, C., Lignocellulosic residues: Biodegradation and bioconversion by fungi (2009) Biotechnol Advances, 27, pp. 185-194Sugano, Y., DyP-type peroxidases comprise a novel heme peroxidase family (2009) Cellular and Molecular Life Sciences, 66, pp. 1387-1403Roberts, J.N., Singh, R., Grigg, J.C., Murphy, M.E.P., Bugg, T.D.H., Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1 (2011) Biochemistry, 50, pp. 5108-5119Ahmad, M., Taylor, C.R., Pink, D., Burton, K., Eastwood, D., Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders (2010) Molecular Biosystems, 6, pp. 815-821Brown, M.E., Walker, M.C., Nakashige, T.G., Iavarone, A.T., Chang, M.C.Y., Discovery and characterization of heme enzymes from unsequenced Bacteria: Application to microbial lignin degradation (2011) Journal of the American Chemical Society, 133, pp. 18006-18009Markowitz, V.M., Ivanova, N.N., Szeto, E., Palaniappan, K., Chu, K., IMG/M: a data management and analysis system for metagenomes (2008) Nucleic Acids Research, 36, pp. D534-D538Lamendella, R., Domingo, J.W., Ghosh, S., Martinson, J., Oerther, D.B., Comparative fecal metagenomics unveils unique functional capacity of the swine gut (2011) BMC Microbiology, 11, p. 103van der Lelie, D., Taghavi, S., McCorkle, S.M., Li, L.L., Malfatti, S.A., The metagenome of an anaerobic microbial community decomposing poplar wood chips (2012) PloS ONE, 7, pp. e36740Edwards, M.C., Doran-Peterson, J., Pectin-rich biomass as feedstock for fuel ethanol production (2012) Applied Microbiology and Biotechnology, 95, pp. 565-575Rynk, R., van de Kamp, M., Willson, G.B., Singley, M.E., Richard, T.L., (1992) On-Farm Composting Handbook, Northeast Regional Agricultural Engineering Service - Cooperative Extension, p. 186. , Rynk R, editor. Ithaca, NY: Northeast Regional Agricultural Engineering ServiceBitencourt, A.L.V., Vallim, M.A., Maia, D., Spinelli, R., Angeloni, R., Core sampling test in large-scale compost cells for microorganism isolation (2010) African Journal of Microbiology Research, 4, pp. 1631-1634Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., Metagenomic microbial community profiling using unique clade-specific marker genes (2012) Nat Methods, 9, pp. 811-814Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Database resources of the National Center for Biotechnology Information (2012) Nucleic Acids Research, 40, pp. D13-D25Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs (1997) Nucleic Acids Research, 25, pp. 3389-3402Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., Clustal W and clustal X version 2.0 (2007) Bioinformatics, 23, pp. 2947-294