A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves

AMB Express

Volumn 3, Issue , 2013, Pages 1-35

  Thompson, Claudia Elizabeth ^a,b   Beys da Silva, Walter Orlando ^b   Santi, Lucélia ^b   Berger, Markus ^b   Vainstein, Marilene Henning ^b   Guimarães, Jorge Almeida ^b   Vasconcelos, Ana Tereza Ribeiro ^a  

^a LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^b FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

Author keywords

Bacterial diversity; Biomass decomposition; Brazilian mangrove; Cellulase; Metagenomics

Indexed keywords

ALCOHOL DEHYDROGENASE; CARBOHYDRATE; CELLULASE; HYDROGEN DEHYDROGENASE; METHANE; METHANOL; NAPHTHALENE; UNSPECIFIC MONOOXYGENASE;

AGAR GEL ELECTROPHORESIS; ALGORITHM; ARTICLE; BIODIVERSITY; CLIMATE; DNA EXTRACTION; ENVIRONMENTAL FACTOR; MANGROVE; METAGENOMICS; MICROBIOME; MICROORGANISM; NITROGEN METABOLISM; NONHUMAN; PHYSICAL CHEMISTRY; POLYMERASE CHAIN REACTION; PROTEIN METABOLISM; PYROSEQUENCING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SUCROSE METABOLISM; TAXONOMY;

EID: 84887162848     PISSN: None     EISSN: 21910855     Source Type: Journal    
DOI: 10.1186/2191-0855-3-65     Document Type: Article

References (77)

1. Almeida LG, Paixão R, Souza RC, da Costa GC, Barrientos FJA, dos Santos MT, de Almeida D, Vasconcelos ATR (2004) A System for Automated Bacterial (genome) Integrated Annotation -SABIA. Bioinformatics 20:2832-2833
2. Alongi DM (2002) Present state and future of the world's mangrove forests. Environ Conserv 29:331-349
3. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST (1997) a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
4. Andreote FD, Jiménez DJ, Chaves D, Dias ACF, Luvizotto DM, Dini-Andreote Fasanella CC, Lopez MV, Baena S, Taketani RG, de Melo IS (2012) The microbiome of brazilian mangrove sediments as revealed by metagenomics. PLOS ONE 7:e38600
5. Angelov A, Loderer C, Pompei S, Liebl W (2011) Novel family of carbohydrate-binding modules revealed by the genome sequence of Spirochaeta thermophila DSM 6192. Appl Environ Microbiol 77(15):5483-5489
6. Arias AH, Vazquez-Botello A, Tombesi N, Ponce-Vélez G, Freije H, Marcovecchio J (2010) Presence, distribution, and origins of polycyclic aromatic hydrocarbons (PAHs) in sediments from Bahía Blanca estuary, Argentina. Environ Monit Assess 160:301-314
7. Bensmihen S, de Billy F, Gough C (2011) Contribution of NFP LysM domains to the recognition of Nod factors during the Medicago truncatula/Sinorhizobium meliloti symbiosis. PLOS ONE 6(11):e26114
8. Bernard D, Pascaline H, Jeremie JJ (1996) Distribution and origin of hydrocarbons in sediments from lagoons with fringing mangrove communities. Mar Pollut Bull 32:734-739
9. Brulc JM, Antonopoulos DA, Miller MEB, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA (2009) Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci U S A 106:1948-1953
10. Butchart SHM, Walpole M, Collen B, van Strien A, Scharlemann JPW, Almond REA, Baillie JEM, Bomhard B, Brown C, Bruno J, Carpenter KE, Carr GM, Chanson J, Chenery AM, Csirke J, Davidson NC, Dentener F, Foster M, Galli A, Galloway JN, Genovesi P, Gregory RD, Hockings M, Kapos V, Lamarque J-F, Leverington F, Loh J, McGeoch MA, McRae L, Minasyan A et al (2010) Global biodiversity: indicators of recent declines. Science 328:1164-1168
11. 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 37:233-238
12. Cha J, Matsuoka S, Chan H, Yukawa H, Inui M, Roy H (2007) Effect of multiple copies of cohesins on cellulase and hemicellulase activities of Clostridium cellulovorans mini-cellulosomes. J Microbiol Biotechnol 17(11):1782-1788
13. Challacombe JF, Eichorst SA, Hauser L, Land M, Xie G, Kuske CR (2011) Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076. PLOS ONE 6(9):e24882
14. Chou HH, Holmes MH (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104
15. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh TL, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:141-145
16. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503
17. Dias ACF, Andreote FD, Dini-Andreote F, Lacava PT, Sá ALB, Melo IS, Azevedo JL, Araújo WL (2009) Diversity and biotechnological potential of culturable bacteria from Brazilian mangrove sediment. World J Microb Biot 25(7):1305-1311
18. Dias ACF, Andreote FD, Rigonato J, Fiore MF, Melo IS, Araujo W (2010) The bacterial diversity in a Brazilian non-disturbed mangrove sediment. Antoine van Leeuwenhoek 98:541-551
19. Dittmar T, Hertkorn N, Kattner G, Lara RJ (2006) Mangroves, a major source of dissolved organic carbon to the oceans. Global Biogeochem Cy 20:GB1012-GB1019
20. Doi RH, Kosugi A (2004) Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat Rev Microbiol 2(7):541-551
21. Dourado MN, Ferreira A, Araújo WL, Azevedo JL, Lacava PT (2012) The diversity of endophytic methylotrophic bacteria in an oil-contaminated and an oil-free mangrove ecosystem and their tolerance to heavy metals. Biotechnol Res Int 2012:1-8
22. Duan CJ, Feng JX (2010) Mining metagenomes for novel cellulose genes. Biotechnol Lett 32:1765-1775
23. Duke NC, Meynecke JO, Dittmann S, Ellison AM, Anger K, Berger U, Cannici S, Diele K, Ewel KC, Field CD, Koedam N, Lee SY, Marchand C, Nordhaus I, Dahdouh-Guebas F (2007) A world without mangroves? Science 317:41-42
24. Faure D, Henrissat B, Ptacek D, Bekri MA, Vanderleyden J (2011) The celA gene, encoding a glycosyl hydrolase family 3 β-glucosidase in Azospirillum irakense is required for optimal growth on cellobiosides. Appl Environ Microbiol 67(5):2380-2383
25. Feller IC, Lovelock CE, Berger U, McKee KL, Joye SB, Ball MC (2010) Biocomplexity in mangrove ecosystems. Ann Rev Mar Sci 2:395-417
26. Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:29-37, M
27. Fontes CM, Gilbert HJ (2010) Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annu Rev Biochem 79:655-681
28. Gao Z, Ruan L, Chen X, Zhang Y, Xu X (2010) A novel salt-tolerant endo-β-1,4-glucanase Cel5A in Vibrio sp. G21 isolated from mangrove soil. Appl Microbiol Biotechnol 87:1373- 1382
29. Giri C, Ochieng E, Tieszen LL, Singh A, Loveland T, Masek J, Duke N (2011)) Status and distribution of mangrove forests of the world using earth observation satellite data. Global Ecol Biogeogr 20:154-159
30. Gomes NCM, Borges LR, Paranhos R, Pinto FN, Mendonça-Hagler LCS, Smalla K (2008) Exporing the diversity of bacterial communities in sediments of urban mangrove forests. FEMS Microbiol Ecology 2008(66):96-109
31. Gomez-Alvarez V, Teal TK, Schmidt TM (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J 3:1314-1317
32. Gonzales-Acosta B, Bashan Y, Hernandez-Saavedra NY, Ascencio F, De la Cruz-guero G (2006) Seasonal seawater temperature as the major determinant for populations of culturable bacteria in the sediments of an intact mangrove in an arid region. FEMS Microbiol Ecol 55:311-321
33. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:463-467
34. Holguin G, Vazquez P, Bashan Y (2001) The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol Fert Soils 33(4):265-278
35. Hooper DU, Chapin FS III, Ewel JJ, Hector A, Inchausti P, Lavorel S, Lawton JH, Lodge DM, Loreau M, Naeem S, Schmid B, Setälä H, Symstad AJ, Vandermeer J, Wardle DA (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75:3-35
36. Huang Y, Gilna P, Li W (2009) Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25:1338-1340
37. Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21:1552-1560
38. International Agency for Research on Cancer (IARC) (2002) Traditional Herbal Medicines, Some Mycotoxins, Naphthalene and Styrene. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, vol 82. IARC, Lyon, France
39. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109-D114
40. Koch EW, Barbier EB, Silliman BR, Reed DJ, Perillo GME, Hacker SD, Granek EF, Primavera JH, Muthiga N, Polasky S, Halpern BS, Kennedy CJ, Kappel CV, Wolanski E (2009) Nonlinearity in ecosystem services: temporal and spatial variability in coastal protection. Front Ecol Environ 7:29-37
41. Kumar R, Singht S, Singh OV (2008) Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol 35:377-391
42. Medie FM, Davies GJ, Drancourt M, Henrissat B (2012) Genome analyses highlight the different biological roles of cellulases. Nature Rev Microbiol 10:227-234
43. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386-394
44. Mitra S, Klar B, Huson DH (2009) Visual and statistical comparison of metagenomes. Bioinform 25:1849-1855
45. Ong JE (1993) Mangroves - a carbon source and sink. Chemosphere 27:1097-1107
46. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang H-Y, Cohoon M, 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, Mc-Hardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V et al (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33:5691-5702
47. Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26:715-721
48. Patthra P, Chon GH, Ratanakhanokchai K, Kyu KL, Jhee O-H, Juseop K, Kim WH, Kyung-Min C, Gil-Soon P, Jin-Sang L, Hyun P, Rho MS, Yun-Sik L (2006) Selection of multienzyme complex-producing bacteria under aerobic cultivation. J Microbiol Biotechnol 16:1269-1275
49. Peixoto R, Chaer GM, Carmo FL, Araújo FV, Paes JE, Volpon A, Santiago GA, Rosado AS 2011) Bacterial communities reflect the spatial variation in pollutant levels in Brazilian mangrove sediment. Antonie van Leeuwenhoek 99:341-354
50. Pointing SB, Buswell JA, Jones EBG, Vrijmoed LLP (1999) Extracellular cellulolytic enzyme profiles of five lignicolous mangrove fungi. Mycol Res 103:696-700
51. Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci U S A 107(33):14793-14798
52. 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 40:290-301
53. Raghukumar S, Sathe-Pathak V, Sharma S, Raghukumar C (1995) Thraustochytrid and fungal component of marine detritus. III. Field studies on decomposition of leaves of the mangrove Rhizophora apicula. Aquatic Microbial Ecology 9:117-125
54. Rho M, Tang H, Ye Y (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38:e121
55. Sahoo K, Dhal NK (2009) Potential microbial diversity in mangrove ecosystems: a review. Indian J Mar Sci 38:249-256
56. Santos H, Cury JC, Carmo FL, Santos AL, Tiedje J, van Elsas JD, Rosado AS, Peixoto RS (2011) Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLOS ONE 6:e16943
57. Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y (2003) Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53(Pt 6):1843-1851
58. Slutzki M, Ruimy V, Morag E, Barak Y, Haimovitz R, Lamed R, Bayer EA (2012) High-throughput screening of cohesin mutant libraries on cellulose microarrays. Methods Enzymol 510:453-463
59. Spalding MD, Blasco F, Field CD (eds) (1997) World mangrove atlas. The International Society for Mangrove Ecosystems, Okinawa, Japan
60. Spiers AG (1999) Review of international/continental wetland resources. Global review of wetland resources and priorities for wetland inventory. In: Finlayson CM, Spiers AG (eds) Supervising Scientist Report 144. Australian Government, Department of The Environment -Supervising Scientist Division, Canberra, Australia, pp 63-104
61. Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR (2010) An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet 6:e1001129
62. Sun FL, Wang YS, Sun CC, Peng YL, Deng C (2012) Effects of three different PAHs on nitrogen-fixing bacterial diversity in mangrove sediment. Ecotoxicol 21:1651-1660
63. Takagi M, Hashida S, Goldstein MA, Doi RH (1993) The hydrophobic repeated domain of the Clostridium cellulovorans cellulose-binding protein (CbpA) has specific interactions with endoglucanases. J Bacteriol 175:7119-7122
64. Taketani RG, Franco NO, Rosado AS, van Elsas JD (2010a) Microbial community response to a simulated hydrocarbon spill in mangrove sediments. J Microbiol 48(1):7-15
65. Taketani RG, Yoshiura CA, Dias ACF, Andreote FD, Tsai SM (2010b) Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove. Antonie van Leeuwenhoek 97(4):401-411
66. Teather RM, Wood PJ (1982) Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43(4):777-780
67. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308:554-557
68. Walters BB, Ronnback P, Knovacs JM, Crona B, Hussain SA, Badola R, Primavera JH, Barbier E, Dahdouh-Guebas F (2008) Ethobiology, socio-economics and management of mangrove forests: a review. Aquat Bot 89:220-236
69. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267
70. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernándes M, Murillo C, Acosta LG et al (2007) Metagenomic and functional analysis of hindgut micro-biota of a wood-feeding higher termite. Nature 450:560-565
71. Willner D, Thurber RV, Rohwer F (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol 11:1752-1766
72. Xu J (2011) Biomolecules produced by mangrove-associated microbes. Curr Med Chem 18:5224-5266
73. Yang ZY, Chen RZ, Yang F, Xu X (2001) Cloning and DNA sequencing of Bacillus pumilus endo-1, 4-β-glucanase gene. Wei Sheng Wu Xue Bao 41:76-81
74. Yun T, Yuan-rong L, Tian-ling Z, Li-xhe C, Xiao-xing C, Chong-ling Y (2008) Contamination and potential biodegradation of polycyclic aromatic hydrocarbons in mangrove sediments of Xiamen, China. Mar Pollut Bull 56:1184-1191
75. Zhou HW, Wong AHY, Yu RMK, Park YD, Wong YS, Tam NFY (2008) Polycyclic aromatic hydrocarbon-induced structural shift of bacterial communities in mangrove sediment. Microbiol Ecol 58:153-160
76. Zhu W, Lomsadze A, Borodovsky M (2010) Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38:e132
77. Zhu L, Wu Q, Dai J, Zhang S, Wei F (2011) Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci USA 108:17714-17719