Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

• Published in: Applied microbiology and biotechnology Vol. 98; no. 23; pp. 9527 - 9544
• Main Authors: Tian, Jiang-Hao, Pourcher, Anne-Marie, Bouchez, Théodore, Gelhaye, Eric, Peu, Pascal
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.12.2014; Springer Berlin Heidelberg; Springer; Springer Nature B.V; Springer Verlag
• Subjects: Analysis; Archaea - classification; Archaea - genetics; Archaea - metabolism; Bacteria - classification; Bacteria - genetics; Bacteria - metabolism; Biodegradation; Biodiesel fuels; Biogas; Bioinformatics; biomass; Biomedical and Life Sciences; biopulping; Biotechnology; Biotransformation; Carbon; Cluster Analysis; Culture; Decomposition; Degradation; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Enzymes; Genetic aspects; Genotype; Hydrolysis; Life Sciences; Lignin; Lignin - metabolism; Lignocellulose; Microbial Genetics and Genomics; Microbiology; Microorganisms; Mini-Review; Molecular weight; nucleotide sequences; Phenotype; Phylogenetics; Phylogeny; Physiological aspects; Polymers; Prokaryotes; prokaryotic cells; ribosomal DNA; RNA, Ribosomal, 16S - genetics; Screening; Sequence Analysis, DNA; Studies; France; Degradation; Culture-independent; Lignin; Screening; Culture-dependent; Prokaryotes; Phylogenetic distribution; POLYCYCLIC AROMATIC-HYDROCARBONS; KRAFT LIGNIN; BIOCHEMICAL-CHARACTERIZATION; RHODOCOCCUS-JOSTII RHA1; MODEL COMPOUNDS; MICROBIAL-DEGRADATION; LIGNOCELLULOSE-DEGRADING ENZYMES; PHANEROCHAETE-CHRYSOSPORIUM; SPHINGOMONAS-PAUCIMOBILIS SYK-6; GEOBACTER-METALLIREDUCENS
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-014-6142-4

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.