Comparative Analyses Of Xanthomonas And Xylella Complete Genomes

Computational analyses of four bacterial genomes of the Xanthomonadaceae family reveal new unique genes that may be involved in adaptation, pathogenicity, and host specificity. The Xanthomonas genus presents 3636 unique genes distributed in 1470 families, while Xylella genus presents 1026 unique genes distributed in 375 families. Among Xanthomonas-specific genes, we highlight a large number of cell wall degrading enzymes, proteases, and iron receptors, a set of energy metabolism genes, second copy of the type II secretion system, type III secretion system, flagella and chemotactic machinery, and the xanthomonadin synthesis gene cluster. Important genes unique to the Xylella genus are an additional copy of a type IV pili gene cluster and the complete machinery of colicin V synthesis and secretion. Intersections of gene sets from both genera reveal a cluster of genes homologous to Salmonella's SPI-7 island in Xanthomonas axonopodis pv citri and Xylella fastidiosa 9a5c, which might be involved in host specificity. Each genome also presents important unique genes, such as an HMS cluster, the kdgT gene, and O-antigen in Xanthomonas axonopodis pv citri; a number of avrBS genes and a distinct O-antigen in Xanthomonas campestris pv campestris, a type I restriction- modification system and a nickase gene in Xylella fastidiosa 9a5c, and a type II restriction-modification system and two genes related to peptidoglycan biosynthesis in Xylella fastidiosa temecula 1. All these differences imply a considerable number of gene gains and losses during the divergence of the four lineages, and are associated with structural genome modifications that may have a direct relation with the mode of transmission, adaptation to specific environments and pathogenicity of each organism.914376Adachi, J., Hasegawa, M., (1996) MOLPHY Version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood, , J. Adachi, ed. (Institute of Statistical Mathematics, Tokyo)Almra, Mattick, J.S., Genes involved in the biogenesis and function of type-4 fimbriae in Pseudomonas aeruginosa (1997) Gene, 192, pp. 89-98Almeida, R.P., Mann, R., Purcell, A.H., Xylella fastidiosa cultivation on a minimal solid defined medium (2004) Curr Microbiol, 48, pp. 368-372Almeida, R.P., Purcell, A.H., Biological traits of Xylella fastidiosa strains from grapes and almonds (2003) Appl Environ Microbiol, 69, pp. 7447-7452Altschul, S.F., Madden, T.L., Schaffer, A.A., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs (1997) Nucleic Acids Res, 25, pp. 3389-3402Apweiler, R., Attwood, T.K., Bairoch, A., InterPro: An integrated documentation resource for protein families, domains and functional sites (2000) Bioinformatics, 16, pp. 1145-1150Apweiler, R., Bairoch, A., Wu, C.H., UniProt: The Universal Protein knowledgebase (2004) Nucleic Acids Res, 32, pp. D115-D119Araujo, W.L., Marcon, J., Maccheroni Jr., W., Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants (2002) Appl Environ Microbiol, 68, pp. 4906-4914Barber, C.E., Tang, J.L., Feng, J.X., A novel regulatory system required for pathogenicity of Xanthomonas campestris is mediated by a small diffusible signal molecule (1997) Mol Microbiol, 24, pp. 555-566Bhattacharyya, A., Stilwagen, S., Ivanova, N., Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains (2002) Proc Natl Acad Sci USA, 99, pp. 12403-12408Bhattacharyya, A., Stilwagen, S., Reznik, G., Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights (2002) Genome Res, 12, pp. 1556-1563Bradley, D.E., Shortening of Pseudomonas aeruginosa pili after RNA-phage adsorption (1972) J Gen Microbiol, 72, pp. 303-319Bradley, D.E., The adsorption of Pseudomonas aeruginosa pilus-dependent bacteriophages to a host mutant with nonretractile pili (1974) Virology, 58, pp. 149-163Braun, V., Braun, M., Iron transport and signaling in Escherichia coll (2002) FEBS Lett, 529, pp. 78-85Braun, V., Hancock, R.E., Hantke, K., Functional organization of the outer membrane of Escherichia coli: Phage and colicin receptors as components of iron uptake systems (1976) J Supramol Struct, 5, pp. 37-58Buyer, J.S., Leong, J., Iron transport-mediated antagonism between plant growth-promoting and plant-deleterious Pseudomonas strains (1986) J Biol Chem, 261, pp. 791-794Campbell, A., Prophage insertion sites (2003) Res Microbiol, 154, pp. 277-282Castresana, J., Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis (2000) Mol Biol Evol, 17, pp. 540-552Chang, C.J., Donaldson, R.C., Nutritional requirements of Xylella fastidiosa, which causes Pierce's disease in grapes (2000) Can J Microbiol, 46, pp. 291-293Chang, C.J., Garner, M., Zreik, L., Culture and serological detection of the xylem-limited bacterium causing citrus variegated chlorosis and identification as a strain of Xylella fastidiosa (1993) Curr Microbiol, 27, pp. 137-142Collmer, A., Badel, J.L., Charkowski, A.O., Pseudomonas syringae Hrp type III secretion system and effector proteins (2000) Proc Natl Acad Sci USA, 97, pp. 8770-8777Cornelis, P., Matthijs, S., Diversity of siderophore-mediated iron uptake systems in fluorescent pseudomonads: Not only pyoverdines (2002) Environ Microbiol, 4, pp. 787-798Crow, J.F., Kimura, M., (1970) An Introduction to Population Genetics Theory, , Harper and Row, New YorkSilva, D.A., Ferro, A.C., Reinach, J.A., Comparison of the genomes of two Xanthomonas pathogens with differing host specificities (2002) Nature, 417, pp. 459-463Silva, D.A., Vettore, F.R., Kemper, A.L., Fastidian gum: The Xylellafastidiosa exopolysaccharide possibly involved in bacterial pathogenicity (2001) FEMS Microbiol Lett, 203, pp. 165-171Daubin, V., Ochman, H., Start-up entities in the origin of new genes (2004) Curr Opin Genet Dev, 14, pp. 616-619Delver, E.P., Kotova, V.U., Zavilgelsky, G.B., Nucleotide sequence of the gene (ard) encoding the antirestriction protein of plasmid colIb-P9 (1991) J Bacteriol, 173, pp. 5887-5892Digiampietrl, L.A., Medeiros, C.B., Setubal, J.C., A data model for comparative genomics (2003) Rev Tecnol Inform, 3, pp. 35-40Dow, J.M., Feng, J.X., Barber, C.E., Novel genes involved in the regulation of pathogenicity factor production within the rpf gene cluster of Xanthomonas campestris (2000) Microbiology, 146, pp. 885-891Fath, M.J., Mahanty, H.K., Kolter, R., Characterization of a purF operon mutation which affects colicin V production (1989) J Bacteriol, 171, pp. 3158-3161Gelfand, M.S., Koonin, E.V., Avoidance of palindromic words in bacterial and archaeal genomes: A close connection with restriction enzymes (1997) Nucleic Acids Res, 25, pp. 2430-2439Gobert, A.P., Cheng, Y., Wang, J.Y., Helicobacter pylori induces macrophage apoptosis by activation of arginase II (2002) J Immunol, 168, pp. 4692-4700Gobert, A.P., Mcgee, D.J., Akhtar, M., Helicobacter pylori arginase inhibits nitric oxide production by eukaryotic cells: A strategy for bacterial survival (2001) Proc Natl Acad Sci USA, 98, pp. 13844-13849Goel, A.K., Rajagopal, L., Nagesh, N., Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in Xanthomonas oryzae pv. oryzae (2002) J Bacteriol, 184, pp. 3539-3548Gomez, P., Ribas-Aparicio, R.M., Pelaez, A.I., Isolation and nucleotide sequence of the gene encoding the Xaml DNA methyltransferase of Xanthomonas campestris pv. amaranthicola (1997) Biochim Biophys Acta, 1351, pp. 261-266Gottwald, T., Graham, J., Bacteria diseases (2000) Compendium of Citrus Diseases, , L. W. Timmer, S.M. Garnsey, and J.H. Graham, eds. (APS Press, St. Paul)Graham, J.H., Gottwald, T.R., Cubero, J., Xanthomonas axonopodis pv. citri: Factors affecting successful eradiction of citrus canker (2004) Mol Plant Pathol, 5, pp. 1-15Heidelberg, J.F., Eisen, J.A., Nelson, W.C., DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae (2000) Nature, 406, pp. 477-483Hendricks, E.C., Szerlong, H., Hill, T., Cell division, guillotining of dimer chromosomes and SOS induction in resolution mutants (dif, xerC and xerD) of Escherichia coli (2000) Mol Microbiol, 36, pp. 973-981Hendson, M., Purcell, A.H., Chen, D., Genetic diversity of Pierce's disease strains and other pathotypes of Xylella fastidiosa (2001) Appl Environ Microbiol, 67, pp. 895-903Holt, J.G., (1994) Xylella. Bergey's Manual of Determinative Bacteriology, 9th Ed., pp. 100-115. , J.G. Holt, ed. (Williams and Wilkins, London)Hopkins, D.L., Xylella fastidiosa: Xylem-limited bacaterial pathogen of plants (1989) Annu Rev Phytopathol, 27, pp. 271-290Housby, J.N., Thomas, J.D., Wharam, S.D., Conditional mutations in OutE and OutL block exoenzyme secretion across the Erwinia carotovora outer membrane (1998) FEMS Microbiol Lett, 165, pp. 91-102Hung, C.H., Yang, C.F., Yang, C.Y., Involvement of tonB-exbBD1D2 operon in infection of Xanthomonas campestris nhaee phi L7 (2003) Biochem and Biophys Res Commun, 302, pp. 878-884Jenkins, C.L., Starr, M.P., Formation of halogenated aryl-polyene (xanthomonadin) pigments by the type and other yellow-pigmented strains of Xanthomonas maltophilia (1985) Ann l'Institut Pasteur Microbiol, 136 B, pp. 257-264Kanehisa, M., Goto, S., Kawashima, S., The KEGG resource for deciphering the genome (2004) Nucleic Acids Res, 32, pp. D277-D280Karlin, S., Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes (2001) Trends Microbiol, 9, pp. 335-343Kelly, M.J., Poole, R.K., Yates, M.G., Cloning and mutagenesis of genes encoding the cytochrome bd terminal oxidase complex in Azotobacter vinelandii: Mutants deficient in the cytochrome d complex are unable to fix nitrogen in air (1990) J Bacteriol, 172, pp. 6010-6019Khalil-Rizvi, S., Toth, S.I., Van Der Helm, D., Structures and characteristics of novel siderophores from plant deleterious Pseudomonas fluorescens A225 and Pseudomonas putida ATCC 39167 (1997) Biochemistry, 36, pp. 4163-4171Koide, T., Zaini, P.A., Moreira, L.M., DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence (2004) J Bacteriol, 186, pp. 5442-5449Koster, M., Ovaa, W., Bitter, W., Multiple outer membrane receptors for uptake of ferric pseudobactins in Pseudomonas putida WCS358 (1995) Mol Gen Genet, 248, pp. 735-743Lacava, P.T., Araujo, W.L., Marcon, J., Interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria Xylella fastidiosa, causal agent of citrus-variegated chlorosis (2004) Lett Appl Microbiol, 39, pp. 55-59Lazdunski, C.J., Bouveret, E., Rigal, A., Colicin import into Escherichia coli cells (1998) J Bacteriol, 180, pp. 4993-5002Lee, H.M., Chen, J.R., Lee, H.L., Functional dissection of the XpsN (GspC) protein of the Xanthomonas campestris pv. campestris type II secretion machinery (2004) J Bacteriol, 186, pp. 2946-2955Lee, H.M., Wang, K.C., Liu, Y.L., Association of the cytoplasmic membrane protein XpsN with the outer membrane protein XpsD in the type II protein secretion apparatus of Xanthomonas campestris pv. campestris (2000) J Bacteriol, 182, pp. 1549-1557Lee, R.F.E.A., Beretta, M.J.G., Hartung, J.H., Citrus variegated chlorosis: Confirmation of a Xylella fastidiosa as the causal agent (1993) Summa Phytopathol, pp. 123-125. , 19.2Leite, B., Andersen, P.C., Ishida, M.L., Colony aggregation and biofilm formation in xylem chemistry-based media for Xylella fastidiosa (2004) FEMS Microbiol Lett, 230, pp. 283-290Lerat, E., Daubin, V., Moran, N.A., From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria (2003) PLoS Biol, 1, pp. E19Lima, W.C., Paquola, A.C.M., Van Sluys, M.-A., Non-gamma proteobacteria gene islands contribution to Xanthomonas genome (2005) OMICS, , this issueLin, R.J., Capage, M., Hill, C.W., A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome (1984) J Mol Biol, 177, pp. 1-18Lobry, J.R., Asymmetric substitution patterns in the two DNA strands of bacteria (1996) Mol Biol Evol, 13, pp. 660-665Long, S.R., Staskawicz, B.J., Prokaryotic plant parasites (1993) Cell, 73, pp. 921-935Lopes, J.R.S., Beretta, M.J.G., Harakava, R., Confirmação da transmissão por cigarrinhas do agente causal da clorose variegada dos citros, Xylella fastidiosa (1996) Fitopatol Brasil, 21 (SUPPL.), p. 343Lopez, N.I., Haedo, A.S., Mendez, B.S., Evaluation of Xanthomonas campestris survival in a soil microcosm system (1999) Int Microbiol, 2, pp. 111-114Minet, A.D., Chiquet-Ehrismann, R., Phylogenetic analysis of teneurin genes and comparison to the rearrangement hot spot elements of E. coli (2000) Gene, 257, pp. 87-97Moreira, L.M., De Souza, R.F., Almeida, N.F., Comparative genomics analyses of citrus-associated bacteria (2004) Annu Rev Phytopathol, 42, pp. 163-184Noel, L., Thieme, F., Gabler, J., XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria (2003) J Bacteriol, 185, pp. 7092-7102Nunes, L.R., Rosato, Y.B., Muto, N.H., Microarray analyses of Xylella fastidiosa provide evidence of coordinated transcription control of laterally transferred elements (2003) Genome Res, 13, pp. 570-578Page, R.D., Charleston, M.A., From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem (1997) Mol Phylogenet Evol, 7, pp. 231-240Pashalidis, S., Moreira, L.M., Zaini, P.A., Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose (2005) OMICS, , this issuePendrak, M.L., Perry, R.D., Characterization of a hemin-storage locus of Yersinia pestis (1991) Biol Met, 4, pp. 41-47Plckard, D., Wain, J., Baker, S., Composition, acquisition, and distribution of the Vi exopolysaccharide- encoding Salmonella enterica pathogenicity island SPI-7 (2003) J Bacteriol, 185, pp. 5055-5065Poplawsky, A.R., Chun, W., pigB determines a diffusible factor needed for extracellular polysaccharide slime and xanthomonadin production in Xanthomonas campestris pv. campestris (1997) J Bacteriol, 179, pp. 439-444Poplawsky, A.R., Urban, S.C., Chun, W., Biological role of xanthomonadin pigments in Xanthomonas campestris pv. campestris (2000) Appl Environ Microbiol, 66, pp. 5123-5127Purcell, A.H., Almond leaf scorch: Leafhooper and spittle bug vectors (1980) J Econ Entomol, 73, pp. 834-838Rajagopal, L., Sundari, C.S., Balasubramanian, D., The bacterial pigment xanthomonadin offers protection against photodamage (1997) FEBS Lett, 415, pp. 125-128Rossetti, V., Garnier, M., Bové, J.M., Presence de bacteries dans le xyleme d'oranges atteints de chlorose variegee, une nouvelle maladie des agrumes au Bresil (1990) CRAcad Paris, 310, pp. 345-349Scarpari, L.M., Lambais, M.R., Silva, D.S., Expression of putative pathogenicity-related genes in Xylella fastidiosa grown at low and high cell density conditions in vitro (2003) FEMS Microbiol Lett, 222, pp. 83-92Schaad, N.W., Alvarez, A., Xanthomonas campestris pv. campestris: Cause of black rot of crucifers (1993) Xanthomonas, 1st Ed., pp. 51-53. , J.G. Swings and E.L. Civerolo, eds. London: Chapman & HallSchaad, N.W., Postnikova, E., Lacy, G., Xylella fastidiosa subspecies: X. fastidiosa subsp piercei, subsp. nov., and X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov (2004) Syst Appl Microbiol, 27, pp. 290-300Schubert, S., Rakln, A., Karch, H., Prevalence of the "high-pathogenicity island" of Yersinia species among Escherichia coli strains that are pathogenic to humans (1998) Infect Immun, 66, pp. 480-485Sekizaki, T., Otani, Y., Osaki, M., Evidence for horizontal transfer of SsuDAT1I restriction-modification genes to the Streptococcus suis genome (2001) J Bacteriol, 183, pp. 500-511Sharp, P.M., Kelleher, J.E., Daniel, A.S., Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria (1992) Proc Natl Acad Sci USA, 89, pp. 9836-9840Simpson, A.J., Reinach, F.C., Arruda, P., The genome sequence of the plant pathogen Xylella fastidiosa (2000) Nature, 406, pp. 151-157. , The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and AnalysisSivonen, K., Namikoshi, M., Evans, W.R., Three new microcystins, cyclic heptapeptide hepatotoxins, from Nostoc sp. strain 152 (1992) Chem Res Toxicol, 5, pp. 464-469Starr, M.P., Jenkins, C.L., Bussey, L.B., Chemotaxonomic significance of the xanthomonadins, novel brominated aryl-polyene pigments produced by bacteria of the genus Xanthomonas (1977) Arch Microbiol, 113, pp. 1-9Steinmann, D., Koplin, R., Puhler, A., Xanthomonas campestris pv. campestris 1psI and 1psJ genes encoding putative proteins with sequence similarity to the alpha- and beta-subunits of 3-oxoacid CoA-transferases are involved in LPS biosynthesis (1997) Arch Microbiol, 168, pp. 441-447Stock, J., Surette, M., Bacterial chemotaxis. The motor connection (1994) Curr Biol, 4, pp. 143-144Stock, J., Surette, M., Park, P., Chemosensing and signal transduction in bacteria (1994) Curr Opin Neurobiol, 4, pp. 474-480Stock, J.B., Surette, M.G., Mccleary, W.R., Signal transduction in bacterial chemotaxis (1992) J Biol Chem, 267, pp. 19753-19756Strom, M.S., Lory, S., Structure-function and biogenesis of the type IV pili (1993) Annu Rev Microbiol, 47, pp. 565-596Swings, J.G., Civerolo, E.L., (1993) Xanthomonas, 1st Ed., , Chapman & Hall, LondonTang, J.L., Liu, Y.N., Barber, C.E., Genetic and molecular analysis of a cluster of rpf genes involved in positive regulation of synthesis of extracellular enzymes and polysaccharide in Xanthomonas campestris pathovar campestris (1991) Mol Gen Genet, 226, pp. 409-417Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., The COG database: New developments in phylogenetic classification of proteins from complete genomes (2001) Nucleic Acids Res, 29, pp. 22-28Thomas, J.D., Reeves, P.J., Salmond, G.P., The general secretion pathway of Erwinia carotovora subsp. carotovora: Analysis of the membrane topology of OutC and OutF (1997) Microbiology, 143, pp. 713-720Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice (1994) Nucleic Acids Res, 22, pp. 4673-4680Van Sluys, M.A., De Oliveira, M.C., Monteiro-Vitorello, C.B., Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa (2003) J Bacteriol, 185, pp. 1018-1026Van Sluys, M.A., Monteiro-Vitorello, C.B., Camargo, L.E., Comparative genomic analysis of plant-associated bacteria (2002) Annu Rev Phytopathol, 40, pp. 169-189Vojnov, A.A., Slater, H., Newman, M.A., Regulation of the synthesis of cyclic glucan in Xanthomonas campestris by a diffusible signal molecule (2001) Arch Microbiol, 176, pp. 415-420Vorholter, F.J., Niehaus, K., Puhler, A., Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: A cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core (2001) Mol Genet Genomics, 266, pp. 79-95Waters, V.L., Crosa, J.H., Colicin V virulence plasmids (1991) Microbiol Rev, 55, pp. 437-450Wells, J.M., Raju, B.C., Hung, H.Y., Xylella fastidiosa gen. nov., sp. nov.: Gram-negative, xylem-limited, fastidious plant bacteria related to Xanthomonas spp (1987) Int J Syst Bacteriol, 37, pp. 136-143Wells, J.M., Raju, B.C., Thompson, J.M., Etiology of phony peach and plum leaf scald diseases (1981) Phytopathology, 71, pp. 1156-1161Wiggerich, H.G., Klauke, B., Koplin, R., Unusual structure of the tonB-exb DNA region of Xanthomonas campestris pv. campestris: tonB, exbB, and exbD1 are essential for ferric iron uptake, but exbD2 is not (1997) J Bacteriol, 179, pp. 7103-7110Wiggerich, H.G., Puhler, A., The exbD2 gene as well as the iron-uptake genes tonB, exbB and exbD1 of Xanthomonas campestris pv. campestris are essential for the induction of a hypersensitive response on pepper (Capsicum annuum) (2000) Microbiology, 146, pp. 1053-1060Williams, K.P., Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: Sublocation preference of integrase subfamilies (2002) Nucleic Acids Res, 30, pp. 866-875Woolfit, M., Bromham, L., Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes (2003) Mol Biol Evol, 20, pp. 1545-155

Fact And Task Oriented System For Genome Assembly And Annotation

We present a preliminary description and results of a system to help the curation of genome assembly and annotation. Standard tools are used for these tasks, and our methodology focuses on user guidance, data visualization and integration, and data browsing aspects. © Springer-Verlag Berlin Heidzelberg 2005.3594238241http://www2.iq.usp.br/bioquimica/(2004) Extensible Markup Language (XML) 1.0 (Third Edition), , http://www.w3.org/TR/2004/REC-xml-20040204Phrap, G.P., Phragment Assembly Program, , http://www.phrap.orghttp://www.lbi.ic.unicamp.brhttp://www.lbm.fcav.unesp.br/Setubal, J., Werneck, R., A program for building contig scaffolds in double-barreled shotgun genome sequencing (2001) Technical Report, IC-01-05. , Institute of Computing, Unicam

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

Genome features of Leptospira interrogans serovar Copenhageni

We report novel features of the genome sequence of Leptospira interrogans serovar Copenhageni, a highly invasive spirochete. Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in mammals. Genomic sequence analysis reveals the presence of a competent transport system with 13 families of genes encoding for major transporters including a three-member component efflux system compatible with the long-term survival of this organism. The leptospiral genome contains a broad array of genes encoding regulatory system, signal transduction and methyl-accepting chemotaxis proteins, reflecting the organism's ability to respond to diverse environmental stimuli. The identification of a complete set of genes encoding the enzymes for the cobalamin biosynthetic pathway and the novel coding genes related to lipopolysaccharide biosynthesis should bring new light to the study of Leptospira physiology. Genes related to toxins, lipoproteins and several surface-exposed proteins may facilitate a better understanding of the Leptospira pathogenesis and may serve as potential candidates for vaccine