1932

Abstract

The ancient phylum is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.

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2016-09-08
2024-04-19
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Literature Cited

  1. Adams AS, Jordan MS, Adams SM, Suen G, Goodwin LA. 1.  et al. 2011. Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio. ISME J. 5:81323–31 [Google Scholar]
  2. Ahmed A, Earl J, Retchless A, Hillier SL, Rabe LK. 2.  et al. 2012. Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J. Bacteriol. 194:153922–37 [Google Scholar]
  3. Andam CP, Doroghazi JR, Campbell AN, Kelly PJ, Choudoir MJ, Buckley DH. 2.  2016. A latitudinal diversity gradient in terrestrial bacteria of the genus Streptomyces. mBio 7:2e02200–15 [Google Scholar]
  4. Atabani AE, Silitonga AS, Badruddin IA, Mahlia TMI, Masjuki HH, Mekhilef S. 3.  2012. A comprehensive review on biodiesel as an alternative energy resource and its characteristics. Renew. Sustain. Energy Rev. 16:2070–93 [Google Scholar]
  5. Atsumi S, Hanai T, Liao JC. 4.  2008. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86–89 [Google Scholar]
  6. Barabas G, Vargha G, Szabo IM, Penyige A, Damjanovich S. 5.  et al. 2001. n-Alkane uptake and utilisation by Streptomyces strains. Antonie Van Leeuwenhoek 79:269–76 [Google Scholar]
  7. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C. 6.  et al. 2016. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol. Mol. Biol. Rev. 80:11–43 [Google Scholar]
  8. Barr BK, Hsieh YL, Ganem B, Wilson DB. 7.  1996. Identification of two functionally different classes of exocellulases. Biochemistry 35:2586–92 [Google Scholar]
  9. Battistuzzi FU, Feijao A, Hedges SB. 8.  2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4:44 [Google Scholar]
  10. Beier S, Bertilsson S. 9.  2011. Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton. Limnol. Oceanogr. 56:41179–88 [Google Scholar]
  11. Bell KS, Philp JC, Aw DWJ, Christofi N. 10.  1998. A review: the genus Rhodococcus. J. Appl. Microbiol. 85:195–210 [Google Scholar]
  12. Beller HR, Lee TS, Katz L. 11.  2015. Natural products as biofuels and bio-based chemicals: fatty acids and isoprenoids. Nat. Prod. Rep. 32:1508–26 [Google Scholar]
  13. Berenbaum MR, Eisner T. 12.  2008. Bugs' bugs. Science 322:52–53 [Google Scholar]
  14. Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL. 13.  et al. 2014. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Front. Microbiol. 5:639 [Google Scholar]
  15. Berlemont R, Martiny AC. 14.  2013. Phylogenetic distribution of potential cellulases in bacteria. Appl. Environ. Microbiol. 79:51545–54 [Google Scholar]
  16. Blombach B, Riester T, Wieschalka S, Ziert C, Youn J-W. 15.  et al. 2011. Corynebacterium glutamicum tailored for efficient isobutanol production. Appl. Environ. Microbiol. 77:103300–10 [Google Scholar]
  17. Bontemps C, Toussaint M, Revol P-V, Hotel L, Jeanbille M. 16.  et al. 2013. Taxonomic and functional diversity of Streptomyces in a forest soil. FEMS Microbiol. Lett. 342:2157–67 [Google Scholar]
  18. Book AJ, Lewin GR, McDonald BR, Takasuka TE, Doering DT. 17.  et al. 2014. Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically linked capacity to degrade lignocellulose. Appl. Environ. Microbiol. 80:154692–701 [Google Scholar]
  19. Book AJ, Lewin GR, McDonald BR, Takasuka TE, Wendt-Pienkowski E. 18.  et al. 2016. Evolution of high cellulolytic activity in symbiotic Streptomyces through selection of expanded gene content and coordinated gene expression. PLOS Biol. 146e1002475
  20. Book AJ, Yennamalli RM, Takasuka TE, Currie CR, Phillips GN Jr, Fox BG. 19.  2014. Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases. Biotechnol. Biofuels 7:109 [Google Scholar]
  21. Brecher G, Wigglesworth VB. 20.  1944. The transmission of Actinomyces rhodnii Erikson in Rhodnius prolixus stål (Hemiptera) and its influence on the growth of the host. Parasitology 35:04220–24 [Google Scholar]
  22. Brumbley SM, Petrasovits LA, Hermann SR, Young AJ, Croft BJ. 21.  2006. Recent advances in the molecular biology of Leifsonia xyli subsp. xyli, causal organism of ratoon stunting disease. Australas. Plant Pathol. 35:6681–89 [Google Scholar]
  23. Cafaro MJ, Currie CR. 22.  2005. Phylogenetic analysis of mutualistic filamentous bacteria associated with fungus-growing ants. Can. J. Microbiol. 51:6441–46 [Google Scholar]
  24. Cafaro MJ, Poulsen M, Little AEF, Price SL, Gerardo NM. 23.  et al. 2011. Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria. Proc. R. Soc. B 278:1814–22 [Google Scholar]
  25. Caldera EJ, Currie CR. 24.  2012. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis. Am. Nat. 180:5604–17 [Google Scholar]
  26. Caspeta L, Nielsen J. 25.  2013. Economic and environmental impacts of microbial biodiesel. Nat. Biotechnol. 31:9789–93 [Google Scholar]
  27. Chandra G, Chater KF. 26.  2014. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol. Rev. 38:345–79 [Google Scholar]
  28. Choi YJ, Lee J, Jang Y-S, Lee SY. 27.  2014. Metabolic engineering of microorganisms for the production of higher alcohols. mBio 5:5e01524–14 [Google Scholar]
  29. Christopherson MR, Suen G, Bramhacharya S, Jewell KA, Aylward FO. 28.  et al. 2013. The genome sequences of Cellulomonas fimi and “Cellvibrio gilvus” reveal the cellulolytic strategies of two facultative anaerobes, transfer of “Cellvibrio gilvus” to the genus Cellulomonas, and proposal of Cellulomonas gilvus sp. nov. PLOS ONE 8:1e53954 [Google Scholar]
  30. Chu S, Majumdar A. 29.  2012. Opportunities and challenges for a sustainable energy future. Nature 488:294–303 [Google Scholar]
  31. Clawson ML, Bourret A, Benson DR. 30.  2004. Assessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences. Mol. Phylogenet. Evol. 31:131–38 [Google Scholar]
  32. Colman DR, Toolson EC, Takacs-Vesbach CD. 31.  2012. Do diet and taxonomy influence insect gut bacterial communities?. Mol. Ecol. 21:5124–37 [Google Scholar]
  33. Conn VM, Walker AR, Franco CM. 32.  2008. Endophytic Actinobacteria induce defense pathways in Arabidopsis thaliana. Mol. Plant-Microbe Interact. 21:2208–18 [Google Scholar]
  34. Coombs JT, Michelsen PP, Franco CMM. 33.  2004. Evaluation of endophytic Actinobacteria as antagonists of Gaeumannomyces graminis var. tritici in wheat. Biol. Control 29:3359–66 [Google Scholar]
  35. Crawford DL. 34.  1978. Lignocellulose decomposition by selected Streptomyces strains. Appl. Environ. Microbiol. 35:61041–45 [Google Scholar]
  36. Cross T. 35.  1981. Aquatic actinomycetes: a critical survey of the occurrence, growth and role of actinomycetes in aquatic habitats. J. Appl. Bacteriol. 50:3397–423 [Google Scholar]
  37. Currie CR, Mueller UG, Malloch D. 36.  1999. The agricultural pathology of ant fungus gardens. PNAS 96:147998–8002 [Google Scholar]
  38. Currie CR, Poulsen M, Mendenhall J, Boomsma JJ, Billen J. 37.  2006. Coevolved crypts and exocrine glands support mutualistic bacteria in fungus-growing ants. Science 311:575781–83 [Google Scholar]
  39. Currie CR, Scott JA, Summerbell RC, Malloch D. 38.  1999. Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature 398:701–4 [Google Scholar]
  40. d'Espaux L, Mendez-Perez D, Li R, Keasling JD. 39.  2015. Synthetic biology for microbial production of lipid-based biofuels. Curr. Opin. Chem. Biol. 29:58–65 [Google Scholar]
  41. Dale BE, Ong RG. 40.  2012. Energy, wealth, and human development: Why and how biomass pretreatment research must improve. Biotechnol. Prog. 28:4893–98 [Google Scholar]
  42. de Boer W, Folman LB, Summerbell RC, Boddy L. 41.  2005. Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol. Rev. 29:795–811 [Google Scholar]
  43. Demain AL. 42.  2007. The business of biotechnology. Ind. Biotechnol. 3:3269–83 [Google Scholar]
  44. Deng Y, Fisher AB, Fong SS. 43.  2015. Systematic analysis of intracellular mechanisms of propanol production in the engineered Thermobifida fusca B6 strain. Appl. Microbiol. Biotechnol. 99:198089–8100 [Google Scholar]
  45. Deng Y, Fong SS. 44.  2011. Metabolic engineering of Thermobifida fusca for direct aerobic bioconversion of untreated lignocellulosic biomass to 1-propanol. Metab. Eng. 13:570–77 [Google Scholar]
  46. Ding CH, Jiang ZQ, Li XT, Li LT, Kusakabe I. 45.  2004. High activity xylanase production by Streptomyces olivaceoviridis E-86. World J. Microbiol. Biotechnol. 20:7–10 [Google Scholar]
  47. Doroghazi JR, Metcalf WW. 45a.  2013. Comparative genomics of actinomycetes with a focus on natural product biosynthesis genes. BMC Genomics 14:611 [Google Scholar]
  48. Eckert EM, Baumgartner M, Huber IM, Pernthaler J. 46.  2013. Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon. Environ. Microbiol. 15:72019–30 [Google Scholar]
  49. Eichenlaub R, Gartemann K-H. 47.  2011. The Clavibacter michiganensis subspecies: molecular investigation of gram-positive bacterial plant pathogens. Annu. Rev. Phytopathol. 49:445–64 [Google Scholar]
  50. Erikson D. 48.  1941. Some studies on lake-mud strains of Micromonospora. J. Bacteriol. 41:3277–300 [Google Scholar]
  51. Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. 49.  2015. Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms. Nat. Prod. Rep. 32:904–36 [Google Scholar]
  52. Franco C, Michelsen P, Percy N, Conn V, Listiana E. 50.  et al. 2007. Actinobacterial endophytes for improved crop performance. Australas. Plant Pathol. 36:524–31 [Google Scholar]
  53. Fulton LM, Lynd LR, Korner A, Greene N, Tonachel LR. 51.  2015. The need for biofuels as part of a low carbon energy future. Biofuels Bioprod. Biorefining 9:476–83 [Google Scholar]
  54. Gao B, Gupta RS. 52.  2012. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol. Mol. Biol. Rev. 76:166–112 [Google Scholar]
  55. Gelfand I, Snapp SS, Robertson GP. 53.  2010. Energy efficiency of conventional, organic, and alternative cropping systems at a site in the U.S. Midwest. Environ. Sci. Technol. 44:104006–11 [Google Scholar]
  56. Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S. 54.  et al. 2014. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J. 8:841–53 [Google Scholar]
  57. Harris PV, Xu F, Kreel NE, Kang C, Fukuyama S. 55.  2014. New enzyme insights drive advances in commercial ethanol production. Curr. Opin. Chem. Biol. 19:162–70 [Google Scholar]
  58. Herrmann RF, Shann JF. 56.  1997. Microbial community changes during the composting of municipal solid waste. Microb. Ecol. 33:78–85 [Google Scholar]
  59. Hirsch AM, Valdés M. 57.  2010. Micromonospora: an important microbe for biomedicine and potentially for biocontrol and biofuels. Soil Biol. Biochem. 42:536–42 [Google Scholar]
  60. Hopwood DA. 58.  2007. Streptomyces in Nature and Medicine: The Antibiotic Makers. New York: Oxford Univ. Press [Google Scholar]
  61. Hsing W, Canale-Parola E. 59.  1992. Cellobiose chemotaxis by the cellulolytic bacterium Cellulomonas gelida. J. Bacteriol. 174:247996–8002 [Google Scholar]
  62. 60. Int. Energy Agency 2015. 2015 Key World Energy Statistics. Paris: Int. Energy Agency
  63. Ishaque M, Kluepfel D. 61.  1981. Production of xylanolytic enzymes by Streptomyces flavogriseus. Biotechnol. Lett. 3:9481–86 [Google Scholar]
  64. Janssen PH. 62.  2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:31719–28 [Google Scholar]
  65. Johansen KS. 63.  2016. Discovery and industrial applications of lytic polysaccharide mono-oxygenases. Biochem. Soc. Trans. 44:143–49 [Google Scholar]
  66. Jones RT, Sanchez LG, Fierer N. 64.  2013. A cross-taxon analysis of insect-associated bacterial diversity. PLOS ONE 8:4e61218 [Google Scholar]
  67. Kaltenpoth M. 65.  2009. Actinobacteria as mutualists: general healthcare for insects?. Trends Microbiol. 17:12529–35 [Google Scholar]
  68. Kaltenpoth M, Gottler W, Herzner G, Strohm E. 66.  2005. Symbiotic bacteria protect wasp larvae from fungal infestation. Curr. Biol. 15:475–79 [Google Scholar]
  69. Katoh K, Standley DM. 67.  2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30:4772–80 [Google Scholar]
  70. Kawase T, Saito A, Sato T, Kanai R, Fujii T. 68.  et al. 2004. Distribution and phylogenetic analysis of family 19 chitinases in Actinobacteria. Appl. Environ. Microbiol. 70:21135–44 [Google Scholar]
  71. Kers JA, Cameron KD, Joshi MV, Bukhalid RA, Morello JE. 69.  et al. 2005. A large, mobile pathogenicity island confers plant pathogenicity on Streptomyces species. Mol. Microbiol. 55:41025–33 [Google Scholar]
  72. Kim M, Kim W-S, Tripathi BM, Adams J. 70.  2014. Distinct bacterial communities dominate tropical and temperate zone leaf litter. Microb. Ecol. 67:4837–48 [Google Scholar]
  73. Klaus M, Ostrowski MP, Austerjost J, Robbins T, Lowry B. 71.  et al. 2016. Protein–protein interactions, not substrate recognition, dominates the turnover of chimeric assembly line polyketide synthases. J. Biol. Chem. In press. doi: 10.1074/jbc.M116.730531
  74. Kroiss J, Kaltenpoth M, Schneider B, Schwinger M-G, Hertweck C. 72.  et al. 2010. Symbiotic streptomycetes provide antibiotic combination prophylaxis for wasp offspring. Nat. Chem. Biol. 6:4261–63 [Google Scholar]
  75. Kung Y, Runguphan W, Keasling JD. 73.  2012. From fields to fuels: recent advances in the microbial production of biofuels. ACS Synth. Biol. 1:498–513 [Google Scholar]
  76. Kurosawa K, Boccazzi P, de Almeida NM, Sinskey AJ. 74.  2010. High-cell-density batch fermentation of Rhodococcus opacus PD630 using a high glucose concentration for triacylglycerol production. J. Biotechnol. 147:212–18 [Google Scholar]
  77. Kurosawa K, Laser J, Sinskey AJ. 75.  2015. Tolerance and adaptive evolution of triacylglycerol-producing Rhodococcus opacus to lignocellulose-derived inhibitors. Biotechnol. Biofuels 8:76 [Google Scholar]
  78. Kurosawa K, Wewetzer SJ, Sinskey AJ. 76.  2013. Engineering xylose metabolism in triacylglycerol-producing Rhodococcus opacus for lignocellulosic fuel production. Biotechnol. Biofuels 6:134 [Google Scholar]
  79. Lauber CL, Hamady M, Knight R, Fierer N. 77.  2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75:155111–20 [Google Scholar]
  80. Lawrence DB, Schoenike RE, Quispel A, Bond G. 78.  1967. The role of Dryas drummondii in vegetation development following ice recession at Glacier Bay, Alaska, with special reference to its nitrogen fixation by root nodules. J. Ecol. 55:3793–813 [Google Scholar]
  81. Liu J, Rice A, Mcglew K, Shaw V, Park H. 79.  et al. 2015. Metabolic engineering of oilseed crops to produce high levels of novel acetyl glyceride oils with reduced viscosity, freezing point and calorific value. Plant Biotechnol. J. 13:858–65 [Google Scholar]
  82. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 80.  2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42:1D490–95 [Google Scholar]
  83. Loqman S, Barka EA, Clément C, Ouhdouch Y. 81.  2009. Antagonistic actinomycetes from Moroccan soil to control the grapevine gray mold. World J. Microbiol. Biotechnol. 25:81–91 [Google Scholar]
  84. Loria R, Kers J, Joshi M. 82.  2006. Evolution of plant pathogenicity in Streptomyces. Annu. Rev. Phytopathol. 44:469–87 [Google Scholar]
  85. Lu Y, Wang J, Deng Z, Wu H, Deng Q. 83.  et al. 2013. Isolation and characterization of fatty acid methyl ester (FAME)-producing Streptomyces sp. S161 from sheep (Ovis aries) faeces. Lett. Appl. Microbiol. 57:200–5 [Google Scholar]
  86. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J. 84.  et al. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90 [Google Scholar]
  87. Margesin R, Mörtelmaier C, Mair J. 85.  2013. Low-temperature biodegradation of petroleum hydrocarbons (n-alkanes, phenol, anthracene, pyrene) by four actinobacterial strains. Int. Biodeterior. Biodegrad. 84:185–91 [Google Scholar]
  88. Marin ML, Lee JH, Murtha J, Ustunol Z, Pestka JJ. 86.  1997. Differential cytokine production in clonal macrophage and T-cell lines cultured with Bifidobacteria. J. Dairy Sci. 80:112713–20 [Google Scholar]
  89. Marsh SE, Poulsen M, Pinto-Tomás A, Currie CR. 87.  2014. Interaction between workers during a short time window is required for bacterial symbiont transmission in Acromyrmex leaf-cutting ants. PLOS ONE 9:7e103269 [Google Scholar]
  90. Marushima K, Ohnishi Y, Horinouchi S. 88.  2009. CebR as a master regulator for cellulose/cellooligosaccharide catabolism affects morphological development in Streptomyces griseus. J. Bacteriol. 191:195930–40 [Google Scholar]
  91. Matulich KL, Weihe C, Allison SD, Amend AS, Berlemont R. 89.  et al. 2015. Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME J. 9:112477–89 [Google Scholar]
  92. McCarthy AJ. 90.  1987. Lignocellulose-degrading actinomycetes. FEMS Microbiol. Rev. 46:145–63 [Google Scholar]
  93. McCarthy AJ, Williams ST. 91.  1992. Actinomycetes as agents of biodegradation in the environment—a review. Gene 115:189–92 [Google Scholar]
  94. Metcalfe AC, Krsek M, Gooday GW, Prosser JI, Wellington EMH. 92.  2002. Molecular analysis of a bacterial chitinolytic community in an upland pasture. Appl. Environ. Microbiol. 68:105042–50 [Google Scholar]
  95. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM. 93.  et al. 2008. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386 [Google Scholar]
  96. Milani C, Turroni F, Duranti S, Lugli GA, Mancabelli L. 94.  et al. 2016. Genomics of the genus Bifidobacterium reveals species-specific adaptation to the glycan-rich gut environment. Appl. Environ. Microbiol. 82:4980–91 [Google Scholar]
  97. Noda S, Kawai Y, Tanaka T, Kondo A. 95.  2015. 4-Vinylphenol biosynthesis from cellulose as the sole carbon source using phenolic acid decarboxylase- and tyrosine ammonia lyase-expressing Streptomyces lividans. Bioresour. Technol. 180:59–65 [Google Scholar]
  98. Noda S, Kitazono E, Tanaka T, Ogino C, Kondo A. 96.  2012. Benzoic acid fermentation from starch and cellulose via a plant-like β-oxidation pathway in Streptomyces maritimus. Microb. Cell Fact. 11:49 [Google Scholar]
  99. Oh D-C, Poulsen M, Currie CR, Clardy J. 97.  2009. Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis. Nat. Chem. Biol. 5:6391–93 [Google Scholar]
  100. Pasti MB, Pometto AL III, Nuti MP, Crawford DL. 98.  1990. Lignin-solubilizing ability of actinomycetes isolated from termite (Termitidae) gut. Appl. Environ. Microbiol. 56:72213–18 [Google Scholar]
  101. Pauly M, Keegstra K. 99.  2008. Cell-wall carbohydrates and their modification as a resource for biofuels. Plant J. 54:559–68 [Google Scholar]
  102. Paye JMD, Guseva A, Hammer SK, Gjersing E, Davis MF. 100.  et al. 2016. Biological lignocellulose solubilization: comparative evaluation of biocatalysts and enhancement via cotreatment. Biotechnol. Biofuels 9:8 [Google Scholar]
  103. Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME. 101.  et al. 2015. Fungal cellulases. Chem. Rev. 115:1308–448 [Google Scholar]
  104. Peralta-Yahya PP, Zhang F. Cardayre SB, Keasling JD. 102. , del 2012. Microbial engineering for the production of advanced biofuels. Nature 488:7411320–28 [Google Scholar]
  105. Phelan RM, Sekurova ON, Keasling JD, Zotchev SB. 103.  2014. Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene. ACS Synth. Biol. 4:393–99 [Google Scholar]
  106. Phillips CM, Beeson WT IV, Cate JH, Marletta MA. 104.  2011. Cellobiose dehydrogenase and a copper-dependent polysaccharide monooxygenase potentiate cellulose degradation by Neurospora crassa. ACS Chem. Biol. 6:1399–406 [Google Scholar]
  107. Pokusaeva K, Fitzgerald GF, van Sinderen D. 105.  2011. Carbohydrate metabolism in Bifidobacteria. Genes Nutr. 6:285–306 [Google Scholar]
  108. Poulsen M, Oh D-C, Clardy J, Currie CR. 106.  2011. Chemical analyses of wasp-associated Streptomyces bacteria reveal a prolific potential for natural products discovery. PLOS ONE 6:2e16763 [Google Scholar]
  109. Ransom C, Balan V, Biswas G, Dale B, Crockett E, Sticklen M. 107.  2007. Heterologous Acidothermus cellulolyticus 1,4-β-endoglucanase E1 produced within the corn biomass converts corn stover into glucose. Appl. Biochem. Biotechnol. 136–140:207–19 [Google Scholar]
  110. Razeghifard R. 108.  2013. Algal biofuels. Photosynth. Res. 117:207–19 [Google Scholar]
  111. Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B, Neyrolles O. 109.  2006. Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis. Mol. Biol. Evol. 23:61129–35 [Google Scholar]
  112. Salem H, Bauer E, Strauss AS, Vogel H, Marz M, Kaltenpoth M. 110.  2014. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. Proc. R. Soc. B 281:20141838 [Google Scholar]
  113. Saviola B, Bishai W. 111.  2006. The genus Mycobacterium—medical. The Prokaryotes 3 M Dworkin, S Falkow, E Rosenberg, K-H Schleifer, E Stackebrandt 919–33 New York: Springer, 3rd ed.. [Google Scholar]
  114. Schlosser A, Jantos J, Hackmann K, Schrempf H. 112.  1999. Characterization of the binding protein-dependent cellobiose and cellotriose transport system of the cellulose degrader Streptomyces reticuli. Appl. Environ. Microbiol. 65:62636–43 [Google Scholar]
  115. Schlosser A, Kampers T, Schrempf H. 113.  1997. The Streptomyces ATP-binding component MsiK assists in cellobiose and maltose transport. J. Bacteriol. 179:62092–95 [Google Scholar]
  116. Schrempf H, Walter S. 114.  1995. The cellulolytic system of Streptomyces reticuli. Int. J. Biol. Macromol. 17:6353–55 [Google Scholar]
  117. Schrey SD, Erkenbrack E, Früh E, Fengler S, Hommel K. 115.  et al. 2012. Production of fungal and bacterial growth modulating secondary metabolites is widespread among mycorrhiza-associated streptomycetes. BMC Microbiol. 12:164 [Google Scholar]
  118. Scott JJ, Budsberg KJ, Suen G, Wixon DL, Balser TC, Currie CR. 116.  2010. Microbial community structure of leaf-cutter ant fungus gardens and refuse dumps. PLOS ONE 5:3e9922 [Google Scholar]
  119. Scott JJ, Oh DC, Yuceer MC, Klepzig KD, Clardy J, Currie CR. 117.  2008. Bacterial protection of beetle-fungus mutualism. Science 322:63 [Google Scholar]
  120. Seeds JD, Bishop JG. 118.  2009. Low Frankia inoculation potentials in primary successional sites at Mount St. Helens, Washington, USA. Plant Soil 323:225–33 [Google Scholar]
  121. Seipke RF, Kaltenpoth M, Hutchings MI. 119.  2012. Streptomyces as symbionts: an emerging and widespread theme?. FEMS Microbiol. Rev. 36:862–76 [Google Scholar]
  122. Semedo LTAS, Gomes RC, Linhares AA, Duarte GF, Nascimento RP. 120.  et al. 2004. Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil. Int. J. Syst. Evol. Microbiol. 54:1323–28 [Google Scholar]
  123. Servin AL. 121.  2004. Antagonistic activities of lactobacilli and Bifidobacteria against microbial pathogens. FEMS Microbiol. Rev. 28:405–40 [Google Scholar]
  124. Smanski MJ, Schlatter DC, Kinkel LL. 122.  2015. Leveraging ecological theory to guide natural product discovery. J. Ind. Microbiol. Biotechnol. 43:115–28 [Google Scholar]
  125. Smith KM, Cho K-M, Liao JC. 123.  2010. Engineering Corynebacterium glutamicum for isobutanol production. Appl. Microbiol. Biotechnol. 87:1045–55 [Google Scholar]
  126. Stamatakis A. 124.  2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:91312–13 [Google Scholar]
  127. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A. 125.  et al. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559–62 [Google Scholar]
  128. Steffan SA, Chikaraishi Y, Currie CR, Horn H, Gaines-Day HR. 126.  et al. 2015. Microbes are trophic analogs of animals. PNAS 112:4915119–24 [Google Scholar]
  129. Steger K, Jarvis Å, Vasara T, Romantschuk M, Sundh I. 127.  2007. Effects of differing temperature management on development of Actinobacteria populations during composting. Res. Microbiol. 158:7617–24 [Google Scholar]
  130. Stes E, Francis I, Pertry I, Dolzblasz A, Depuydt S, Vereecke D. 128.  2013. The leafy gall syndrome induced by Rhodococcus fascians. FEMS Microbiol. Lett. 342:2187–94 [Google Scholar]
  131. Stes E, Vandeputte OM, El Jaziri M, Holsters M, Vereecke D. 129.  2011. A successful bacterial coup d'état: how Rhodococcus fascians redirects plant development. Annu. Rev. Phytopathol. 49:69–86 [Google Scholar]
  132. Stutzenberger FJ. 130.  1972. Cellulolytic activity of Thermomonospora curvata: nutritional requirements for cellulase production. Appl. Microbiol. 24:177–82 [Google Scholar]
  133. Takahashi T, Oka T, Iwana H, Kuwata T, Yamamoto Y. 131.  1993. Immune response of mice to orally administered lactic acid bacteria. Biosci. Biotechnol. Biochem. 57:91557–60 [Google Scholar]
  134. Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. 132.  2013. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci. Rep. 3:1–10 [Google Scholar]
  135. Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. 133.  2012. Estimating divergence times in large molecular phylogenies.. PNAS 109:4719333–38 [Google Scholar]
  136. Thompson JN. 134.  1994. The Coevolutionary Process Chicago: Univ. Chicago Press
  137. Thompson PB. 135.  2012. The agricultural ethics of biofuels: climate ethics and mitigation arguments. Poiesis Prax. 8:169–89 [Google Scholar]
  138. Tucker MP, Mohagheghi A, Grohmann K, Himmel ME. 136.  1989. Ultra-thermostable cellulases from Acidothermus cellulolyticus: comparison of temperature optima with previously reported cellulases. Nat. Biotechnol. 7:817–20 [Google Scholar]
  139. Turroni F, van Sinderen D, Ventura M. 137.  2011. Genomics and ecological overview of the genus Bifidobacterium. Int. J. Food Microbiol. 149:37–44 [Google Scholar]
  140. Tveit AT, Urich T, Svenning MM. 138.  2014. Metatranscriptomic analysis of Arctic peat soil microbiota. Appl. Environ. Microbiol. 80:185761–72 [Google Scholar]
  141. 139. US Energy Inf. Adm 2016. January 2016 Monthly Energy Review. Washington, DC: US Energy Inf. Adm.
  142. Vaaje-Kolstad G, Westereng B, Horn SJ, Liu Z, Zhai H. 140.  et al. 2010. An oxidative enzyme boosting the enzymatic conversion of recalcitrant polysaccharides. Science 330:219–22 [Google Scholar]
  143. Vitousek PM, Walker LR. 141.  1989. Biological invasion by Myrica faya in Hawai'i: plant demography, nitrogen fixation, ecosystem effects. Ecol. Monogr. 59:3247–65 [Google Scholar]
  144. Vollmann J, Eynck C. 142.  2015. Camelina as a sustainable oilseed crop: contributions of plant breeding and genetic engineering. Biotechnol. J. 10:525–35 [Google Scholar]
  145. von Graeventiz A, Bernard K. 143.  2006. The genus Corynebacterium—medical. See Ref. 111 819–42
  146. Wachinger G, Bronnenmeier K, Staudenbauer WL, Schrempf H. 144.  1989. Identification of mycelium-associated cellulase from Streptomyces reticuli. Appl. Environ. Microbiol. 55:102653–57 [Google Scholar]
  147. Waksman SA. 145.  1918. Studies in the metabolism of actinomycetes II. J. Bacteriol. 4:307–30 [Google Scholar]
  148. Waksman SA. 146.  1931. Decomposition of the various chemical constituents etc. of complex plant materials by pure cultures of fungi and bacteria. Arch. Mikrobiol. 2:1136–54 [Google Scholar]
  149. Walter S, Schrempf H. 147.  1996. The synthesis of the Streptomyces reticuli cellulase (avicelase) is regulated by both activation and repression mechanisms. Mol. Gen. Genet. 251:2186–95 [Google Scholar]
  150. Wang B, Wang J, Zhang W, Meldrum DR. 148.  2012. Application of synthetic biology in cyanobacteria and algae. Front. Microbiol. 3:344 [Google Scholar]
  151. Wang C, Dong D, Wang H, Müller K, Qin Y. 149.  et al. 2016. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition. Biotechnol. Biofuels 9:1–17 [Google Scholar]
  152. Watanabe Y, Martini JE, Ohmoto H. 150.  2000. Geochemical evidence for terrestrial ecosystems 2.6 billion years ago. Nature 408:574–78 [Google Scholar]
  153. Watanabe Y, Shinzato N, Fukatsu T. 151.  2003. Isolation of actinomycetes from termites' guts. Biosci. Biotechnol. Biochem. 67:81797–801 [Google Scholar]
  154. Weber NA. 152.  1966. Fungus-growing ants. Science 153:3736587–604 [Google Scholar]
  155. Webster NS, Taylor MW. 153.  2012. Marine sponges and their microbial symbionts: love and other relationships. Environ. Microbiol. 14:2335–46 [Google Scholar]
  156. Weise SE, van Wijk KJ, Sharkey TD. 154.  2011. The role of transitory starch in C3, CAM, and C4 metabolism and opportunities for engineering leaf starch accumulation. J. Exp. Bot. 62:93109–18 [Google Scholar]
  157. Wilson DB. 155.  2004. Studies of Thermobifida fusca plant cell wall degrading enzymes. Chem. Rec. 4:272–82 [Google Scholar]
  158. Wilson DB. 156.  2011. Microbial diversity of cellulose hydrolysis. Curr. Opin. Microbiol. 14:259–63 [Google Scholar]
  159. Wu M, Bu L, Vuong TV, Wilson DB, Crowley MF. 157.  et al. 2013. Loop motions important to product expulsion in the Thermobifida fusca glycoside hydrolase family 6 cellobiohydrolase from structural and computational studies. J. Biol. Chem. 288:4633107–17 [Google Scholar]
  160. Yamamoto S, Suda M, Niimi S, Inui M, Yukawa H. 158.  2013. Strain optimization for efficient isobutanol production using Corynebacterium glutamicum under oxygen deprivation. Biotechnol. Bioeng. 110:112938–48 [Google Scholar]
  161. Yu H, Zeng G, Huang H, Xi X, Wang R. 159.  et al. 2007. Microbial community succession and lignocellulose degradation during agricultural waste composting. Biodegradation 18:793–802 [Google Scholar]
  162. Yuzawa S, Keasling JD, Katz L. 160.  2016. Insights into polyketide biosynthesis gained from repurposing antibiotic-producing polyketide synthases to produce fuels and chemicals. J. Antibiot. In press. doi: 10.1038/ja.2016.64
  163. Ziemert N, Lechner A, Wietz M, Millán-Aguiñaga N, Chavarria KL, Jensen PR. 161.  2014. Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. PNAS 111:12E1130–39 [Google Scholar]
  164. Žifčáková L, Větrovský T, Howe A, Baldrian P. 162.  2015. Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter. Environ. Microbiol. 18:1288–301 [Google Scholar]
  165. Zimmermann W. 163.  1990. Degradation of lignin by bacteria. J. Biotechnol. 13:119–30 [Google Scholar]
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