Isolation and characterization of lignin‐degrading bacteria from rainforest soils

Huang, Xing‐Feng; Santhanam, Navaneetha; Badri, Dayakar V.; Hunter, William J.; Manter, Daniel K.; Decker, Stephen R.; Vivanco, Jorge M.; Reardon, Kenneth F.

doi:10.1002/bit.24833

Cited by 148 publications

(130 citation statements)

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“…ISTKB was higher than the earlier reported activity for bacterial consortia (Chandra and Singh 2012). Although, intracellular laccase production in bacteria has been reported earlier (Huang et al 2013), the production of intracellular laccase in Pandoraea sp. is being reported for the first time in this study.…”

Section: Oxidative Ligninolytic Enzyme Assaycontrasting

confidence: 51%

Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Kumar

Singh

et al. 2015

Environ Sci Pollut Res

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The present study investigates the kraft lignin (KL) degrading potential of novel alkalotolerant Pandoraea sp. ISTKB utilizing KL as sole carbon source. The results displayed 50.2 % reduction in chemical oxygen demand (COD) and 41.1 % decolorization after bacterial treatment. The maximum lignin peroxidase (LiP) and manganese peroxidase (MnP) activity detected was 2.73 and 4.33 U ml(-1), respectively, on day 3. The maximum extracellular and intracellular laccase activities observed were 1.32 U ml(-1) on day 5 and 4.53 U ml(-1) on day 4, respectively. The decolorization and degradation was maximum on day 2. Further, it registered an increase with the production of extracellular laccase. This unusual trend of decolorization and degradation was studied using various aromatic compounds and dyes. SEM and FTIR results indicated significant change in surface morphology and functional group composition during the course of degradation. Gas chromatography and mass spectroscopy (GC-MS) analysis confirmed KL degradation by emergence of new peaks and the identification of low molecular weight aromatic intermediates in treated sample. The degradation of KL progressed through the generation of phenolic intermediates. The identified intermediates implied the degradation of hydroxyphenyl, ferulic acid, guaiacyl, syringyl, phenylcoumarane, and pinoresinol components commonly found in lignin. The degradation, decolorization, and GC-MS analysis indicated potential application of the isolate Pandoraea sp. ISTKB in treatment of lignin-containing pollutants and KL valorization.

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Section: Oxidative Ligninolytic Enzyme Assaycontrasting

confidence: 51%

Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Kumar

Singh

et al. 2015

Environ Sci Pollut Res

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“…For one, the products of SCF1 anaerobic lignin reduction remain unclear. These products could include phenolic aldehyde, acid, or ketone monomers that are observed to be released during alkaline CuO oxidation (Thevenot et al, 2010), or any of the catabolic pathway intermediates that have observed during anaerobic lignin degradation of other bacteria, such as the catabolic pathways described for degradation of lignin and lignin-derived compounds in S. paucimobilis SYK-6 (Masai et al, 2007) and others (Harwood and Parales, 1996; DeRito et al, 2005; McLeod et al, 2006; Bugg et al, 2011b; Huang et al, 2013). The use of lignin dimers or model lignin compounds such as artificial or naturally occurring aromatics would permit measurement of specific rates of degradation of specific bonds present in lignin (Kato et al, 1998; Koga et al, 1999; Chang, 2008).…”

Section: Resultsmentioning

confidence: 99%

“…Known potential lignin-degrading bacteria are in the groups α-proteobacteria, γ-proteobacteria, Firmicutes and Actinomycetes (Bugg et al, 2011b) and most bacteria employ extracellular peroxidases, which require oxygen availability (Bugg et al, 2011a). For example, the novel isolates in the phylum Firmicutes Bacillus pumilus strain C6 and Bacillus atrophaeus strain B7 were identified to have very high laccase activity as well as the ability to aerobically degrade Kraft lignin and the lignin model dimer guaiacylglycerol-b-guaiacyl ether (Huang et al, 2013). Many bacterial processes have been successfully engineered into consolidated bioprocessing for biofuels, such as cellulose conversion to sugars (saccharification) and ionic liquid pretreatment tolerance (Blanch et al, 2008; Lee et al, 2008; Singh et al, 2009), with an emerging role for bacterial lignin degradation (Bugg et al, 2011b).…”

Section: Introductionmentioning

confidence: 99%

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

DeAngelis¹,

Sharma²,

Varney³

et al. 2013

Front. Microbiol.

101

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Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.

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“…B-9, which was isolated from eroded bamboo slips, was found able to degrade kraft lignin to low molecular weight compounds and use these as the sole source of carbon (Chen et al 2012). In another study, 140 bacterial strains were isolated from soil of a rainforest rich in biodiversity, and Bacillus pumilus as well as Bacillus atrophaeus were shown capable of degrading kraft lignin and lignin model dimers (Huang et al 2013). Amycolatopsis sp., Pseudomonas putida strains, Acinetobacter ADP1, and Rhodococcus jostii were found able to depolymerize high molecular weight lignins and also catabolize a wide variety of low molecular weight lignin aromatics (Salvachúa et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost

Ravi

García-Hidalgo

Gorwa-Grauslund

et al. 2017

Appl Microbiol Biotechnol

101

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Starting from mature vegetable compost, four bacterial strains were selected using a lignin-rich medium. 16S ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. for three out of four isolates. Further characterization of growth on mixtures of six selected lignin model compounds (vanillin, vanillate, 4-hydroxybenzoate, p-coumarate, benzoate, and ferulate) was carried out with three of the Pseudomonas isolates and in addition with the strain Pseudomonas putida KT2440 from a culture collection. The specific growth rates on benzoate, p-coumarate, and 4-hydroxybenzoate were considerably higher (0.26–0.27 h−1) than those on ferulate and vanillate (0.21 and 0.22 h−1), as were the uptake rates. There was no direct growth of P. putida KT2440 on vanillin, but instead, vanillin was rapidly converted into vanillate at a rate of 4.87 mmol (gCDW h)−1 after which the accumulated vanillate was taken up. The growth curve reflected a diauxic growth when mixtures of the model compounds were used as carbon source. Vanillin, 4-hydroxybenzoate, and benzoate were preferentially consumed first, whereas ferulate was always the last substrate to be taken in. These results contribute to a better understanding of the aromatic metabolism of P. putida in terms of growth and uptake rates, which will be helpful for the utilization of these bacteria as cell factories for upgrading lignin-derived mixtures of aromatic molecules.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-017-8211-y) contains supplementary material, which is available to authorized users.

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Isolation and characterization of lignin‐degrading bacteria from rainforest soils

Cited by 148 publications

References 100 publications

Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Investigating the degradation process of kraft lignin by β-proteobacterium, Pandoraea sp. ISTKB

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost

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