Genomic potential for polysaccharide deconstruction in bacteria

Applied and Environmental Microbiology

Volumn 81, Issue 4, 2015, Pages 1513-1519

  Berlemont, Renaud ^a   Martiny, Adam C ^b  

^a CALIFORNIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIODEGRADATION; CELLULOSE; CHITIN; GENES; OLIGOSACCHARIDES; PLANTS (BOTANY); POLYSACCHARIDES; STARCH;

BACTERIAL GENOMES; BACTERIAL GROWTH; GLYCOSIDE HYDROLASES; MICROBIAL ASSEMBLAGE; MICROBIAL COMMUNITIES; PHYLOGENETIC DISTRIBUTION; STRUCTURAL POLYMERS; TAXONOMIC GROUPS;

HYDROLASES;

BACTERIUM; ENZYME ACTIVITY; GENOMICS; MICROBIAL COMMUNITY; PHYLOGENETICS; PHYLOGENY; POLYMER; POLYSACCHARIDE; TAXONOMY;

BACTERIA (MICROORGANISMS);

BACTERIAL PROTEIN; GLYCOSIDASE; POLYSACCHARIDE;

BACTERIUM; CLASSIFICATION; ENZYMOLOGY; GENETICS; GENOMICS; METABOLISM; PHYLOGENY;

BACTERIA; BACTERIAL PROTEINS; GENOMICS; GLYCOSIDE HYDROLASES; PHYLOGENY; POLYSACCHARIDES;

EID: 84922032029     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03718-14     Document Type: Article

References (50)

1. Thomas F, Hehemann J-H, Rebuffet E, Czjzek M, Michel G. 2011. Environmental and gut bacteroidetes: the food connection. Front Microbiol 2:93. http://dx.doi.org/10.3389/fmicb.2011.00093.
2. Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL. 2011. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:94. http://dx.doi.org/10.3389/fmicb.2011 .00094.
3. Johnson DR, Goldschmidt F, Lilja EE, Ackermann M. 2012. Metabolic specialization and the assembly of microbial communities. ISME J 6:1985-1991. http://dx.doi.org/10.1038/ismej.2012.46.
4. Haichar FEZ, Achouak W, Christen R, Heulin T, Marol C, Marais M-F, Mougel C, Ranjard L, Balesdent J, Berge O. 2007. Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 9:625-634. http://dx.doi.org/10.1111/j.1462-2920.2006.01182.x.
5. Wilson DB. 2011. Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol 14:259-263. http://dx.doi.org/10.1016/j.mib.2011.04.004.
6. Anderson I, Abt B, Lykidis A, Klenk HP, Kyrpides N, Ivanova N. 2012. Genomics of aerobic cellulose utilization systems in actinobacteria. PLoS One 7:e39331. http://dx.doi.org/10.1371/journal.pone.0039331.
7. Hou Bin P, Li YZ, Wu BH, Yan ZC, Yan BX, Gao PJ. 2006. Cellulolytic complex exists in cellulolytic myxobacterium Sorangium. Enzyme Microb Technol 38:273-278. http://dx.doi.org/10.1016/j.enzmictec.2004.08.044.
8. Berlemont R, Martiny AC. 2013. Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol 79:1545-1554. http://dx .doi.org/10.1128/AEM.03305-12.
9. Eichlerová I, Homolka L, Žifčáková L, Lisá L, Dobiášová P, Baldrian P. 2015. Enzymatic systems involved in decomposition reflects the ecology and taxonomy of saprotrophic fungi. Fungal Ecol 13:10-22. http://dx.doi .org/10.1016/j.funeco.2014.08.002.
10. Stursová M, Zifčáková L, Leigh MB, Burgess R, Baldrian P. 2012. Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers. FEMS Microbiol Ecol 80:735-746. http://dx.doi.org /10.1111/j.1574-6941.2012.01343.x.
11. Allison SD, Lu Y, Weihe C, Goulden ML, Martiny AC, Treseder KK, Martiny JBH. 2013. Microbial abundance and composition influence litter decomposition response to environmental change. Ecology 94:714- 725. http://dx.doi.org/10.1890/12-1243.1.
12. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490-D495. http://dx.doi.org/10.1093/nar/gkt1178.
13. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M. 2014. Pfam: the protein families database. Nucleic Acids Res 42:D222-D230. http://dx.doi.org/10.1093/nar/gkt1223.
14. DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE. 2008. Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 190:5455-5463. http://dx.doi.org/10.1128/JB.01701-07.
15. Trivedi P, Anderson IC, Singh BK. 2013. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol 21:641-651. http://dx.doi.org/10.1016/j .tim.2013.09.005.
16. Lynd LR, Weimer PJ, Van Zyl WH, Pretorius IS. 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66: 506-577. http://dx.doi.org/10.1128/MMBR.66.3.506-577.2002.
17. Zimmerman AE, Martiny AC, Allison SD. 2013. Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes. ISME J 7:1187-1199. http://dx.doi.org/10.1038/ismej.2012.176.
18. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233-D238. http://dx.doi.org/10.1093/nar/gkn663.
19. Cantarel BL, Lombard V, Henrissat B. 2012. Complex carbohydrate utilization by the healthy human microbiome. PLoS One 7:e28742. http: //dx.doi.org/10.1371/journal.pone.0028742.
20. Martiny AC, Treseder K, Pusch G. 2013. Phylogenetic conservatism of functional traits in microorganisms. ISME J 7:830-838. http://dx.doi.org /10.1038/ismej.2012.160.
21. Gillespie JJ, Wattam AR, Cammer SA, Gabbard JL, Shukla MP, Dalay O, Driscoll T, Hix D, Mane SP, Mao C, Nordberg EK, Scott M, Schulman JR, Snyder EE, Sullivan DE, Wang C, Warren A, Williams KP, Xue T, Yoo HS, Zhang C, Zhang Y, Will R, Kenyon RW, Sobral BW. 2011. PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect Immun 79:4286-4298. http://dx.doi.org/10.1128/IAI.00207-11.
22. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA. 2010. Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11:319. http: //dx.doi.org/10.1186/1471-2105-11-319.
23. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702. http://dx.doi.org/10.1093/nar/gki866.
24. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Res 40:D290-D301. http://dx.doi.org/10.1093 /nar/gkr1065.
25. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195. http://dx.doi.org/10.1371/journal.pcbi.1002195.
26. Chen W, Xie T, Shao Y, Chen F. 2012. Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi. PLoS One 7:e49679. http://dx.doi.org/10.1371/journal.pone.0049679.
27. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-D596. http://dx.doi.org/10.1093/nar/gks1219.
28. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973. http://dx.doi.org/10.1093/bioinformatics/btp348.
29. Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5:164-166.
30. Fritz SA, Purvis A. 2010. Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits. Conserv Biol 24:1042-1051. http://dx.doi.org/10.1111/j.1523-1739.2010 .01455.x.
31. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. 2012. vegan: Community Ecology Package. R Package version 2.0-8. http://vegan.r-forge.r-project.org/.
32. R Development Core Team. 2012. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
33. Baldrian P, López-Mondéjar R. 2014. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 98:1531-1537. http: //dx.doi.org/10.1007/s00253-013-5457-x.
34. Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JBH, Martiny AC, Brodie EL. 2013. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front Microbiol 4:282. http://dx.doi.org/10.3389/fmicb.2013.00282.
35. Woo HL, Hazen TC, Simmons BA, DeAngelis KM. 2014. Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol 37:60-67. http://dx.doi.org/10.1016/j .syapm.2013.10.001.
36. Whitaker J, Ostle N, Nottingham AT, Ccahuana A, Salinas N, Bardgett RD, Meir P, McNamara NP. 2014. Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient. J Ecol 102:1058-1071. http://dx .doi.org/10.1111/1365-2745.12247.
37. Henrissat B, Deleury E, Coutinho PM. 2002. Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria? Trends Genet 18: 437-440. http://dx.doi.org/10.1016/S0168-9525(02)02734-8.
38. Beier S, Bertilsson S. 2013. Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol 4:149. http://dx.doi.org /10.3389/fmicb.2013.00149.
39. Wilmes P, Bond PL. 2006. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14:92-97. http://dx .doi.org/10.1016/j.tim.2005.12.006.
40. Davies GJ, Gloster TM, Henrissat B. 2005. Recent structural insights into the expanding world of carbohydrate-active enzymes. Curr Opin Struct Biol 15:637-645. http://dx.doi.org/10.1016/j.sbi.2005.10.008.
41. Goh YJ, Klaenhammer TR. 2013. A functional glycogen biosynthesis pathway in Lactobacillus acidophilus: expression and analysis of the glg operon. Mol Microbiol 89:1187-1200. http://dx.doi.org/10.1111/mmi.12338.
42. Keyhani NO, Roseman S. 1999. Physiological aspects of chitin catabolism in marine bacteria. Biochim Biophys Acta 1473:108-122. http://dx.doi .org/10.1016/S0304-4165(99)00172-5.
43. Vaaje-Kolstad G, Horn SJ, Sørlie M, Eijsink VGH. 2013. The chitinolytic machinery of Serratia marcescens-a model system for enzymatic degradation of recalcitrant polysaccharides. FEBS J 280:3028-3049. http://dx .doi.org/10.1111/febs.12181.
44. Hjort K, Bergström M, Adesina MF, Jansson JK, Smalla K, Sjöling S. 2010. Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil. FEMS Microbiol Ecol 71:197-207. http://dx.doi.org/10.1111/j.1574 -6941.2009.00801.x.
45. Souza CP, Almeida BC, Colwell RR, Rivera ING. 2011. The importance of chitin in the marine environment. Mar Biotechnol (NY) 13:823-830. http://dx.doi.org/10.1007/s10126-011-9388-1.
46. Larsen MH, Leisner JJ, Ingmer H. 2010. The chitinolytic activity of Listeria monocytogenes EGD is regulated by carbohydrates but also by the virulence regulator PrfA. Appl Environ Microbiol 76:6470-6476. http: //dx.doi.org/10.1128/AEM.00297-10.
47. De Boer W, Leveau JHJ, Kowalchuk GA, Klein Gunnewiek PJA, Abeln ECA, Figge MJ, Sjollema K, Janse JD, van Veen JA. 2004. Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. Int J Syst Evol Microbiol 54:857-864. http://dx.doi.org/10.1099/ijs.0.02920-0.
48. Gefen G, Anbar M, Morag E, Lamed R, Bayer EA. 2012. Enhanced cellulose degradation by targeted integration of a cohesin-fused β-glucosidase into the Clostridium thermocellum cellulosome. Proc Natl Acad Sci U S A 109:10298-10303. http://dx.doi.org/10.1073/pnas.1202747109.
49. Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JBH, Martiny AC. 2014. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Aquat Microbiol 5:639. http: //dx.doi.org/10.3389/fmicb.2014.00639.
50. Allison SD. 2012. A trait-based approach for modelling microbial litter decomposition. Ecol Lett 15:1058-1070. http://dx.doi.org/10.1111/j.1461 -0248.2012.01807.x.