Glycoside Hydrolases across Environmental Microbial Communities

PLoS Computational Biology

Volumn 12, Issue 12, 2016, Pages

  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

HYDROLASES; MICROORGANISMS; RANDOM PROCESSES; STOCHASTIC SYSTEMS; SUGARS;

BACTERIAL GENUS; COMMUNITY COMPOSITION; CRITICAL FUNCTIONS; ENZYMATIC PROCESSING; GLYCOSIDE HYDROLASES; METAGENOMES; METAGENOMICS; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY STRUCTURES; MICROBIAL COMPOSITION;

ECOSYSTEMS;

CELLULOSE; GLYCOSIDASE; OLIGOSACCHARIDE; POLYSACCHARIDE; STARCH; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; CARBOHYDRATE METABOLISM; COMMUNITY STRUCTURE; ECOSYSTEM; ENZYME SPECIFICITY; HUMAN; INTESTINE FLORA; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL DEGRADATION; NONHUMAN; SEQUENCE ANALYSIS; BACTERIUM; ENZYMOLOGY; GENETICS; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY;

BACTERIA; BACTERIAL PROTEINS; CARBOHYDRATE METABOLISM; ENVIRONMENTAL MICROBIOLOGY; GLYCOSIDE HYDROLASES; METAGENOMICS; MICROBIAL CONSORTIA; SUBSTRATE SPECIFICITY;

EID: 85007575525     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005300     Document Type: Article

References (64)

1. Lombard V, Bernard T, Rancurel C, Brumer H, Coutinho PM, Henrissat B, et al. A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J. Portland Press Limited; 2010;432: 437–44.
2. Berlemont R, Martiny AC, Genomic potential for polysaccharides deconstruction in bacteria. Appl Environ Microbiol. 2015;81: 1513–19. doi: 10.1128/AEM.03718-1425527556
3. Wilson DB, Microbial diversity of cellulose hydrolysis. Curr Opin Microbiol. Elsevier Ltd; 2011;14: 259–63.
4. Hemsworth GR, Henrissat B, Davies GJ, Walton PH, Discovery and characterization of a new family of lytic polysaccharide monooxygenases. Nat Chem Biol. 2014;10: 122–6. doi: 10.1038/nchembio.141724362702
5. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B, The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42: D490–5. doi: 10.1093/nar/gkt117824270786
6. Talamantes D, Biabini N, Dang H, Abdoun K, Berlemont R, Natural diversity of cellulases, xylanases, and chitinases in bacteria. Biotechnol Biofuels. BioMed Central; 2016;9: 133.
7. Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JBH, et al. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Front Microbiol. 2014;5: 639. doi: 10.3389/fmicb.2014.0063925505459
8. Medie FM, Davies GJ, Drancourt M, Henrissat B, Genome analyses highlight the different biological roles of cellulases. Nature Reviews Microbiology. 2012. pp. 227–234. doi: 10.1038/nrmicro272922266780
9. Berlemont R, Martiny AC, Phylogenetic distribution of potential cellulases in bacteria. Appl Environ Microbiol. 2013;79: 1545–54. doi: 10.1128/AEM.03305-1223263967
10. Martiny JBH, Jones SE, Lennon JT, Martiny AC, Microbiomes in light of traits: A phylogenetic perspective. Science (80-). 2015;350: aac9323–aac9323.
11. Delgado-Baquerizo M, Maestre FT, Reich PB, Trivedi P, Osanai Y, Liu Y-R, et al. Carbon content and climate variability drive global soil bacterial diversity patterns. Ecol Monogr. 2016;86: 373–390.
12. Souza RC, Cantão ME, Vasconcelos ATR, Nogueira MA, Hungria M, Soil metagenomics reveals differences under conventional and no-tillage with crop rotation or succession. Appl Soil Ecol. Elsevier B.V.; 2013;72: 49–61.
13. Fierer N, Leff JW, Adams BJ, Nielsen UN, Thomas S, Lauber CL, et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. 2012; 2–7.
14. Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford M a, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. Nature Publishing Group; 2012;6: 1007–17.
15. Baldrian P, Head IM, Prosser JI, Schloter M, Smalla K, Tebbe CC, Ecology and metagenomics of soil microorganisms. FEMS Microbiol Ecol. 2011;78: 1–2. doi: 10.1111/j.1574-6941.2011.01184.x22092139
16. Tringe SG, von Mering C, Kobayashi A, Salamov A a, Chen K, Chang HW, et al. Comparative metagenomics of microbial communities. Science. 2005;308: 554–7. doi: 10.1126/science.110785115845853
17. Vivanco L, Irvine IC, Martiny JBH, Nonlinear responses in salt marsh functioning to increased nitrogen addition. Ecology. 2015;96: 936–47. 26230015
18. Lomas MW, Bonachela JA, Levin SA, Martiny AC, Impact of ocean phytoplankton diversity on phosphate uptake. Proc Natl Acad Sci U S A. 2014;111: 17540–5. doi: 10.1073/pnas.142076011125422472
19. Allison SD, Lu Y, Weihe C, Goulden ML, Martiny AC, Treseder KK, et al. Microbial abundance and composition influence litter decomposition response to environmental change. Ecology. 2013;94: 714–25. 23687897
20. Boon E, Meehan CJ, Whidden C, Wong DH-J, Langille MGI, Beiko RG, Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev. 2014;38: 90–118. doi: 10.1111/1574-6976.1203523909933
21. Vranova V, Rejsek K, Formanek P, Aliphatic, cyclic, and aromatic organic acids, vitamins, and carbohydrates in soil: a review. ScientificWorldJournal. 2013;2013: 524239. doi: 10.1155/2013/52423924319374
22. Jouraiphy A, Amir S, El Gharous M, Revel J-C, Hafidi M, Chemical and spectroscopic analysis of organic matter transformation during composting of sewage sludge and green plant waste. Int Biodeterior Biodegradation. 2005;56: 101–108.
23. Leveau JH, Lindow SE, Appetite of an epiphyte: quantitative monitoring of bacterial sugar consumption in the phyllosphere. Proc Natl Acad Sci U S A. 2001;98: 3446–53. doi: 10.1073/pnas.06162959811248098
24. McCarthy M, Hedges J, Benner R, Major biochemical composition of dissolved high molecular weight organic matter in seawater. Mar Chem. 1996;55: 281–297.
25. Souza CP, Almeida BC, Colwell RR, Rivera ING, The importance of chitin in the marine environment. Mar Biotechnol (NY). 2011;13: 823–30.
26. Stuart RK, Mayali X, Lee JZ, Craig Everroad R, Hwang M, Bebout BM, et al. Cyanobacterial reuse of extracellular organic carbon in microbial mats. ISME J. International Society for Microbial Ecology; 2015;
27. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332: 970–4. doi: 10.1126/science.119871921596990
28. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.; 2014;505: 559–63.
29. Lozupone C a, Stombaugh JI, Gordon JI, Jansson JK, Knight R, Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489: 220–30. doi: 10.1038/nature1155022972295
30. Mathieu A, Delmont TO, Vogel TM, Robe P, Nalin R, Simonet P, Life on human surfaces: skin metagenomics. PLoS One. Public Library of Science; 2013;8: e65288.
31. Kamke J, Sczyrba A, Ivanova N, Schwientek P, Rinke C, Mavromatis K, et al. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J. International Society for Microbial Ecology; 2013;7: 2287–300.
32. Wilson W a, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, et al. Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiol Rev. 2010;34: 952–85. doi: 10.1111/j.1574-6976.2010.00220.x20412306
33. Henrissat B, Deleury E, Coutinho PM, Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria?Trends Genet. 2002;18: 437–40. 12175798
34. Khalikova E, Susi P, Korpela T, Microbial dextran-hydrolyzing enzymes: fundamentals and applications. Microbiol Mol Biol Rev. 2005;69: 306–25. doi: 10.1128/MMBR.69.2.306-325.200515944458
35. Wilke A, Bischof J, Harrison T, Brettin T, D’Souza M, Gerlach W, et al. A RESTful API for accessing microbial community data for MG-RAST. PLoS Comput Biol. 2015;11: e1004008. doi: 10.1371/journal.pcbi.100400825569221
36. Wilmes P, Bond PL, Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol. 2006;14: 92–7. doi: 10.1016/j.tim.2005.12.00616406790
37. Frank JA, Sørensen SJ, Quantitative metagenomic analyses based on average genome size normalization. Appl Environ Microbiol. 2011;77: 2513–2521. doi: 10.1128/AEM.02167-1021317268
38. Giovannoni SJ, Cameron Thrash J, Temperton B, Implications of streamlining theory for microbial ecology. ISME J. 2014;8: 1553–65. doi: 10.1038/ismej.2014.6024739623
39. Cantarel BL, Lombard V, Henrissat B, Complex carbohydrate utilization by the healthy human microbiome. PLoS One. 2012;7: e28742. doi: 10.1371/journal.pone.002874222719820
40. Burns JH, Anacker BL, Strauss SY, Burke DJ, Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus. AoB Plants. 2015;7: plv030-.
41. Pommier T, Douzery EJP, Mouillot D, Environment drives high phylogenetic turnover among oceanic bacterial communities. Biol Lett. 2012;8: 562–6. doi: 10.1098/rsbl.2011.099022258446
42. Folse HJ, Allison SD, Cooperation, competition, and coalitions in enzyme-producing microbes: social evolution and nutrient depolymerization rates. Front Microbiol. 2012;3: 338. doi: 10.3389/fmicb.2012.0033823060866
43. Griffiths BS, Philippot L, Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev. The Oxford University Press; 2013;37: 112–29.
44. Allison SD, Martiny JBH, Colloquium paper: resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci U S A. 2008;105Suppl: 11512–11519.
45. Ferrenberg S, Knelman JE, Jones JM, Beals SC, Bowman WD, Nemergut DR, Soil bacterial community structure remains stable over a 5-year chronosequence of insect-induced tree mortality. Front Microbiol. Frontiers; 2014;5: 681.
46. Nayfach S, Pollard KS, Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16: 51. doi: 10.1186/s13059-015-0611-725853934
47. Martens EC, Kelly AG, Tauzin AS, Brumer H, The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes. J Mol Biol. Elsevier Ltd; 2014;426: 3851–3865.
48. Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, et al. The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J. International Society for Microbial Ecology; 2015;
49. Brown K, DeCoffe D, Molcan E, Gibson DL, Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients. 2012;4: 1095–119. doi: 10.3390/nu408109523016134
50. Lebeer S, Vanderleyden J, De Keersmaecker SCJ, Genes and molecules of lactobacilli supporting probiotic action. Microbiol Mol Biol Rev. American Society for Microbiology (ASM); 2008;72: 728–64, Table of Contents.
51. Holland C, Mak TN, Zimny-Arndt U, Schmid M, Meyer TF, Jungblut PR, et al. Proteomic identification of secreted proteins of Propionibacterium acnes. BMC Microbiol. BioMed Central; 2010;10: 230.
52. Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T, Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci U S A. 2011;108: 14288–93. doi: 10.1073/pnas.110159110821825123
53. Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS, et al. Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. Proc Natl Acad Sci U S A. 2012;109: E1878–87. doi: 10.1073/pnas.120328710922699508
54. Delmont TO, Malandain C, Prestat E, Larose C, Monier J-M, Simonet P, et al. Metagenomic mining for microbiologists. ISME J. 2011;5: 1837–43. doi: 10.1038/ismej.2011.6121593798
55. Ferrenberg S, O’Neill SP, Knelman JE, Todd B, Duggan S, Bradley D, et al. Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J. Nature Publishing Group; 2013;7: 1102–1111.
56. Human-Microbiome-Project-ConsortiumStructure, function and diversity of the healthy human microbiome. Nature. 2012;486: 207–214. doi: 10.1038/nature1123422699609
57. Thomas F, Hehemann J-H, Rebuffet E, Czjzek M, Michel G, Environmental and gut bacteroidetes: the food connection. Front Microbiol. Frontiers Media SA; 2011;2: 93.
58. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, et al. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9: 386. doi: 10.1186/1471-2105-9-38618803844
59. Glass EM, Meyer F, The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. 2011. pp. 325–331.
60. Overbeek R, Begley T, Butler RM, Choudhuri J V, Chuang H-Y, Cohoon M, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33: 5691–702. doi: 10.1093/nar/gki86616214803
61. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42: D222–30. doi: 10.1093/nar/gkt122324288371
62. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, et al. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics. 2012;13: 141. doi: 10.1186/1471-2105-13-14122720753
63. Oksanen J, Blanchet FG, Kindt R, Legendre P, O’Hara RB, Simpson GL, et al. vegan: Community Ecology Package. R package version. 2012. p. R package version 2.0–4.
64. R Development Core TeamR: A language and environment for statistical computing. R Found Stat Comput Vienna, Austria. 2012;