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Kato, Kinya; Kozaki, Shinya; Sakuranaga, Masanori

doi:10.1023/a:1005432027603

Cited by 41 publications

(15 citation statements)

References 10 publications

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“…; Table S1 in Supplementary Material). These versatile taxa responded mostly to sucrose, lignin, and tannin–protein and this agrees with previous studies that demonstrated either an ability to metabolize lignin/lignin monomers (Krishna and Sunil, 1993; Nigel et al, 1995; Kato et al, 1998; Mitsui et al, 2003) or presence of lignin peroxidase gene homologs (in the case of Acidovorax avenae ). Many Rhodocyclales (including Azoarcus and Thauera spp.)…”

Section: Discussionsupporting

confidence: 91%

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

Goldfarb¹,

Karaöz²,

Hanson³

et al. 2011

Front. Microbio.

496

355

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Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin–protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

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Section: Discussionsupporting

confidence: 91%

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

Goldfarb¹,

Karaöz²,

Hanson³

et al. 2011

Front. Microbio.

496

355

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“…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). However, dissimilatory reduction of the complex heteropolymer lignin might result in increased saturation of bonds or hydrolysis of end groups, which would not result in production small molecules.…”

Section: Resultsmentioning

confidence: 99%

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

DeAngelis¹,

Sharma²,

Varney³

et al. 2013

Front. Microbiol.

105

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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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“…CCA53. Several Burkholderia species, including B. cepacia KK01 [40] and Burkholderia sp. LIG30 [41] also have a capacity to degrade lignin.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of Burkholderia multivorans CCA53

et al. 2017

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ObjectiveA lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53.ResultsMultilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

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Cited by 41 publications

References 10 publications

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

Identification and characterization of Burkholderia multivorans CCA53

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