eLignin Database

All references in database (by first author):

Today, the bibliome of eLignin consists of 337 scientific references (peer-reviewed articles, reviews and books). New references are continuously added.

Quick navigation: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z


• Abe, T., Masai, E., Miyauchi, K., Katayama, Y., & Fukuda, M. (2005) A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6 Journal of bacteriology 187(6): 2030-2037.
PubMed: 15743951
PMC: PMC1064056

• Acevedo, F., Pizzul, L., del Pilar Castillo, M., Cuevas, R., & Diez, M. C. (2011) Degradation of polycyclic aromatic hydrocarbons by the Chilean white-rot fungus Anthracophyllum discolor. Journal of hazardous materials 185(1): 212-219.
PubMed: 20934253

• Adav, S. S., Chao, L. T., & Sze, S. K. (2012) Quantitative secretomic analysis of Trichoderma reesei strains reveals enzymatic composition for lignocellulosic biomass degradation. Molecular & cellular proteomics 11(7): M111-012419.
PubMed: 22355001
PMC: PMC3394936

• Alexieva, Z., Yemendzhiev, H., & Zlateva, P. (2010) Cresols utilization by Trametes versicolor and substrate interactions in the mixture with phenol. Biodegradation 21(4): 625-635.
PubMed: 20127146

• Alvarez, H. M., Mayer, F., Fabritius, D., & Steinbüchel, A. (1996) Formation of intracytoplasmic lipid inclusions by Rhodococcus opacus strain PD630. Archives of microbiology 165(6): 377-386.
PubMed: 8661931

• Anderson, J. J., & Dagley, S. (1980) Catabolism of aromatic acids in Trichosporon cutaneum. Journal of bacteriology 141(2): 534-543.
PubMed: 7364712
PMC: PMC293656

• Antai, S. P., & Crawford, D. L. (1981) Degradation of softwood, hardwood, and grass lignocelluloses by two Streptomyces strains. Applied and environmental microbiology 42(2): 378-380.
PubMed: 16345837

• Antai, S. P., & Crawford, D. L. (1981) Degradation of softwood, hardwood, and grass lignocelluloses by two Streptomyces strains. Applied and environmental microbiology 42(2): 378-380.
PubMed: 16345837
PMC: PMC244017

• Antai, S. P., & Crawford, D. L. (1983) Degradation of phenol by Streptomyces setonii. Canadian Journal of Microbiology 29(1): 142-143.

• Aoyama, A., Yamada, K., Suzuki, Y., Kato, Y., Nagai, K., & Kurane, R. (2014) Newly-isolated laccase high productivity Streptomyces sp. grown in cedar powder as the sole carbon source. International Journal of Waste Resources, 4(2): 1-5.

• Arora, D. S., & Sandhu, D. K. (1985) Laccase production and wood degradation by a white-rot fungus Daedalea flavida. Enzyme and microbial technology 7(8): 405-408.

• Azman, H. (2015) Bioligninolysis: Degradation Of Ionic Liquid Derived Lignin By Rhodococcus PhD Thesis, Department Of Chemistry, Faculty Of Natural Sciences,Imperial College London : .


• Bache, R., & Pfennig, N. (1981) Selective isolation of Acetobacterium woodii on methoxylated aromatic acids and determination of growth yields. Archives of Microbiology 130(3): 255-261.

• Bak, F., & Widdel, F. (1986) Anaerobic degradation of phenol and phenol derivatives by Desulfobacterium phenolicum sp. nov. Archives of microbiology 146(2): 177-180.

• Bak, F., Finster, K., & Rothfuß, F. (1992) Formation of dimethylsulfide and methanethiol from methoxylated aromatic compounds and inorganic sulfide by newly isolated anaerobic bacteria. Archives of microbiology 157(6): 529-534.

• Balkwill, D. L., Drake, G. R., Reeves, R. H., Fredrickson, J. K., White, D. C., Ringelberg, D. B., Chandler D. P., Romine M. F., Kennedy D. W., & Spadoni, C. M. (1997) Taxonomic Study of Aromatic-Degrading Bacteria from Deep-Terrestrial-Subsurface Sediments and Description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. International Journal of Systematic and Evolutionary Microbiology, 47(1): 191-201.
PubMed: 8995822

• Bandounas, L., Wierckx, N. J., de Winde, J. H., & Ruijssenaars, H. J. (2011) Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. BMC Biotechnology 11(1): 94.
PubMed: 21995752
PMC: PMC3212925

• Barapatre, A., & Jha, H. (2017) Degradation of alkali lignin by two ascomycetes and free radical scavenging activity of the products. Biocatalysis and Biotransformation 35(4): 269-286.

• Barbe, V., Vallenet, D., Fonknechten, N., Kreimeyer, A., Oztas, S., Labarre, L., ... & Ornston, L. N. (2004) Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Research 32(19): 5766-5779.
PubMed: 15514110
PMC: PMC528795

• Barton, N., Horbal, L., Starck, S., Kohlstedt, M., Luzhetskyy, A., & Wittmann, C. (2018) Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis, cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116. Metabolic engineering 45: 200-210.
PubMed: 29246517

• Belda E., van Heck R.G., José Lopez-Sanchez M., Cruveiller S., Barbe V., Fraser C., Klenk H.P., Petersen J., Morgat A., Nikel P.I., Vallenet D., Rouy Z., Sekowska A., Martins Dos Santos V.A., de Lorenzo V., Danchin A., Médigue C.. (2016) The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environmental microbiology. 18(10): 3403-3424.
PubMed: 26913973

• Benjamin, S., Kamimura, N., Takahashi, K., & Masai, E. (2016) Achromobacter denitrificans SP1 efficiently utilizes 16 phthalate diesters and their downstream products through protocatechuate 3, 4-cleavage pathway. Ecotoxicology and Environmental Safety 134: 172-178.
PubMed: 27619352

• Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3 (2). Nature 417(6885): 141-147.
PubMed: 12000953

• Bergauer, P., Fonteyne, P. A., Nolard, N., Schinner, F., & Margesin, R. (2005) Biodegradation of phenol and phenol-related compounds by psychrophilic and cold-tolerant alpine yeasts. Chemosphere 59(7): 909-918.
PubMed: 15823324

• Bi, R., Lawoko, M., & Henriksson, G. (2016) Phoma herbarum, a soil fungus able to grow on natural lignin and synthetic lignin (DHP) as sole carbon source and cause lignin degradation. Journal of industrial microbiology & biotechnology 43(8): 1175-1182.
PubMed: 27260523

• Billings, A. F., Fortney, J. L., Hazen, T. C., Simmons, B., Davenport, K. W., Goodwin, L., Ivanova N., Kyrpides N. C., Mavromatis K., Woyke T., DeAngelis K.M. (2015) Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Standards in genomic sciences 10(1): 106.
PubMed: 26594307
PMC: PMC4653933

• Bleichrodt, F. S., Fischer, R., & Gerischer, U. C. (2010) The β-ketoadipate pathway of Acinetobacter baylyi undergoes carbon catabolite repression, cross-regulation and vertical regulation, and is affected by Crc. Microbiology 156(5): 1313-1322.
PubMed: 20110298

• Butler, G., Rasmussen, M. D., Lin, M. F., Santos, M. A. S., Sakthikumar, S., Munro, C. A., Rheinbay, E., Grabherr, M., Forche, A., Reedy, J. L., Agrafioti, I., Arnaud /.../ & Cuomo, C. A. (2009) Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature. 459(7247): 657-662.
PubMed: 19465905
PMC: PMC2834264


• Cámara, B., Bielecki, P., Kaminski, F., dos Santos, V. M., Plumeier, I., Nikodem, P., & Pieper, D. H. (2007) A gene cluster involved in degradation of substituted salicylates via ortho cleavage in Pseudomonas sp. strain MT1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate. Journal of bacteriology 189(5): 1664-1674.
PubMed: 17172348
PMC: PMC1855727

• Causer, M. J., Hopper, D. J., McIntire, W. S., & SINGER, T. P. (1984) Azurin from Pseudomonas putida: an electron acceptor for p-cresol methylhydroxylase. Biochem. Soc. Trans. 12: 1131-1132.

• Cecil, J. H., Garcia, D. C., Giannone, R. J., & Michener, J. K. (2018) Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans Applied and Environmental Microbiology 84(22): e01185-18.
PubMed: 30217841
PMC: PMC6210112

• Chan, J. Z., Halachev, M. R., Loman, N. J., Constantinidou, C., & Pallen, M. J. (2012) Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC microbiology, 12(1): 302.
PubMed: 23259572
PMC: PMC3556118

• Chandra, R., & Bharagava, R. N. (2013) Bacterial degradation of synthetic and kraft lignin by axenic and mixed culture and their metabolic products. Journal of Environmental Biology 34(6): 991.
PubMed: 24555327

• Chandra, R., Raj, A., Purohit, H. J., & Kapley, A. (2007) Characterisation and optimisation of three potential aerobic bacterial strains for kraft lignin degradation from pulp paper waste. Chemosphere 67(4): 839-846.
PubMed: 17150240

• Chang, A. J., Fan, J., & Wen, X. (2012) Screening of fungi capable of highly selective degradation of lignin in rice straw. International Biodeterioration & Biodegradation 72: 26-30.

• Chang, Y. C., Choi, D., Takamizawa, K., & Kikuchi, S. (2014) Isolation of Bacillus sp. strains capable of decomposing alkali lignin and their application in combination with lactic acid bacteria for enhancing cellulase performance. Bioresource technology 152: 429-436.
PubMed: 24316485

• Chang, Y. C., Choi, D., Takamizawa, K., & Kikuchi, S. (2014) Isolation of Bacillus sp. strains capable of decomposing alkali lignin and their application in combination with lactic acid bacteria for enhancing cellulase performance. Bioresource technology 152: 429-436.
PubMed: 24316485

• Chapman, P. J., & Ribbons, D. W. (1976) Metabolism of resorcinylic compounds by bacteria: orcinol pathway in Pseudomonas putida. Journal of bacteriology 125(3): 975-984.
PubMed: 1254564
PMC: PMC236174

• Chapman, P. J., & Ribbons, D. W. (1976). (1976) Metabolism of resorcinylic compounds by bacteria: alternative pathways for resorcinol catabolism in Pseudomonas putida. Journal of bacteriology 125(3): 985-998.
PubMed: 942589
PMC: PMC236175

• Chaudhry, M. T., Huang, Y., Shen, X. H., Poetsch, A., Jiang, C. Y., & Liu, S. J. (2007) Genome-wide investigation of aromatic acid transporters in Corynebacterium glutamicum. Microbiology 153(3): 857-865.
PubMed: 17322206

• Chen, H. P., Chow, M., Liu, C. C., Lau, A., Liu, J., & Eltis, L. D. (2012) Vanillin catabolism in Rhodococcus jostii RHA1. Applied and environmental microbiology 78(2): 586-588.
PubMed: 22057861
PMC: PMC3255756

• Chen, Y. H., Chai, L. Y., Zhu, Y. H., Yang, Z. H., Zheng, Y., & Zhang, H. (2012) Biodegradation of kraft lignin by a bacterial strain Comamonas sp. B-9 isolated from eroded bamboo slips. Journal of applied microbiology 112(5): 900-906.
PubMed: 22380656

• Chen, Y., Chai, L., Tang, C., Yang, Z., Zheng, Y., Shi, Y., & Zhang, H. (2012) Kraft lignin biodegradation by Novosphingobium sp. B-7 and analysis of the degradation process. Bioresource technology 123: 682-685.
PubMed: 22921251

• Chong, G. G., Huang, X. J., Di, J. H., Xu, D. Z., He, Y. C., Pei, Y. N., Tang, Y. & Ma, C. L. (2018) Biodegradation of alkali lignin by a newly isolated Rhodococcus pyridinivorans CCZU-B16. Bioprocess and biosystems engineering 41(4): 501-510.
PubMed: 7641141

• Chow, K. T., Pope, M. K., & Davies, J. (1999) Characterization of a vanillic acid non-oxidative decarboxylation gene cluster from Streptomyces sp. D7. Microbiology 145(9): 2393-2403..
PubMed: 10517592

• Chowdhury, S. P., Khanna, S., Verma, S. C., & Tripathi, A. K. (2004) Molecular diversity of tannic acid degrading bacteria isolated from tannery soil. Journal of applied microbiology 97(6): 1210-1219.
PubMed: 15546412

• Chung, S. Y., Maeda, M., Song, E., Horikoshij, K., & Kudo, T. (1994) A Gram-positive polychlorinated biphenyl-degrading bacterium, Rhodococcus erythropolis strain TA421, isolated from a termite ecosystem. Bioscience, biotechnology, and biochemistry 58(11): 2111-2113.

• Collier, L. S., Nichols, N. N., & Neidle, E. L. (1997) benK encodes a hydrophobic permease-like protein involved in benzoate degradation by Acinetobacter sp. strain ADP1. Journal of bacteriology 179(18): 5943-5946.
PubMed: 9294456
PMC: PMC179488

• Cook, K. A., & Cain, R. B. (1974) Regulation of aromatic metabolism in the fungi: metabolic control of the 3-oxoadipate pathway in the yeast Rhodotorula mucilaginosa. Microbiology 85(1): 37-50.
PubMed: 4474356

• Cowles, C. E., Nichols, N. N., & Harwood, C. S. (2000) BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. Journal of bacteriology 182(22): 6339-6346.
PubMed: 11053377
PMC: PMC94779

• Crawford, R. L., Bromley, J. W., & Perkins-Olson, P. E. (1979) Catabolism of protocatechuate by Bacillus macerans. Applied and environmental microbiology 37(3): 614-618.
PubMed: 453834
PMC: PMC243264

• Crawford, R. L., McCoy, E., Harkin, J. M., Kirk, T. K., & Obst, J. R. (1973) Degradation of methoxylated benzoic acids by a Nocardia from a lignin-rich environment: significance to lignin degradation and effect of chloro substituents. Applied microbiology 26(2): 176-184.
PubMed: 4743871
PMC: PMC379747

• Cronin, C. N., Kim, J., Fuller, J. H., Zhang, X., & Mcintire, W. S. (1999) Organization and sequences of p-hydroxybenzaldehyde dehydrogenase and other plasmid-encoded genes for early enzymes of the p-cresol degradative pathway in Pseudomonas putida NCIMB 9866 and 9869. DNA Sequence 10(1): 7-17.
PubMed: 10565539


• D'Argenio, D. A., Segura, A., Coco, W. M., Bünz, P. V., & Ornston, L. N. (1999) The Physiological Contribution of Acinetobacter PcaK, a Transport System That Acts upon Protocatechuate, Can Be Masked by the Overlapping Specificity of VanK. Journal of bacteriology 181(11): 3505-3515.

• Daina, S., Orlandi, M., Bestetti, G., Wiik, C., & Elegir, G. (2002) Degradation of beta-5 lignin model dimers by Ceriporiopsis subvermispora. Enzyme and Microbial Technology 30(4): 499-505.

• Daniel, S. L., Wu, Z., & Drake, H. L. (1988) Growth of thermophilic acetogenic bacteria on methoxylated aromatic acids. FEMS microbiology letters 52(1-2): 25-28.

• Dardas, A., Gal, D., Barrelle, M., Sauret-Ignazi, G., Sterjiades, R., & Pelmont, J. (1985) The demethylation of guaiacol by a new bacterial cytochrome P-450. Archives of biochemistry and biophysics 236(2): 585-592.
PubMed: 3970527

• Davis J.R., Goodwin L.A., Woyke T., Teshima H., Bruce D., Detter C., Tapia R., Han S., Han J., Pitluck S., Nolan M., Mikhailova N., Land M.L., Sello J.K. (2012) Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. Journal of bacteriology 194(9): 2396-2397.
PubMed: 22493203
PMC: PMC3347045

• Davis, J. R., & Sello, J. K. (2010) Regulation of genes in Streptomyces bacteria required for catabolism of lignin-derived aromatic compounds. Applied microbiology and biotechnology 86(3): 921-929.
PubMed: 20012281

• Davis, J.R., Goodwin, L., Teshima, H., Detter, C., Tapia, R., Han, C., Huntemann, M., Wei, C.-L., Han, J., Chen, A. (2013) Genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a lignin-degrading actinomycete. Genome announcements 1(4): e00416-00413.
PubMed: 23833133
PMC: PMC3703594

• DeAngelis, K.M., D'Haeseleer, P., Chivian, D., Fortney, J.L., Khudyakov, J., Simmons, B., Woo, H., Arkin, A.P., Davenport, K.W., Goodwin, L., Chen, A., Ivanova, N., Kyrpides, N.C., Mavromatis, K., Woyke, T., Hazen, T.C. (2011) Complete genome sequence of "Enterobacter lignolyticus" SCF1 Stand Genomic Sci 5(1): 69-85.
PubMed: 22180812
PMC: PMC3236048

• DeAngelis, K.M., Sharma, D., Varney, R., Simmons, B., Isern, N.G., Markilllie, L.M., Nicora, C., Norbeck, A.D., Taylor, R.C., Aldrich, J.T. & Robinson, E.W. (2013) Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1 Frontiers in microbiology, 4: 280.
PubMed: 24065962
PMC: PMC3777014

• Defnoun, S., Labat, M., Ambrosio, M., Garcia, J. L., & Patel, B. K. (2000) Papillibacter cinnamivorans gen. nov., sp. nov., a cinnamate-transforming bacterium from a shea cake digester. International journal of systematic and evolutionary microbiology 50(3): 1221-1228.
PubMed: 10843066
PMC: 10.1099/00207713-50-3-1221

• Deligios, M., Fraumene, C., Abbondio, M., Mannazzu, I., Tanca, A., Addis, M.F., Uzzau, S. (2015) Draft genome sequence of Rhodotorula mucilaginosa, an emergent opportunistic pathogen. Genome announcements 3(2): e00201-00215.

• Delneri, D., Degrassi, G., Rizzo, R., & Bruschi, C. V. (1995) Degradation of trans-ferulic and p-coumaric acid byAcinetobacter calcoaceticus DSM 586. Biochimica et Biophysica Acta (BBA)-General Subjects 1244(2-3: 363-367.
PubMed: 7599157

• Deschamps, A. M., Mahoudeau, G., & Lebeault, J. M. (1980) Fast degradation of kraft lignin by bacteria. Applied Microbiology and Biotechnology, 9(1): 45-51.

• Divari, S., Valetti, F., Caposio, P., Pessione, E., Cavaletto, M., Griva, E., Gribaudo G, Gilardi G & Giunta C. (2003) The oxygenase component of phenol hydroxylase from Acinetobacter radioresistens S13. European journal of biochemistry 270(10): 2244-2253.
PubMed: 12752444

• Duan, J., Huo, X., Du, W. J., Liang, J. D., Wang, D. Q., & Yang, S. C. (2016) Biodegradation of kraft lignin by a newly isolated anaerobic bacterial strain, Acetoanaerobium sp. WJDL-Y2. Letters in applied microbiology 62(1): 55-62.
PubMed: 26465801

• Duan, J., Liang, J., Wang, Y., Du, W., & Wang, D. (2016) Kraft Lignin Biodegradation by Dysgonomonas sp. WJDL-Y1, a New Anaerobic Bacterial Strain Isolated from Sludge of a Pulp and Paper Mill. Journal of microbiology and biotechnology 26(10): 1765-1773.
PubMed: 27381334

• Durham, D.R., Mcnamee, C.G. & Stewart, D.B. (1984) Dissimilation of Aromatic-Compounds in Rhodotorula graminis - Biochemical-Characterization of Pleiotropically Negative Mutants J Bacteriol 160(2): 771-777.
PubMed: 6542098
PMC: PMC214803


• Edlin, D. A., Narbad, A., Dickinson, J. R., & Lloyd, D. (1995) The biotransformation of simple phenolic compounds by Brettanomyces anomalus. FEMS Microbiology Letters 125(2-3): 311-315.

• Eggeling, L., & Sahm, H. (1980) Degradation of coniferyl alcohol and other lignin-related aromatic compounds by Nocardia sp. DSM 1069. Archives of Microbiology 126(2): 141-148.

• Eggert, C., Temp, U., & Eriksson, K. E. (1996) The ligninolytic system of the white rot fungus Pycnoporus cinnabarinus: purification and characterization of the laccase. Applied and Environmental Microbiology 62(4): 1151-1158.
PubMed: 8919775
PMC: PMC167880

• Elena, S., & Božena, K. (2001) Modification of lignin by Geotrichum klebahnii. World Journal of Microbiology and Biotechnology, 17(1): 1-3.

• Emerson, D., Chauhan, S., Oriel, P., & Breznak, J. A. (1994) Haloferax sp. D1227, a halophilic Archaeon capable of growth on aromatic compounds. Archives of microbiology 161(6): 445-452.

• Engelmann T., Kaufmann F., Diekert G. (2001) Isolation and characterization of a veratrol:corrinoid protein methyl transferase from Acetobacterium dehalogenans Archives of microbiology 175(5): 376-383..
PubMed: 11409548

• Erdoğmuş, S. F., Mutlu, B., Korcan, S. E., Güven, K., & Konuk, M. (2013) Aromatic hydrocarbon degradation by halophilic archaea isolated from Çamaltı Saltern, Turkey. Water, Air, & Soil Pollution, 224(3): 1449.

• Eriksson, K. E., Gupta, J. K., Nishida, A., & Rao, M. (1984) Syringic acid metabolism by some white-rot, soft-rot and brown-rot fungi. Microbiology 130(10): 2457-2464.

• Eriksson, K. E., Johnsrud, S. C., & Vallander, L. (1983) Degradation of lignin and lignin model compounds by various mutants of the white-rot fungus Sporotrichum pulverulentum. Archives of Microbiology 135(3): 161-168.

• Eulberg, D., Golovleva, L. A., & Schlömann, M. (1997) Characterization of catechol catabolic genes from Rhodococcus erythropolis 1CP. Journal of bacteriology 179(2): 370-381.
PubMed: 8990288
PMC: PMC178706


• Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C. R., Morgan, P., & Larkin, M. J. (2002) Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Applied and environmental microbiology 68(12): 6246-6255.
PubMed: 12450849

• Falcon, M. A., Rodriguez, A., Carnicero, A., Regalado, V., Perestelo, F., Milstein, O., & De la Fuente, G. (1995) Isolation of microorganisms with lignin transformation potential from soil of Tenerife Island. Soil Biology and Biochemistry 27(2): 121-126.

• Fialová, A., Boschke, E., & Bley, T. (2004) Rapid monitoring of the biodegradation of phenol-like compounds by the yeast Candida maltosa using BOD measurements. International biodeterioration & biodegradation 54(1): 69-76.

• Firrincieli, A., Otillar, R., Salamov, A., Schmutz, J., Khan, Z., Redman, R.S., Fleck, N.D., Lindquist, E., Grigoriev, I.V., Doty, S.L. (2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1 Front Microbiol 6: .

• Fischer, R., Bleichrodt, F. S., & Gerischer, U. C. (2008) Aromatic degradative pathways in Acinetobacter baylyi underlie carbon catabolite repression. Microbiology 154(10): 3095-3103.
PubMed: 18832315

• Fleige, C., Hansen, G., Kroll, J., & Steinbüchel, A. (2013) Investigation of the Amycolatopsis sp. strain ATCC 39116 vanillin dehydrogenase and its impact on the biotechnical production of vanillin. Applied and environmental microbiology 79(1): 81-90.
PubMed: 23064333
PMC: PMC3536076

• Floudas D., Binder M., Riley R., Barry K., Blanchette R.A., Henrissat B., Martínez A.T., Otillar R., Spatafora J.W., Yadav J.S., Aerts A., Benoit I., Boyd A., Carlson A., Copeland A., Coutinho P.M., de Vries R.P., Ferreira P., Findley K., Foster B., Gaskell J., Glotzer D., Górecki P., Heitman J., Hesse C., Hori C., Igarashi K., Jurgens J.A., Kallen N., Kersten P., Kohler A., Kües U., Kumar T.K., Kuo A., LaButti K., Larrondo L.F., Lindquist E., Ling A., Lombard V., Lucas S., Lundell T., Martin R., McLaughlin D.J., Morgenstern I., Morin E., Murat C., Nagy L.G., Nolan M., Ohm R.A., Patyshakuliyeva A., Rokas A., Ruiz-Dueñas F.J., Sabat G., Salamov A., Samejima M., Schmutz J., Slot J.C., St John F., Stenlid J., Sun H., Sun S., Syed K., Tsang A., Wiebenga A., Young D., Pisabarro A., Eastwood D.C., Martin F., Cullen D., Grigoriev I.V., Hibbett D.S. (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336(6089): 1715-1719.
PubMed: 22745431

• Fontaine, F. E., Peterson, W. H., McCoy, E., Johnson, M. J., & Ritter, G. J. (1942) A new type of glucose fermentation by Clostridium thermoaceticum. Journal of bacteriology 43(6): 701.
PubMed: 16560531
PMC: PMC373636

• França, L. , Sannino, C., Turchetti, B. , Buzzini, P. & Margesin, R. (2016) Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils Extremophiles 20(6): 855-873.
PubMed: 27620454
PMC: PMC5085987

• Fukasawa, Y., Osono, T., & Takeda, H. (2011) Wood decomposing abilities of diverse lignicolous fungi on nondecayed and decayed beech wood. Mycologia 103(3): 474-482.
PubMed: 21262989
PMC: 10.3852/10-246

• Fukuhara Y., Kamimura N., Nakajima M., Hishiyama S., Hara H., Kasai D., Tsuji Y., Narita-Yamada S., Nakamura S., Katano Y., Fujita N., Katayama Y., Fukuda M., Kajita S., Masai E. (2013) Discovery of pinoresinol reductase genes in sphingomonads. Enzyme and microbial technology 52(1): 38-43.
PubMed: 23199737

• Furukawa, K., Hayase, N., Taira, K., & Tomizuka, N. (1989) Molecular relationship of chromosomal genes encoding biphenyl/polychlorinated biphenyl catabolism: some soil bacteria possess a highly conserved bph operon. Journal of bacteriology 171(10): 5467-5472.
PubMed: 2507526


• Gérecová G., Neboháčová M., Zeman I., Pryszcz L.P., Tomáška, L., Gabaldón T., Nosek J. (2015) Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans. FEMS Yeast Res. 15(3): .
PubMed: 25743787

• Galagan J.E., Calvo S.E., Cuomo C., Ma L.J., Wortman J.R., Batzoglou S., Lee S.I., Basturkmen M., Spevak C.C., Clutterbuck J., Kapitonov V., Jurka J., Scazzocchio C., Farman M., Butler J., Purcell S., Harris S., Braus G.H., Draht O., Busch S., D'Enfert C., Bouchier C., Goldman G.H., Bell-Pedersen D., Griffiths-Jones S., Doonan J.H., Yu J., Vienken K., Pain A., Freitag M., Selker E.U., Archer D.B., Peñalva M.A., Oakley B.R., Momany M., Tanaka T., Kumagai T., Asai K., Machida M., Nierman W.C., Denning D.W., Caddick M., Hynes M., Paoletti M., Fischer R., Miller B., Dyer P., Sachs M.S., Osmani S.A. & Birren B.W. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438(7071): 1105-1115.
PubMed: 16372000

• Gao, X., Tan, C. L., Yeo, C. C., & Poh, C. L. (2005) Molecular and biochemical characterization of the xlnD-encoded 3-hydroxybenzoate 6-hydroxylase involved in the degradation of 2, 5-xylenol via the gentisate pathway in Pseudomonas alcaligenes NCIMB 9867. Journal of bacteriology 187(22): 7696-7702.
PubMed: 16267294
PMC: PMC1280293

• Giroux, H., Vidal, P., Bouchard, J., & Lamy, F. (1988) Degradation of Kraft indulin lignin by Streptomyces viridosporus and Streptomyces badius. Applied and environmental microbiology 54(12): 3064-3070.
PubMed: 16347796
PMC: PMC204428

• González, J. M., Mayer, F., Moran, M. A., Hodson, R. E., & Whitman, W. B. (1997) Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. International Journal of Systematic and Evolutionary Microbiology 47(2): 369-376.
PubMed: 9103623

• González, B., Acevedo, C., Brezny, R., & Joyce, T. (1993) Metabolism of chlorinated guaiacols by a guaiacol-degrading Acinetobacter junii strain. Applied and environmental microbiology 59(10): 3424-3429.
PubMed: 8250564
PMC: PMC182469

• Gonzalez, J. M., Mayer, F., Moran, M. A., Hodson, R. E., & Whitman, W. B. (1997) Sagittula stellata gen. nov., sp. nov., a lignin-transforming bacterium from a coastal environment. International Journal of Systematic and Evolutionary Microbiology 47(3): 773-780.
PubMed: 9226910

• Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M., Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C., Gurson J., Lomo C., Sear C., Strub G., Cielo C., & Slater S. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294(5550): 2323-2328.
PubMed: 11743194

• Gorny, N., Wahl, G., Brune, A., & Schink, B. (1992) A strictly anaerobic nitrate-reducing bacterium growing with resorcinol and other aromatic compounds. Archives of microbiology 158(1),: 48-53.
PubMed: 1444713

• Grbić-Galić, D. (1985) Fermentative and oxidative transformation of ferulate by a facultatively anaerobic bacterium isolated from sewage sludge. Applied and environmental microbiology 50(4): 1052-1057.
PubMed: 4083873
PMC: PMC291792

• Groseclose, E. E., & Ribbons, D. W. (1981) Metabolism of resorcinylic compounds by bacteria: new pathway for resorcinol catabolism in Azotobacter vinelandii. Journal of bacteriology 146(2): 460-466.
PubMed: 7217008
PMC: PMC216987

• Gupta J. K., Jebsen, C., & Kneifel, H. (1986) Sinapic acid degradation by the yeast Rhodotorula glutinis. Microbiology 132(10): 2793-2799.

• Gupta, V. K., Minocha, A. K., & Jain, N. (2001) Batch and continuous studies on treatment of pulp mill wastewater by Aeromonas formicans. Journal of Chemical Technology and Biotechnology 76(6): 547-552.


• Haddadin, M. S., Haddadin, J., Arabiyat, O. I., & Hattar, B. (2009) Biological conversion of olive pomace into compost by using Trichoderma harzianum and Phanerochaete chrysosporium. Bioresource technology 100(20): 4773-4782.
PubMed: 19467866

• Hainal, A. R., Capraru, A. M., Volf, I., & Popa, V. I. (2012) Lignin as a carbon source for the cultivation of some Rhodotorula species. Cellul. Chem. Technol 46: 87-96.

• Hammer, E., Krowas, D., Schäfer, A., Specht, M., Francke, W., & Schauer, F. (1988) Isolation and characterization of a dibenzofuran-degrading yeast: identification of oxidation and ring cleavage products. Applied and environmental microbiology 64(6): 2215-2219.
PubMed: 9603837
PMC: PMC106301

• Hamzah, R. Y., & Al-Baharna, B. S. (1994) Catechol ring-cleavage in Pseudomonas cepacia: the simultaneous induction of ortho and meta pathways. Applied microbiology and biotechnology 41(2): 250-256.

• Haq, I., Kumar, S., Kumari, V., Singh, S. K., & Raj, A. (2016) Evaluation of bioremediation potentiality of ligninolytic Serratia liquefaciens for detoxification of pulp and paper mill effluent. Journal of hazardous materials 305: 190-199.
PubMed: 26686478

• Hara, H., Masai, E., Katayama, Y., & Fukuda, M. (2000) The 4-Oxalomesaconate Hydratase Gene, Involved in the Protocatechuate 4, 5-Cleavage Pathway, Is Essential to Vanillate and Syringate Degradation in Sphingomonas paucimobilisSYK-6. Journal of bacteriology 182(24): 6950-6957.
PubMed: 11092855
PMC: PMC94820

• Hara, H., Masai, E., Miyauchi, K., Katayama, Y., & Fukuda, M. (2003) Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4, 5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. Journal of bacteriology 185(1): 41-50.
PubMed: 12486039
PMC: PMC141877

• Harazono, K., Yamashita, N., Shinzato, N., WATANABE, Y., FUKATSU, T., & KURANE, R. (2003) Isolation and characterization of aromatics-degrading microorganisms from the gut of the lower termite Coptotermes formosanus. Bioscience, biotechnology, and biochemistry 67(4): 889-892.
PubMed: 12784634

• Harwood, C. S., & Gibson, J. (1988) Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris. Applied and environmental microbiology 54(3): 712-717.
PubMed: 3377491
PMC: PMC202530

• Harwood, C. S., & Parales, R. E. (1996) The beta-ketoadipate pathway and the biology of self-identity. Annual Reviews in Microbiology 50(1): 553-590.
PubMed: 8905091

• Harwood, C. S., Nichols, N. N., Kim, M. K., Ditty, J. L., & Parales, R. E. (1994) Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. Journal of bacteriology 176(21): 6479-6488.
PubMed: 7961399

• Henson, W. R., Campbell, T., DeLorenzo, D. M., Gao, Y., Berla, B., Kim S.J., Foston M., Moon T.S., Dantas G. (2018) Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus. Metabolic engineering 49: 69-83.
PubMed: 30059786

• Hiratsuka, N., Oyadomari, M., Shinohara, H., Tanaka, H., & Wariishi, H. (2005) Metabolic mechanisms involved in hydroxylation reactions of diphenyl compounds by the lignin-degrading basidiomycete Phanerochaete chrysosporium. Biochemical Engineering Journal 23(3): 241-246.

• Hirose, J., Nagayoshi, A., Yamanaka, N., Araki, Y., & Yokoi, H. (2013) Isolation and characterization of bacteria capable of metabolizing lignin-derived low molecular weight compounds. Biotechnology and bioprocess engineering 18(4): 736-741.

• Hirose, J., Tsuda, N., Miyatake, M., Yokoi, H., & Shimodaira, J. (2018) Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds. Genome announcements 6(16): e00308-18.
PubMed: 29674554
PMC: PMC5908938

• Hirose, J., Tsuda, N., Miyatake, M., Yokoi, H., & Shimodaira, J. (2018) Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds Genome Announcement 6(16): e00308-18.
PubMed: 29674554
PMC: PMC5908938

• Hirose, J., Tsukimata, R., Miyatake, M., & Yokoi, H. (2020) Identification of the Gene Responsible for Lignin-Derived Low-Molecular-Weight Compound Catabolism in Pseudomonas sp. Strain LLC-1 Genes 11(12): 1416.
PubMed: 33260964
PMC: PMC7760541

• Hofrichter, M., & Fritsche, W. (1997) Depolymerization of low-rank coal by extracellular fungal enzyme systems. II. The ligninolytic enzymes of the coal-humic-acid-depolymerizing fungus Nematoloma frowardii b19. Applied microbiology and biotechnology 47(4): 419-424.

• Hofrichter, M., Vares, T., Kalsi, M., Galkin, S., Scheibner, K., Fritsche, W., & Hatakka, A. (1999) Production of manganese peroxidase and organic acids and mineralization of 14C-labelled lignin (14C-DHP) during solid-state fermentation of wheat straw with the white rot fungus Nematoloma frowardii. Applied and Environmental Microbiology 65(5): 1864-1870.
PubMed: 10223971
PMC: PMC91268

• Holder, J.W., Ulrich, J.C., DeBono, A.C., Godfrey, P.A., Desjardins, C.A., Zucker, J., Zeng, Q., Leach, A.L., Ghiviriga, I. & Dancel, C., (2011) Comparative and functional genomics of Rhodococcus opacus PD630 for biofuels development. PLoS Genetics 7(9): e1002219.
PubMed: 21931557
PMC: PMC3169528

• Holesova, Z., Jakubkova, M., Zavadiakova, I., Zeman, I., Tomaska, L., & Nosek, J. (2011) Gentisate and 3-oxoadipate pathways in the yeast Candida parapsilosis: identification and functional analysis of the genes coding for 3-hydroxybenzoate 6-hydroxylase and 4-hydroxybenzoate 1-hydroxylase. Microbiology 157(7): 2152-2163.
PubMed: 21474535

• Hooda, R., Bhardwaj, N. K., & Singh, P. (2015) Screening and identification of ligninolytic bacteria for the treatment of pulp and paper mill effluent. Water, Air, & Soil Pollution 226(9): 305.

• Hooda, R., Bhardwaj, N. K., & Singh, P. (2018) Brevibacillus parabrevis MTCC 12105: a potential bacterium for pulp and paper effluent degradation. World Journal of Microbiology and Biotechnology 34(2): 31.
PubMed: 29380077

• Hopper, D. J., & Chapman, P. J. (1971) Gentisic acid and its 3-and 4-methyl-substituted homologues as intermediates in the bacterial degradation of m-cresol, 3, 5-xylenol and 2, 5-xylenol. Biochemical Journal 122(1): 19-28.
PubMed: 4330964
PMC: PMC1176683

• Huang, H., Zeng, G., Tang, L., Yu, H., Xi, X., Chen, Z., & Huang, G. (2008) Effect of biodelignification of rice straw on humification and humus quality by Phanerochaete chrysosporium and Streptomyces badius. International Biodeterioration & Biodegradation 61(4): 331-336.

• Huang, X.F., Santhanam, N., Badri, D.V., Hunter, W.J., Manter, D.K., Decker, S.R., Vivanco, J.M. & Reardon, K.F. (2013) Isolation and characterization of lignin‐degrading bacteria from rainforest soils. Biotechnology and bioengineering 110(6): 1616-1626.
PubMed: 23297115

• Huang, Y., Zhao, K. X., Shen, X. H., Chaudhry, M. T., Jiang, C. Y., & Liu, S. J. (2006) Genetic characterization of the resorcinol catabolic pathway in Corynebacterium glutamicum. Applied and environmental microbiology 72(11): 7238-7245.
PubMed: 16963551
PMC: PMC1636210

• Huang, Z., Dostal, L., & Rosazza, J. P. (1993) Mechanisms of ferulic acid conversions to vanillic acid and guaiacol by Rhodotorula rubra. Journal of Biological Chemistry 268(32): 23954-23958.
PubMed: 8226936

• Hughes, E. J., & Bayly, R. C. (1983) Control of catechol meta-cleavage pathway in Alcaligenes eutrophus. Journal of bacteriology 154(3): 1363-1370.
PubMed: 6853447
PMC: PMC217612


• Inoue, J., Shaw, J. P., Rekik, M., & Harayama, S. (1995) Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. Journal of bacteriology 177(5): 1196-1201.
PubMed: 7868591
PMC: PMC176723

• Inoue, J., Shaw, J. P., Rekik, M., & Harayama, S. (1995) Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida. Journal of bacteriology 177(5): 1196-1201.
PubMed: 7868591
PMC: PMC176723

• Ishiyama, D., Vujaklija, D., & Davies, J. (2004) Novel pathway of salicylate degradation by Streptomyces sp. strain WA46. Applied and environmental microbiology 70(3): 1297-1306.
PubMed: 15006746
PMC: PMC368302

• Iwabuchi, N., Takiguchi, H., Hamaguchi, T., Takihara, H., Sunairi, M., & Matsufuji, H. (2015) Transformation of Lignin-Derived Aromatics into Nonaromatic Polymeric Substances with Fluorescent Activities (NAPSFA) by Pseudomonas sp. ITH-SA-1. ACS Sustainable Chemistry & Engineering, 3(11): 2678-2685.


• Jackson, C. A., Couger, M. B., Prabhakaran, M., Ramachandriya, K. D., Canaan, P., & Fathepure, B. Z. (2017) Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass. Journal of Applied Microbiology. : .
PubMed: 28092137

• Jimenez, J. I., Minambres, B., Garcia, J. L., & Diaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environmental Microbiology. 4(12): 824-841.
PubMed: 12534466

• Jones, D. C., & Cooper, R. A. (1990) Catabolism of 3-hydroxybenzoate by the gentisate pathway in Klebsiella pneumoniae M5a1. Archives of microbiology 154(5): 489-495.
PubMed: 2256782

• Jurková, M., & Wurst, M. (1993) Biodegradation of aromatic carboxylic acids by Pseudomonas mira. FEMS microbiology letters 111(2-3): 245-250.


• Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., Dusch, N., Eggeling, L., Eikmanns, B.J., Gaigalat, L., Goesmann, A., Hartmann, M., Huthmacher, K., Kramer, R., Linke, B., McHardy, A.C., Meyer, F., Mockel, B., Pfefferle, W., Puhler, A., Rey, D.A., Ruckert, C., Rupp, O., Sahm, H., Wendisch, V.F., Wiegrabe, I., Tauch, A. (2003) The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol 104(1-3): 5-25.

• Kamimura, N., Aoyama, T., Yoshida, R., Takahashi, K., Kasai, D., Abe, T., ... & Masai, E. (2010) Characterization of the protocatechuate 4, 5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene. Applied and environmental microbiology 76(24): 8093-8101.
PubMed: 20952641
PMC: PMC3008244

• Kamimura, N., Goto, T., Takahashi, K., Kasai, D., Otsuka, Y., Nakamura, M., ... & Masai, E. (2017) A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde. Scientific Reports 7: 44422.
PubMed: 28294121

• Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M. & Tabata S.. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA research 9(6): 189-197.
PubMed: 12597275

• Karlson, U., Dwyer, D. F., Hooper, S. W., Moore, E. R., Timmis, K. N., & Eltis, L. D. (1993) Two independently regulated cytochromes P-450 in a Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate. Journal of bacteriology 175(5): 1467-1474.
PubMed: 8444808
PMC: PMC193234

• Kasai, D., Araki, N., Motoi, K., Yoshikawa, S., Iino, T., Imai, S., ... & Fukuda, M. (2015) Gamma-Resorcylate Catabolic Pathway Genes in the Soil Actinomycete Rhodococcus jostii RHA1. Applied and environmental microbiology AEM-02422: .
PubMed: 26319878

• Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M., & Masai, E. (2009) Uncovering the protocatechuate 2, 3-cleavage pathway genes. Journal of bacteriology 191(21): 6758-6768.
PubMed: 19717587
PMC: PMC2795304

• Kasai, D., Fujinami, T., Abe, T., Mase, K., Katayama, Y., Fukuda, M., & Masai, E. (2009) Uncovering the protocatechuate 2, 3-cleavage pathway genes. Journal of bacteriology 191(21): 6758-6768.
PubMed: 19717587

• Kasai, D., Masai, E., Miyauchi, K., Katayama, Y., & Fukuda, M. (2005) Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. Journal of bacteriology 187(15): 5067-5074.
PubMed: 16030198
PMC: PMC1196043

• Kasai, D., Masai, E., Miyauchi, K., Katayama, Y., & Fukuda, M. (2004) Characterization of the 3-O-methylgallate dioxygenase gene and evidence of multiple 3-O-methylgallate catabolic pathways in Sphingomonas paucimobilis SYK-6. Journal of bacteriology 186(15): 4951-4959.
PubMed: 15262932
PMC: PMC451629

• Katayama, Y., Nishikawa, S., Murayama, A., Yamasaki, M., Morohoshi, N., & Haraguchi, T. (1988) The metabolism of biphenyl structures in lignin by the soil bacterium (Pseudomonas paucimobilis SYK-6). FEBS letters, 233(1): 129-133.

• Kato, K., Kozaki, S., & Sakuranaga, M. (1998) Degradation of lignin compounds by bacteria from termite guts. Biotechnology letters 20(5): 459-462.

• Kaufmann, F., Wohlfarth, G., & Diekert, G. (1998) O-demethylase from Acetobacterium dehalogenans--cloning, sequencing, and active expression of the gene encoding the corrinoid protein. European journal of biochemistry/FEBS 257(2): 515-521.
PubMed: 9826201

• Kerr, T. J., Kerr, R. D., & Benner, R. (1983) Isolation of a bacterium capable of degrading peanut hull lignin. Applied and environmental microbiology 46(5): 1201-1206.
PubMed: 16346424
PMC: PMC239541

• Khemili-Talbi, S., Kebbouche-Gana, S., Akmoussi-Toumi, S., Angar, Y., & Gana, M. L. (2015) Isolation of an extremely halophilic arhaeon Natrialba sp. C21 able to degrade aromatic compounds and to produce stable biosurfactant at high salinity. Extremophiles 19(6): 1109-1120.
PubMed: 26334644

• Kim, M. K., & Harwood, C. S. (1991) Regulation of benzoate-CoA ligase in Rhodopseudomonas palustris FEMS microbiology letters 83(2): 199-203.

• Knežević, A., Stajić, M., Milovanović, I., & Vukojević, J. (2018) Wheat Straw Degradation by Trametes gibbosa: The Effect of Calcium Ions. Waste and Biomass Valorization 9(10): 1903-1908.

• Kojima, H., & Fukui, M. (2011) Sulfuritalea hydrogenivorans gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake. International journal of systematic and evolutionary microbiology 61(7): 1651-1655.
PubMed: 20709913

• Kornillowicz-Kowalska, T., & Rybczynska, K. (2015) Screening of microscopic fungi and their enzyme activities for decolorization and biotransformation of some aromatic compounds. International Journal of Environmental Science and Technology 12(8): 2673-2686.

• Kosa, M., & Ragauskas, A. J. (2012) Bioconversion of lignin model compounds with oleaginous Rhodococci. Applied Microbiology and Biotechnology. 93(2): 891-900.
PubMed: 22159607

• Krug, M., Ziegler, H., & Straube, G. (1985) Degradation of Phenolic-Compounds by the Yeast Candida-Tropicalis Hp-15. 1 Physiology of Growth and Substrate Utilization. Journal of Basic Microbiology. 25(2): 103-110.

• Kuhnigk, T., & König, H. (1997) Degradation of dimeric lignin model compounds by aerobic bacteria isolated from the hindgut of xylophagous termites. Journal of basic microbiology 37(3): 205-211.
PubMed: 9265743

• Kumar, M., Gazara, R. K., Verma, S., Kumar, M., Verma, P. K., & Thakur, I. S. (2016) Genome Sequence of Pandoraea sp. ISTKB, a Lignin-Degrading Betaproteobacterium, Isolated from Rhizospheric Soil. Genome announcements 4(6): e01240-16.
PubMed: 27811115
PMC: PMC5095485

• Kumar, M., Singh, J., Singh, M. K., Singhal, A., & Thakur, I. S. (2015) Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB. Environmental Science and Pollution Research, 22(20): 15690-15702 .
PubMed: 26018290

• Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Cordani JJ, Connerton IF, Cummings NJ, Daniel RA, Denziot F, Devine KM, Düsterhöft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim SY, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Hènaut A, Hilbert H, Holsappel S, Hosono S, Hullo MF, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee SM, Levine A, Liu H, Masuda S, Mauél C, Médigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park SH, Parro V, Pohl TM, Portelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin BS, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Togoni A, Tosato V, Uchiyama S, Vandebol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa HF, Zumstein E, Yoshikawa H, Danchin A. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390(6657): 249-256.
PubMed: 9384377


• Larimer, F.W., Chain, P., Hauser, L., Lamerdin, J., Malfatti, S., Do, L., Land, M.L., Pelletier, D.A., Beatty, J.T., Lang, A.S. (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris Nat Biotechnol 22(1): 55-61.

• Li, D., Yan, Y., Ping, S., Chen, M., Zhang, W., Li, L., ... & Lin, M. (2010) Genome-wide investigation and functional characterization of the β-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC microbiology 10(1): 36.
PubMed: 20137101
PMC: PMC2907835

• Liers, C., Arnstadt, T., Ullrich, R., & Hofrichter, M. (2011) Patterns of lignin degradation and oxidative enzyme secretion by different wood-and litter-colonizing basidiomycetes and ascomycetes grown on beech-wood. FEMS microbiology ecology 78(1): 91-102.
PubMed: 21631549

• Liu, F., Sun, W., Su, F., Zhou, K., Li, Z. (2012) Draft genome sequence of the sponge-associated strain Bacillus atrophaeus C89, a potential producer of marine drugs J Bacteriol 194(16): 4454-4454.

• Liu, Z. P., Wang, B. J., Liu, Y. H., & Liu, S. J. (2005) Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. International journal of systematic and evolutionary microbiology 55(3): 1229-1232.
PubMed: 15879260

• Lobos, S., Larraín, J., Salas, L., Cullen, D., & Vicuña, R. (1994) Isoenzymes of manganese-dependent peroxidase and laccase produced by the lignin-degrading basidiomycete Ceriporiopsis subvermispora. Microbiology 140(10): 2691-2698.
PubMed: 8000540

• Lucey, K. S., & Leadbetter, J. R. (2014) Catechol 2, 3‐dioxygenase and other meta‐cleavage catabolic pathway genes in the ‘anaerobic’termite gut spirochete Treponema primitia. Molecular ecology 23(6): 1531-1543.
PubMed: 24261591

• Lykidis A., Mavromatis K., Ivanova N., Anderson I., Land M., DiBartolo G., Martinez M., Lapidus A., Lucas S., Copeland A., Richardson P., Wilson D.B., Kyrpides N. (2007) Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of bacteriology 189(6): 2477-2486.
PubMed: 17209016
PMC: PMC1899369

• Lykidis, A., Perez-Pantoja, D., Ledger, T., Mavromatis, K., Anderson, I. J., Ivanova, N. N., Hooper, S. D., Lapidus, A., Lucas, S., Gonzalez, B., & Kyrpides, N. C. (2010) The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. Plos One. 5(3): .
PubMed: 20339589
PMC: PMC2842291


• Ma L.J., van der Does H.C., Borkovich K.A., Coleman J.J., Daboussi M.J., Di Pietro A., Dufresne M., Freitag M., Grabherr M., Henrissat B., Houterman P.M., Kang S., Shim W.B., Woloshuk C., Xie X., Xu J.R., Antoniw J., Baker S.E., Bluhm B.H., Breakspear A., Brown D.W., Butchko R.A., Chapman S., Coulson R., Coutinho P.M., Danchin E.G., Diener A., Gale L.R., Gardiner D.M., Goff S., Hammond-Kosack K.E., Hilburn K., Hua-Van A., Jonkers W., Kazan K., Kodira C.D., Koehrsen M., Kumar L., Lee Y.H., Li L., Manners J.M., Miranda-Saavedra D., Mukherjee M., Park G., Park J., Park S.Y., Proctor R.H., Regev A., Ruiz-Roldan M.C., Sain D., Sakthikumar S., Sykes S., Schwartz D.C., Turgeon B.G., Wapinski I., Yoder O., Young S., Zeng Q., Zhou S., Galagan J., Cuomo C.A., Kistler H.C., Rep M. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464(7287): 367-373.
PubMed: 20237561
PMC: PMC3048781

• MacLean, A. M., MacPherson, G., Aneja, P., & Finan, T. M. (2006) Characterization of the beta-ketoadipate pathway in Sinorhizobium meliloti. Applied and environmental microbiology 72(8): 5403-5413.
PubMed: 16885292
PMC: PMC1538742

• Mahiudddin, M., & Fakhruddin, A. N. M. (2012) Degradation of phenol via meta cleavage pathway by Pseudomonas fluorescens PU1. ISRN microbiology ID741820: .
PubMed: 23724329
PMC: PMC3658485

• Mallinson, S. J., Machovina, M. M., Silveira, R. L., Garcia-Borràs, M., Gallup, N., Johnson, C. W., Allen M.D., Skaf M.S., Crowley M.F., Neidle E.L., Houk K.N., Beckham G.T., DuBois J.L., McGeehan J.E. (2018) A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion. Nature communications 9(1): 2487.
PubMed: 29950589
PMC: PMC6021390

• Manter, D. K., Hunter, W. J., & Vivanco, J. M. (2011) Enterobacter soli sp. nov.: a lignin-degrading γ-proteobacteria isolated from soil. Current microbiology 62(3): 1044-1049.
PubMed: 21104086

• Margesin, R., Ludwikowsk, T.M., Kutzner, A.,Wagner, A.O. (2022) Low-Temperature Biodegradation of Lignin-Derived Aromatic Model Monomers by the Cold-Adapted Yeast Rhodosporidiobolus colostri Isolated from Alpine Forest Soil Microorganisms 10(3): 515.
PubMed: 35336090

• Margesin, R., Volgger, G., Wagner, A. O., Zhang, D., & Poyntner, C. (2021) Biodegradation of lignin monomers and bioconversion of ferulic acid Applied Microbiology and Biotechnology 105(7): 2967-2977.
PubMed: 33687503
PMC: PMC8007519

• Martinez D., Berka R.M., Henrissat B., Saloheimo M., Arvas M., Baker S.E., Chapman J., Chertkov O., Coutinho P.M., Cullen D., Danchin E.G., Grigoriev I.V., Harris P., Jackson M., Kubicek C.P., Han C.S., Ho I., Larrondo L.F., de Leon A.L., Magnuson J.K., Merino S., Misra M., Nelson B., Putnam N., Robbertse B., Salamov A.A., Schmoll M., Terry A., Thayer N., Westerholm-Parvinen A., Schoch C.L., Yao J., Barabote R., Nelson M.A., Detter C., Bruce D., Kuske C.R., Xie G., Richardson P., Rokhsar D.S., Lucas S.M., Rubin E.M., Dunn-Coleman N., Ward M., Brettin T.S. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature biotechnology 26(5): 553-560.
PubMed: 18454138

• Martinez D., Larrondo L.F., Putnam N., Gelpke M.D., Huang K., Chapman J., Helfenbein K.G., Ramaiya P., Detter J.C., Larimer F., Coutinho P.M., Henrissat B., Berka R., Cullen D., Rokhsar D. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature biotechnology 22(6): 695-700.
PubMed: 15122302

• Martins, T. M., Hartmann, D. O., Planchon, S., Martins, I., Renaut, J., & Pereira, C. S. (2015) The old 3-oxoadipate pathway revisited: new insights in the catabolism of aromatics in the saprophytic fungus Aspergillus nidulans. Fungal Genetics and Biology 74: 32-44.
PubMed: 25479309

• Martins, T. M., Núñez, O., Gallart-Ayala, H., Leitão, M. C., Galceran, M. T., & Pereira, C. S. (2014) New branches in the degradation pathway of monochlorocatechols by Aspergillus nidulans: a metabolomics analysis. Journal of hazardous materials 268: 264-272.
PubMed: 24509097

• Maruyama, K., Ariga, N., Tsuda, M., & Deguchi, K. (1978). (1978) Purification and properties of alpha-hydroxy-gamma-carboxymuconic epsilon-semialdehyde dehydrogenase. The Journal of Biochemistry 83(4): 1125-1134.
PubMed: 26671

• Maruyama, K., Shibayama, T., Ichikawa, A., Sakou, Y., Yamada, S., & Sugisaki, H. (2004) Cloning and characterization of the genes encoding enzymes for the protocatechuate meta-degradation pathway of Pseudomonas ochraceae NGJ1. Bioscience, biotechnology, and biochemistry 68(7): 1434-1441.
PubMed: 15277747

• Masák, J., Čejková, A., & Jirků, V. (1997) Isolation of acetone/ethylene glycol utilizing and biofilm forming strains of bacteria. Journal of microbiological methods 30(2): 133-139.

• Masai, E., Harada, K., Peng, X., Kitayama, H., Katayama, Y., & Fukuda, M. (2002) Cloning and characterization of the ferulic acid catabolic genes of Sphingomonas paucimobilis SYK-6. Applied and environmental microbiology 68(9): 4416-4424.
PubMed: 12200295
PMC: PMC124110

• Masai, E., Kamimura, N., Kasai, D., Oguchi, A., Ankai, A., Fukui, S., Takahashi, M., Yashiro, I., Sasaki, H., Harada, T., Nakamura, S., Katano, Y., Narita-Yamada, S., Nakazawa, H., Hara, H., Katayama, Y., Fukuda, M., Yamazaki, S., & Fujita, N. (2012) Complete Genome Sequence of Sphingobium sp Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls. Journal of Bacteriology. 194(2): 534-535.
PubMed: 22207743
PMC: PMC3256637

• Masai, E., Katayama, Y., & Fukuda, M. (2007) Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Bioscience, biotechnology, and biochemistry 71(1): 1-15.
PubMed: 17213657

• Masai, E., Katayama, Y., Kawai, S., Nishikawa, S., Yamasaki, M., & Morohoshi, N. (1991) Cloning and sequencing of the gene for a Pseudomonas paucimobilis enzyme that cleaves beta-aryl ether. Journal of bacteriology 173(24): 7950-7955.
PubMed: 1744051
PMC: PMC212589

• Masai, E., Katayama, Y., Nishikawa, S., Yamasaki, M., Morohoshi, N., & Haraguchi, T. (1989) Detection and localization of a new enzyme catalyzing the beta-aryl ether cleavage in the soil bacterium (Pseudomonas paucimobilis SYK-6) FEBS letters 249(2): 348-352.
PubMed: 2737293

• Masai, E., Momose, K., Hara, H., Nishikawa, S., Katayama, Y., & Fukuda, M. (2000) Genetic and Biochemical Characterization of 4-Carboxy-2-Hydroxymuconate-6-Semialdehyde Dehydrogenase and Its Role in the Protocatechuate 4, 5-Cleavage Pathway inSphingomonas paucimobilis SYK-6. Journal of bacteriology 182(23): 6651-6658.
PubMed: 11073908
PMC: PMC111406

• Masai, E., Sasaki, M., Minakawa, Y., Abe, T., Sonoki, T., Miyauchi, K., ... & Fukuda, M. (2004) A novel tetrahydrofolate-dependent O-demethylase gene is essential for growth of Sphingomonas paucimobilis SYK-6 with syringate. Journal of bacteriology 186(9): 2757-2765.
PubMed: 15090517
PMC: PMC387776

• Masai, E., Shinohara, S., Hara, H., Nishikawa, S., Katayama, Y., & Fukuda, M. (1999) Genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of Sphingomonas paucimobilis SYK-6. Journal of bacteriology 181(1): 55-62.
PubMed: 9864312
PMC: PMC103531

• Masai, E., Yamamoto, Y., Inoue, T., Takamura, K., Hara, H., Kasai, D., ... & Fukuda, M. (2007). (2007) Characterization of ligV essential for catabolism of vanillin by Sphingomonas paucimobilis SYK-6. Bioscience, biotechnology, and biochemistry 71(10): 2487-2492.
PubMed: 17928721

• Mathews, S. L., Grunden, A. M., & Pawlak, J. (2016) Degradation of lignocellulose and lignin by Paenibacillus glucanolyticus. International Biodeterioration & Biodegradation, 110: 79-86.
PubMed: 24841577

• Mazzoli, R., Pessione, E., Giuffrida, M. G., Fattori, P., Barello, C., Giunta, C., & Lindley, N. D. (2007) Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures. Archives of microbiology 188(1): 55-68.
PubMed: 17483933

• McCarthy, A. J., & Broda, P. (1984) Screening for lignin-degrading actinomycetes and characterization of their activity against [14C] lignin-labelled wheat lignocellulose. Microbiology 130(11): 2905-2913.

• McLeod, M.P., Warren, R.L., Hsiao, W.W.L., Araki, N., Myhre, M., Fernandes, C., Miyazawa, D., Wong, W., Lillquist, A.L., Wang, D., Dosanjh, M., Hara, H., Petrescu, A., Morin, R.D., Yang, G., Stott, J.M., Schein, J.E., Shin, H., Smailus, D., Siddiqui, A.S., Marra, M.A., Jones, S.J.M., Holt, R., Brinkman, F.S.L., Miyauchi, K., Fukuda, M., Davies, J.E., Mohn, W.W., Eltis, L.D. (2006) The complete genome of Rhodococcus sp RHA1 provides insights into a catabolic powerhouse P Natl Acad Sci USA 103(42): 15582-15587.

• Mechichi, T., Labat, M., Patel, B. K., Woo, T. H., Thomas, P., & Garcia, J. L. (1999) Clostridium methoxybenzovorans sp. nov., a new aromatic o-demethylating homoacetogen from an olive mill wastewater treatment digester. International Journal of Systematic and Evolutionary Microbiology 49(3): 1201-1209.
PubMed: 10425780
PMC: 10.1099/00207713-49-3-1201

• Mechichi, T., Patel, B. K., & Sayadi, S. (2005) Anaerobic degradation of methoxylated aromatic compounds by Clostridium methoxybenzovorans and a nitrate-reducing bacterium Thauera sp. strain Cin3, 4. International biodeterioration & biodegradation 56(4): 224-230.

• Mechichi, T., Stackebrandt, E., Gad'on, N., & Fuchs, G. (2002) Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. Archives of microbiology 178(1): 26-35.

• Michielse, C. B., Reijnen, L., Olivain, C., Alabouvette, C., & Rep, M. (2012) Degradation of aromatic compounds through the beta-ketoadipate pathway is required for pathogenicity of the tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici. Molecular plant pathology 13(9): 1089-1100.
PubMed: 22827542

• Middelhoven, W. J. (1993) Catabolism of benzene compounds by ascomycetous and basidiomycetous yeasts and yeastlike fungi. Antonie van Leeuwenhoek 63.2 : 125-144.
PubMed: 8259830

• Middelhoven, W. J., Coenen, A., Kraakman, B., & Gelpke, M. D. S. (1992) Degradation of some phenols and hydroxybenzoates by the imperfect ascomycetous yeasts Candida parapsilosis and Arxula adeninivorans: evidence for an operative gentisate pathway. Antonie van Leeuwenhoek 62(3): 181-187.
PubMed: 1416914

• Murray, K., Duggleby, C. J., Williams, P. A., & Sala-Trepat, J. M. (1972) The Metabolism of Benzoate and Methylbenzoates via the meta-Cleavage Pathway by Pseudomonas arvilla mt-2. The FEBS Journal 28(3): 301-310.
PubMed: 4342906


• Nakai, C., Kagamiyama, H., Nozaki, M., Nakazawa, T., Inouye, S., Ebina, Y., & Nakazawa, A. (1983) Complete nucleotide sequence of the metapyrocatechase gene on the TOI plasmid of Pseudomonas putida mt-2. Journal of Biological Chemistry 258(5): 2923-2928.
PubMed: 6826546

• Nakamura, T., Ichinose, H., & Wariishi, H. (2012) . Flavin-containing monooxygenases from Phanerochaete chrysosporium responsible for fungal metabolism of phenolic compounds. Biodegradation 23(3): 343-350.
PubMed: 22102096

• Narbad, A., & Gasson, M. J. (1998) Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144(5): 1397-1405.
PubMed: 9611814

• Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A., Fouts D.E., Gill S.R., Pop M., Holmes M., Brinkac L., Beanan M., DeBoy R.T., Daugherty S., Kolonay J., Madupu R., Nelson W., White O., Peterson J., Khouri H., Hance I., Chris Lee P., Holtzapple E., Scanlan D., Tran K., Moazzez A., Utterback T., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N., Düsterhöft A., Tümmler B., Fraser C.M. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 Environmental microbiology 4(12): 799-808.
PubMed: 12534463

• Ni, B., Zhang, Y., Chen, D. W., Wang, B. J., & Liu, S. J. (2013) Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4, 5-cleavage pathway in bacteria. Applied microbiology and biotechnology, 97(13): 6031-6041.
PubMed: 22996279

• Nichols, N. N., & Harwood, C. S. (1997) PcaK, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from Pseudomonas putida. Journal of bacteriology 179(16): 5056-5061.
PubMed: 9260946

• Nikodem, P., Hecht, V., Schlömann, M., & Pieper, D. H. (2003) New bacterial pathway for 4-and 5-chlorosalicylate degradation via 4-chlorocatechol and maleylacetate in Pseudomonas sp. strain MT1. Journal of bacteriology 185(23): 6790-6800.
PubMed: 14617643
PMC: PMC262710

• Nishikawa S., Sonoki T., Kasahara T., Obi T., Kubota S., Kawai S., Morohoshi N., Katayama Y. (1998) Cloning and Sequencing of the Sphingomonas (Pseudomonas) paucimobilis Gene Essential for the O Demethylation of Vanillate and Syringate. Applied and environmental microbiology 64(3): 836-842.
PubMed: 9501423
PMC: PMC106335

• Nishikawa, Y., Yasumi, Y., Noguchi, S., Sakamoto, H., & Nikawa, J. I. (2008) Functional analyses of Pseudomonas putida benzoate transporters expressed in the yeast Saccharomyces cerevisiae. Bioscience, biotechnology, and biochemistry 72(8): 2034-2038.
PubMed: 18685209

• Noda Y., Nishikawa S., Shiozuka K., Kadokura H., Nakajima H., Yoda K., Katayama Y., Morohoshi N., Haraguchi T., Yamasaki M. (1990) Molecular cloning of the protocatechuate 4, 5-dioxygenase genes of Pseudomonas paucimobilis Journal of bacteriology 172(5): 2704-2709.
PubMed: 2185230
PMC: PMC208915

• Nogales, J., Canales, A., Jiménez-Barbero, J., García, J. L., & Díaz, E. (2005) Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440 the prototype of a new subgroup of extradiol dioxygenases. Journal of Biological Chemistry 280(42): 35382-35390.
PubMed: 16030014

• Nogales, J., Canales, A., Jiménez-Barbero, J., Serra, B., Pingarrón, J. M., García, J. L., & Díaz, E. (2011) Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Molecular microbiology 79(2): 359-374.
PubMed: 21219457

• Numata, K., Morisaki, K. (2015) Screening of Marine Bacteria To Synthesize Polyhydroxyalkanoate from Lignin: Contribution of Lignin Derivatives to Biosynthesis by Oceanimonas doudoroffii Acs Sustain Chem Eng 3(4): 569-573.


• Ornston, L. N., & Parke, D. (1976) Properties of an inducible uptake system for beta-ketoadipate in Pseudomonas putida. Journal of bacteriology 125(2): 475-488.
PubMed: 1245464
PMC: PMC236106

• Otani, H., Lee, Y. E., Casabon, I., & Eltis, L. D. (2014) Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium. Journal of bacteriology JB-02247: .
PubMed: 25266382
PMC: PMC4248857

• Overhage, J., Priefert, H. & Steinbüchel, A., (1999) Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. strain HR199. Appl. Environ. Microbiol 65 (11): 4837-4847.
PubMed: 10543794
PMC: PMC91652


• Pérez-Pantoja, D., De la Lglesia, R., Pieper, D. H., & Gonzalez, B. (2008) Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. Fems Microbiology Reviews. 32(5): 736-794.
PubMed: 18691224

• Pérez-Pantoja, D., González, B., & Pieper, D. H. (2010) Aerobic degradation of aromatic hydrocarbons. In: Handbook of hydrocarbon and lipid microbiology. : .

• Périé, F. H., & Gold, M. H. (1991) Manganese regulation of manganese peroxidase expression and lignin degradation by the white rot fungus Dichomitus squalens. Applied and Environmental Microbiology 57(8): 2240-2245.
PubMed: 1768094
PMC: PMC183557

• Pang, C., Li, A., Cui, D., Yang, J., Ma, F., Guo, H. (2016) Complete genome sequence of Klebsiella pneumoniae J1, a protein-based microbial flocculant-producing bacterium J Biotechnol 220: 90-91.
PubMed: 26806487

• Parke, D. (1997) . Acquisition, reorganization, and merger of genes: novel management of the beta-ketoadipate pathway in Agrobacterium tumefaciens. FEMS microbiology letters, 146(1): 3-12.

• Parke, D. & Ornston, L. N. (1986) Enzymes of the beta-ketoadipate pathway are inducible in Rhizobium and Agrobacterium spp. and constitutive in Bradyrhizobium spp. Journal of bacteriology 165(1): 288-292.
PubMed: 3941043
PMC: PMC214402

• Paulsen I.T., Press C.M., Ravel J., Kobayashi D.Y., Myers G.S., Mavrodi D.V., DeBoy R.T., Seshadri R., Ren Q., Madupu R., Dodson R.J., Durkin A.S., Brinkac L.M., Daugherty S.C., Sullivan S.A., Rosovitz M.J., Gwinn M.L., Zhou L., Schneider D.J., Cartinhour S.W., Nelson W.C., Weidman J., Watkins K., Tran K., Khouri H., Pierson E.A., Pierson L.S. III, Thomashow L.S., Loper J.E.. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature biotechnology 23(7): 873-878.
PubMed: 15980861

• Pelz, O., Tesar, M., Wittich, R. M., Moore, E. R., Timmis, K. N., & Abraham, W. R. (1999) Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environmental Microbiology 1(2): 167-174.
PubMed: 11207732

• Peng, X., Masai, E., Kasai, D., Miyauchi, K., Katayama, Y., & Fukuda, M. (2005) A second 5-carboxyvanillate decarboxylase gene, ligW2, is important for lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6. Applied and Environmental Microbiology. 71(9): 5014-5021.

• Perestelo, F., Dalcón, M. A., & de la Fuente, G. (1989) Production of vanillic acid from vanillin by resting cells of Serratia marcescens. Applied and Environmental microbiology 55(6): 1660-1662.
PubMed: 2669632
PMC: PMC202925

• Perestelo, F., Falcón, M. A., Pérez, M. L., Roig, E. C., & de la Fuente Martin, G. (1989) Bioalteration of kraft pine lignin by Bacillus megaterium isolated from compost piles. Journal of fermentation and bioengineering 68(2): 151-153.

• Perestelo, F., Falcon, M. A., & de la Fuente, G. (1990) Biotransformation of kraft lignin fractions by Serratia marcescens. Letters in applied microbiology 10(2): 61-64.

• Perestelo, F., Falcon, M. A., Carnicero, A., Rodríguez, A., & De la Fuente, G. (1994) Limited degradation of industrial, synthetic and natural lignins by Serratia marcescens. Biotechnology Letters 16(3): 299-302.

• Perestelo, F., Rodriguez, A., Perez, R., Carnicero, A., De La Fuente, G., & Falcon, M. A. (1996) Isolation of a bacterium capable of limited degradation of industrial and labelled, natural and synthetic lignins. World Journal of Microbiology and Biotechnology 12(1): 111-112.
PubMed: 24415105

• Pernstich, C., Senior, L., MacInnes, K. A., Forsaith, M., & Curnow, P. (2014) Expression, purification and reconstitution of the 4-hydroxybenzoate transporter PcaK from Acinetobacter sp. ADP1. Protein expression and purification 101: 68-75.
PubMed: 24907408
PMC: PMC4148202

• Poblete-Castro, I., Becker, J., Dohnt, K., dos Santos, V. M., & Wittmann, C. (2012) Industrial biotechnology of Pseudomonas putida and related species. Applied Microbiology and Biotechnology. 93(6): 2279-2290.

• Pometto III, A. L., Sutherland, J. B., & Crawford, D. L. (1981) Streptomyces setonii: catabolism of vanillic acid via guaiacol and catechol. Canadian journal of microbiology 27(6): 636-638.
PubMed: 7260738

• Pometto, A. L., & Crawford, D. L. (1983) Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Applied and environmental microbiology 45(5): 1582-1585.
PubMed: 6870241

• Poyntner, C., Zhang, D., & Margesin, R. (2020 ) Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds Microbial Resource Announcement 2;9(27): e00463-20.
PubMed: 32616634
PMC: PMC7330236

• Providenti, M. A., Mampel, J., MacSween, S., Cook, A. M., & Wyndham, R. C. (2001) Comamonas testosteroni BR6020 possesses a single genetic locus for extradiol cleavage of protocatechuate. Microbiology 147(8): 2157-2167.
PubMed: 11495993

• Providenti, M. A., O'Brien, J. M., Ruff, J., Cook, A. M., & Lambert, I. B. (2006) Metabolism of isovanillate, vanillate, and veratrate by Comamonas testosteroni strain BR6020. Journal of bacteriology 188(11): 3862-3869.
PubMed: 16707678
PMC: PMC1482911


• Qi, S.W., Chaudhry, M.T., Zhang, Y., Meng, B., Huang, Y., Zhao, K.X., Poetsch, A., Jiang, C.Y., Liu, S., Liu, S.J. (2007) Comparative proteomes of Corynebacterium glutamicum grown on aromatic compounds revealed novel proteins involved in aromatic degradation and a clear link between aromatic catabolism and gluconeogenesis via fructose-1, 6-bisphosphatase. Proteomics 7(20): 3775-3787.
PubMed: 17880007


• Rabenhorst, J. (1996) Production of methoxyphenol-type natural aroma chemicals by biotransformation of eugenol with a new Pseudomonas sp. Applied Microbiology and Biotechnology 46(5-6): 470-474.

• Rabus, R., & Widdel, F. (1995) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Archives of microbiology 163(2): 96-103.
PubMed: 7710331

• Raj, A., Chandra, R., Reddy, M. M. K., Purohit, H. J., & Kapley, A. (2007) Biodegradation of kraft lignin by a newly isolated bacterial strain, Aneurinibacillus aneurinilyticus from the sludge of a pulp paper mill. World Journal of Microbiology and Biotechnology 23(6): 793-799.

• Ravi K, García-Hidalgo, J., Nöbel M., Gorwa-Grauslund M.F., Lidén G. (2018) Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea AMB Express 8(1): 32.
PubMed: 29500726
PMC: PMC5834416

• Ravi, K., Abdelaziz, O. Y., Nöbel, M., García-Hidalgo, J., Gorwa-Grauslund, M. F., Hulteberg, C. P., & Lidén, G. (2018) Bacterial conversion of depolymerized Kraft lignin. . Biotechnology for biofuels 11(1): 240.
PubMed: 30202435
PMC: PMC6123935

• Ravi, K., García-Hidalgo, J., Gorwa-Grauslund, M. F., & Lidén, G. (2017) Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost. Applied Microbiology and Biotechnology 101(12): 5059-5070.
PubMed: 28299400
PMC: PMC5486835

• Rhoads, T. L., Mikell Jr, A. T., & Eley, M. H. (1995) Investigation of the lignin-degrading activity of Serratia marcescens: biochemical screening and ultrastructural evidence. Canadian journal of microbiology 41(7): 592-600.
PubMed: 7641141

• Rodríguez, A., Carnicero, A., Perestelo, F., De la Fuente, G., Milstein, O., & Falcón, M. A. (1994) Effect of Penicillium chrysogenum on lignin transformation. Applied and environmental microbiology, 60(8): 2971-2976.
PubMed: 16349361
PMC: PMC201751

• Rodriguez, A., Perestelo, F., Carnicero, A., Regalado, V., Perez, R., De la Fuente, G., & Falcon, M. A. (1996) Degradation of natural lignins and lignocellulosic substrates by soil-inhabiting fungi imperfecti. FEMS Microbiology Ecology 21(3): 213-219.

• Rodriguez, A., Perestelo, F., Carnicero, A., Regalado, V., Perez, R., De la Fuente, G., & Falcon, M. A. (1996). (1996) Degradation of natural lignins and lignocellulosic substrates by soil-inhabiting fungi imperfecti. FEMS microbiology ecology 21(3): 213-219.

• Rodriguez, A., Salvachúa, D., Katahira, R., Black, B. A., Cleveland, N. S., Reed, M., Smith, H., Baidoo, E. E. K, Keasling, J. D, Simmons, B.A., Beckham, G. T., Gladden, J. M. (2017) Base-catalyzed depolymerization of solid lignin-rich streams enables microbial conversion ACS Sustainable Chemistry & Engineering 5(9): 8171-8180.

• Ryazanova, T. V., Chuprova, N. A., & Luneva, T. A. (2015) Effect of Trichoderma fungi on lignin from tree species barks. Catalysis in Industry 7(1): 82-89.

• Rüttimann-Johnson, C., Salas, L., Vicuña, R., & Kirk, T. K. (1993) Extracellular enzyme production and synthetic lignin mineralization by Ceriporiopsis subvermispora. Applied and environmental microbiology 59(6): 1792-1797.
PubMed: 16348955
PMC: PMC182163


• Saha, B. C., Qureshi, N., Kennedy, G. J., & Cotta, M. A. (2016) Biological pretreatment of corn stover with white-rot fungus for improved enzymatic hydrolysis. International Biodeterioration & Biodegradation 109: 29-35.

• Sainsbury, P. D., Hardiman, E. M., Ahmad, M., Otani, H., Seghezzi, N., Eltis, L. D., & Bugg, T. D. (2013) Breaking down lignin to high-value chemicals: the conversion of lignocellulose to vanillin in a gene deletion mutant of Rhodococcus jostii RHA1. ACS chemical biology 8(10): 2151-2156.
PubMed: 23898824

• Saito, Y., Tsuchida, H., Matsumoto, T., Makita, Y., Kawashima, M., Kikuchi, J., & Matsui, M. (2018) Screening of fungi for decomposition of lignin-derived products from Japanese cedar. Journal of bioscience and bioengineering. : .
PubMed: 29853299
PMC: 10.1016/j.jbiosc.2018.05.001

• Salmon, R. C., Cliff, M. J., Rafferty, J. B., & Kelly, D. J. (2013) The CouPSTU and TarPQM Transporters in Rhodopseudomonas palustris: redundant, promiscuous uptake systems for lignin-derived aromatic substrates. PloS One 8(3): e59844.
PubMed: 23555803
PMC: PMC3610893

• Salvachúa, D., Karp, E. M., Nimlos, C. T., Vardon, D. R., & Beckham, G. T. (2015) Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria. Green Chemistry 17(11): 4951-4967.

• Sampaio, J. P. (1995) Utilization of low molecular weight lignin-related aromatic compounds for the selective isolation of yeasts: Rhodotorula vanillica, a new basidiomycetous yeast species. Systematic and applied microbiology 17(4): 613-619.

• Sampaio, J.P. (1999) Utilization of low molecular weight aromatic compounds by heterobasidiomycetous yeasts: taxonomic implications. Canadian journal of microbiology 45(6): 491-512.
PubMed: 10453477

• Sasoh, M., Masai, E., Ishibashi, S., Hara, H., Kamimura, N., Miyauchi, K., & Fukuda, M. (2006) Characterization of the terephthalate degradation genes of Comamonas sp. strain E6. Applied and environmental microbiology, 72(3): 1825-1832.
PubMed: 16517628

• Sato, Y., Nishihara, H., Yoshida, M., Watanabe, M., Rondal, J. D., Concepcion, R. N., & Ohta, H. (2006) Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. International journal of systematic and evolutionary microbiology, 56(5): 973-978.
PubMed: 16627640

• Schink, B., & Pfennig, N. (1982) Fermentation of trihydroxybenzenes by Pelobacter acidigallici gen. nov. sp. nov., a new strictly anaerobic, non-sporeforming bacterium. Archives of Microbiology 133(3): 195-201.

• Sethuraman, A., Akin, D. E., & Eriksson, K. E. (1999) Production of ligninolytic enzymes and synthetic lignin mineralization by the bird's nest fungus Cyathus stercoreus. Applied microbiology and biotechnology 52(5): 689-697.
PubMed: 10570816

• Shen, X. H., Huang, Y., & Liu, S. J. (2005) Genomic analysis and identification of catabolic pathways for aromatic compounds in Corynebacterium glutamicum. Microbes and environments 20(3): 160-167.

• Shen, X. H., Jiang, C. Y., Huang, Y., Liu, Z. P., & Liu, S. J. (2005) Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum. Applied and environmental microbiology 71(7): 3442-3452.
PubMed: 16000747
PMC: PMC1169049

• Shen, X. H., Zhou, N. Y., & Liu, S. J. (2012) Degradation and assimilation of aromatic compounds by Corynebacterium glutamicum: another potential for applications for this bacterium? Applied microbiology and biotechnology 95(1): 77-89.
PubMed: 22588501

• Shettigar M., Balotra S., Cahill D., Warden A.C., Lacey M.J., Kohler H.E., Rentsch D., Oakeshott J.G., Pandey G. (2018 ) Isolation of the (+)-Pinoresinol-Mineralizing Pseudomonas sp. Strain SG-MS2 and Elucidation of Its Catabolic Pathway Appl Environ Microbiol 84(4): pii: e02531-17.
PubMed: 29222099
PMC: PMC5795069

• Shi Y., Chai L., Tang C., Yang Z., Zhang H., Chen R., Chen Y., Zheng Y.. (2013) Characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium Cupriavidus basilensis B-8. Biotechnology for biofuels, 6(1): 1.
PubMed: 23298573
PMC: PMC3560178

• Shi, J., Chinn, M. S., & Sharma-Shivappa, R. R. (2008) Microbial pretreatment of cotton stalks by solid state cultivation of Phanerochaete chrysosporium. Bioresource Technology 99(14): 6556-6564.
PubMed: 18242083

• Shi, Y., Chai, L., Tang, C., Yang, Z., Zheng, Y., Chen, Y., & Jing, Q. (2013) Biochemical investigation of kraft lignin degradation by Pandoraea sp. B-6 isolated from bamboo slips. Bioprocess and biosystems engineering 36(12): 1957-1965.
PubMed: 23877715
PMC: PMC3825317

• Sietmann, R., Hammer, E., Specht, M., Cerniglia, C. E., & Schauer, F. (2001) Novel ring cleavage products in the biotransformation of biphenyl by the yeast Trichosporon mucoides. Applied and environmental microbiology 67(9): 4158-4165.
PubMed: 11526019
PMC: PMC93143

• Sláviková, E., Košíková, B., & Mikulášová, M. (2002) Biotransformation of waste lignin products by the soil-inhabiting yeast Trichosporon pullulans. Canadian journal of microbiology 48(3): 200-203.
PubMed: 11989763

• Smith, M. A., Weaver, V. B., Young, D. M., & Ornston, L. N. (2003) Genes for chlorogenate and hydroxycinnamate catabolism (hca) are linked to functionally related genes in the dca-pca-qui-pob-hca chromosomal cluster of Acinetobacter sp. strain ADP1. Applied and environmental microbiology 69(1): 524-532..
PubMed: 12514037
PMC: PMC152463

• Song, Y. J (2009) Characterization of aromatic hydrocarbon degrading bacteria isolated from pine litter. Korean Journal of Microbiology and Biotechnology 37: 333-339.

• Song, Y. J. (2009) Characterization of aromatic hydrocarbon degrading bacteria isolated from pine litter. Korean J Microbiol Biotechnol 37(4): 333-339.

• Sperfeld, M., Diekert, G., & Studenik, S. (2018) Anaerobic aromatic compound degradation in Sulfuritalea hydrogenivorans sk43H. FEMS microbiology ecology 95(1): fiy199.
PubMed: 30304451
PMC: 10.1093/femsec/fiy199

• Stamler, R. A., Vereecke, D., Zhang, Y., Schilkey, F., Devitt, N., & Randall, J. J. (2016) Complete Genome and Plasmid Sequences for Rhodococcus fascians D188 and Draft Sequences for Rhodococcus Isolates PBTS 1 and PBTS 2. Genome Announcements 4(3): e00495-16.
PubMed: 27284129
PMC: PMC4901220

• Sterjiades, R., Sauret-Ignazi, G., Dardas, A., & Pelmont, J. (1982) Properties of a bacterial strain able to grow on guaiacol. FEMS Microbiology Letters 14(1): 57-60.

• Su F., Hua D., Zhang Z., Wang X., Tang H., Tao F., Tai C., Wu Q., Wu G., Xu P. (2011) Genome sequence of Bacillus pumilus S-1, an efficient isoeugenol-utilizing producer for natural vanillin. Journal of bacteriology 193(22): 6400-6401.
PubMed: 22038964
PMC: PMC3209209

• Sudtachat, N., Ito, N., Itakura, M., Masuda, S., Eda, S., Mitsui, H., Kawaharada, Y. & Minamisawa, K. (2009) Aerobic vanillate degradation and C1 compound metabolism in Bradyrhizobium japonicum. Appl. Environ. Microbiol. 75 (15): 5012-5017.
PubMed: 19502448
PMC: PMC2725485

• Suhaila, Y. N., Rosfarizan, M., Ahmad, S. A., Latif, I. A., & Ariff, A. B. (2013) Nutrients and culture conditions requirements for the degradation of phenol by Rhodococcus UKMP-5M. Journal of environmental biology 34(3): 635.
PubMed: 24617152

• Suman, S. K., Dhawaria, M., Tripathi, D., Raturi, V., Adhikari, D. K., & Kanaujia, P. K. (2016) Investigation of lignin biodegradation by Trabulsiella sp. isolated from termite gut. International Biodeterioration & Biodegradation 112: 12-17.

• Sutherland, J. B. (1986) Demethylation of veratrole by cytochrome P-450 in Streptomyces setonii. Applied and environmental microbiology, 52(1): 98-100.
PubMed: 16347120
PMC: PMC203400

• Sutherland, J. B., Crawford, D. L., & Pometto III, A. L. (1983) Metabolism of cinnamic, p-coumaric, and ferulic acids by Streptomyces setonii. Canadian journal of microbiology 29(10): 1253-1257.

• Szewzyk, R., & Pfennig, N. (1987) Complete oxidation of catechol by the strictly anaerobic sulfate-reducing Desulfobacterium catecholicum sp. nov. Archives of microbiology 147(2): 163-168.


• Tao, F., Zhao, P., Li, Q., Su, F., Yu, B., Ma, C., Tang, H., Tai, C., Wu, G., Xu, P. (2011) Genome sequence of Rhodococcus erythropolis XP, a biodesulfurizing bacterium with industrial potential. Journal of bacteriology 193(22): 6422-6423.
PubMed: 22038975
PMC: PMC3209222

• Taylor, C. R., Hardiman, E. M., Ahmad, M., Sainsbury, P. D., Norris, P. R., & Bugg, T. D. (2012) Isolation of bacterial strains able to metabolize lignin from screening of environmental samples. Journal of applied microbiology 113(3): 521-530.
PubMed: 22642383

• Taylor, W. H., & Juni, E. (1964) PATHWAYS FOR BIOSYNTHESIS OF A BACTERIAL CAPSULAR POLYSACCHARIDE I.: Characterization of the Organism and Polysaccharide1. Journal of bacteriology 81(5): 688.
PubMed: 13775654

• Teramoto, H., Tanaka, H., & Wariishi, H. (2004) Degradation of 4-nitrophenol by the lignin-degrading basidiomycete Phanerochaete chrysosporium. Applied microbiology and biotechnology 66(3): 312-317.
PubMed: 15448939

• Tian, J. H., Pourcher, A. M., & Peu, P. (2016) Isolation of bacterial strains able to metabolize lignin and lignin-related compounds. Letters in applied microbiology 63(1): 30-37.
PubMed: 27125750

• Traunecker, J., Preuß, A., & Diekert, G. (1991) Isolation and characterization of a methyl chloride utilizing, strictly anaerobic bacterium. Archives of microbiology, 156(5): 416-421.

• Trojanowski, J., Haider, K., & Sundman, V. (1977) Decomposition of 14C-labelled lignin and phenols by a Nocardia sp. Archives of Microbiology, 114(2): 149-153.
PubMed: 907426

• Tschech, A., & Fuchs, G. (1987) Anaerobic degradation of phenol by pure cultures of newly isolated denitrifying pseudomonads. Archives of Microbiology 148(3): 213-217.
PubMed: 3675113

• Tschech, A., & Pfennig, N. (1984) Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Archives of Microbiology 137(2): 163-167.

• Tsegaye, B., Balomajumder, C., & Roy, P. (2018) Biodelignification and hydrolysis of rice straw by novel bacteria isolated from wood feeding termite. 3 Biotech 8(10): 447.
PubMed: 30333949

• Tumen-Velasquez, M., Johnson, C. W., Ahmed, A., Dominick, G., Fulk, E. M., Khanna, P., Lee S.A., Schmidt A.L., Linger J.G., Eiteman M.A., Beckham G.T., Neidle E.L. (2018) Accelerating pathway evolution by increasing the gene dosage of chromosomal segments. Proceedings of the National Academy of Sciences 201803745: .
PubMed: 29915086
PMC: PMC6142232


• Udayasoorian, C., & Prabu, P. C. (2005) Biodegradation of phenols by ligninolytic fungus Trametes versicolor. J. Biol. Sci 5(5): 558-561.


• Van Dexter, S., & Boopathy, R. (2018) Biodegradation of phenol by Acinetobacter tandoii isolated from the gut of the termite. Environmental Science and Pollution Research, 1-6.: .
PubMed: 30264343

• Vares, T., Niemenmaa, O., & Hatakka, A. (1994) Secretion of ligninolytic enzymes and mineralization of 14C-ring-labelled synthetic lignin by three Phlebia tremellosa strains. Applied and environmental microbiology 60(2): 569-575.
PubMed: 16349186
PMC: PMC201350

• Vasudevan, N., & Mahadevan, A. (1992) Utilization of complex phenolic compounds by Acinetobacter sp. Applied microbiology and biotechnology 37(3): 404-407.


• Wang, J., Gao, Q., & Bao, J. (2016) Genome sequence of Trichosporon cutaneum ACCC 20271: An oleaginous yeast with excellent lignocellulose derived inhibitor tolerance. Journal of biotechnology 228: 50-51.
PubMed: 27130500

• Wang, S. H., Xu, Y., Liu, S. J., & Zhou, N. Y. (2011) Conserved residues in the aromatic acid/H+ symporter family are important for benzoate uptake by NCgl2325 in Corynebacterium glutamicum. International biodeterioration & biodegradation 65(3): 527-532.

• Watanabe, Y., Shinzato, N., & Fukatsu, T. (2003) Isolation of actinomycetes from termites' guts. Bioscience, biotechnology, and biochemistry 67(8): 1797-1801.
PubMed: 12951516

• Wei, Z., Zeng, G., Huang, F., Kosa, M., Huang, D., & Ragauskas, A. J. (2015) Bioconversion of oxygen-pretreated Kraft lignin to microbial lipid with oleaginous Rhodococcus opacus DSM 1069. Green Chemistry, 17(5): 2784-2789.

• Wells, T., Wei, Z., & Ragauskas, A. (2015) Bioconversion of lignocellulosic pretreatment effluent via oleaginous Rhodococcus opacus DSM 1069. Biomass and bioenergy 72: 200-205.

• White-Stevens, R. H., & Kamin, H. (1972) Studies of a flavoprotein, salicylate hydroxylase I. Preparation, properties, and the uncoupling of oxygen reduction from hydroxylation. Journal of Biological Chemistry 247(8): 2358-2370.

• Williams, P. A., & Shaw, L. E. (1997) mucK, a gene in Acinetobacter calcoaceticus ADP1 (BD413), encodes the ability to grow on exogenous cis, cis-muconate as the sole carbon source. Journal of bacteriology 179(18): 5935-5942.
PubMed: 9294455
PMC: PMC179487

• Woo, H. L., Ballor, N. R., Hazen, T. C., Fortney, J. L., Simmons, B., Davenport, K. W., ... & Woyke, T. (2014) Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. . Standards in genomic sciences 9(1) : 19.
PubMed: 25566348
PMC: PMC4273726

• Woo, H. L., Utturkar, S., Klingeman, D., Simmons, B. A., DeAngelis, K. M., Brown, S. D., & Hazen, T. C. (2014) Draft genome sequence of the lignin-degrading Burkholderia sp. strain LIG30, isolated from wet tropical forest soil. Genome announcements 2(3): e00637-14.
PubMed: 24948777
PMC: PMC4064042

• Wöhlbrand, L., Kallerhoff, B., Lange, D., Hufnagel, P., Thiermann, J., Reinhardt, R., & Rabus, R. (2007) Functional proteomic view of metabolic regulation in “Aromatoleum aromaticum” strain EbN1. Proteomics 7(13): 2222-2239.
PubMed: 17549795


• Xiong, X. Q., Liao, H. D., Ma, J. S., Liu, X. M., Zhang, L. Y., Shi, X. W., ... & Zhu, Y. H. (2014) Isolation of a rice endophytic bacterium, Pantoea sp. Sd-1, with ligninolytic activity and characterization of its rice straw degradation ability. Letters in applied microbiology 58(2): 123-129.
PubMed: 24111687

• Xu, C., Ma, F., & Zhang, X. (2009) Xu, C., Ma, F., & Zhang, X. (2009). Lignocellulose degradation and enzyme production by Irpex lacteus CD2 during solid-state fermentation of corn stover. Journal of bioscience and bioengineering 108(5): 372-375.
PubMed: 19804859

• Xu, Y., Gao, X., Wang, S. H., Liu, H., Williams, P. A., & Zhou, N. Y. (2012) MhbT is a specific transporter for 3-hydroxybenzoate uptake by Gram-negative bacteria. Applied and environmental microbiology, AEM-01511.: .
PubMed: 22729544
PMC: PMC3416623

• Xu, Y., Yan, D. Z., & Zhou, N. Y. (2006) Heterologous expression and localization of gentisate transporter Ncg12922 from Corynebacterium glutamicum ATCC 13032. Biochemical and biophysical research communications 346(2): 555-561.
PubMed: 16765316

• Xu, Z., Qin, L., Cai, M., Hua, W., & Jin, M. (2018) Biodegradation of kraft lignin by newly isolated Klebsiella pneumoniae, Pseudomonas putida, and Ochrobactrum tritici strains. Environmental Science and Pollution Research 25(14): 14171-14181.
PubMed: 29524172


• Yaegashi J., Kirby J., Ito M., Sun J., Dutta T., Mirsiaghi M., Sundstrom E.R., Rodriguez A., Baidoo E., Tanjore D., Pray T., Sale K., Singh S., Keasling J.D., Simmons B.A., Singer S.W., Magnuson J.K., Arkin A.P., Skerker J.M., Gladden J.M. (2017) Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnol Biofuels. 10: 241.
PubMed: 29075325
PMC: PMC5651578

• Yaguchi A1, Robinson A1, Mihealsick E1, Blenner M2. (2017) Metabolism of aromatics by Trichosporon oleaginosus while remaining oleaginous. Microb Cell Fact 16(1): 206.
PubMed: 29149902
PMC: PMC5693591

• Yang, C. X., Wang, T., Gao, L. N., Yin, H. J., & Lü, X. (2017) Isolation identification and characterization of lignin-degrading bacteria from Qinling, China Journal of applied microbiology 123(6): 1447-1460.

• Yang, Y. F., Zhang, J. J., Wang, S. H., & Zhou, N. Y. (2010) Purification and characterization of the ncg12932-encoded 3-hydroxybenzoate 6-hydroxylase from Corynebacterium glutamicum Journal of basic microbiology, 50(6): 599-604.
PubMed: 20806251

• Yang, Y. S., Zhou, J. T., Lu, H., Yuan, Y. L., & Zhao, L. H. (2012) Isolation and characterization of Streptomyces spp. strains F-6 and F-7 capable of decomposing alkali lignin. Environmental technology 33(23): 2603-2609.
PubMed: 23437660

• Yang, Y. S., Zhou, J. T., Lu, H., Yuan, Y. L., & Zhao, L. H. (2011) Isolation and characterization of a fungus Aspergillus sp. strain F-3 capable of degrading alkali lignin. Biodegradation 22(5): 1017-1027.
PubMed: 21350882

• Yoshida, T., Inami, Y., Matsui, T., & Nagasawa, T. (2010) Regioselective carboxylation of catechol by 3, 4-dihydroxybenzoate decarboxylase of Enterobacter cloacae P. Biotechnology letters 32(5): 701-705.
PubMed: 20131080

• Young M., Artsatbanov V., Beller H.R., Chandra G., Chater K.F., Dover L.G., Goh E.B., Kahan T., Kaprelyants A.S., Kyrpides N., Lapidus A., Lowry S.R., Lykidis A., Mahillon J., Markowitz V., Mavromatis K., Mukamolova G.V., Oren A., Rokem J.S., Smith M.C., Young D.I., Greenblatt C.L. (2010) Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium. Journal of bacteriology 192(3): 841-860.
PubMed: 19948807
PMC: PMC2812450


• Zeida, M., Wieser, M., Yoshida, T., Sugio, T., & Nagasawa, T. (1998) Purification and characterization of gallic acid decarboxylase from Pantoea agglomerans T71. Applied and environmental microbiology 64(12): 4743-4747.
PubMed: 9835557
PMC: PMC90917

• Zeng, J., Singh, D., Laskar, D. D., & Chen, S (2013) Degradation of native wheat straw lignin by Streptomyces viridosporus T7A. International Journal of Environmental Science and Technology 10(1): 165-174.

• Zhao L., Cao G.L., Wang A.J., Ren H.Y., Dong D., Liu Z.N., Guan X.Y., Xu C.J., Ren N.Q. (2012) Fungal pretreatment of cornstalk with Phanerochaete chrysosporium for enhancing enzymatic saccharification and hydrogen production. Bioresource technology 114: 365-369.
PubMed: 22516249

• Zhu, D., Tanabe, S. H., Xie, C., Honda, D., Sun, J., & Ai, L. (2014) Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea. International journal of systematic and evolutionary microbiology 64(5): 1712-1717.
PubMed: 24554634

• Zhu, D., Zhang, P., Xie, C., Zhang, W., Sun, J., Qian, W. J., & Yang, B. (2017) Biodegradation of alkaline lignin by Bacillus ligniniphilus L1. Biotechnology for biofuels, 10(1): 44.
PubMed: 28239416
PMC: PMC5320714