Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia

Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

doi:10.1007/s00253-013-4699-y

Cited by 62 publications

(47 citation statements)

References 39 publications

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“…Thus, DNA-based high-throughput sequencing techniques have been recently applied to lignocellulolytic consortia [20,21]. The studies performed so far have, however, only addressed the role of bacteria, to the exclusion of fungal players.…”

Section: Introductionmentioning

confidence: 99%

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

Jiménez

Dini‐Andreote

Elsas

2014

Biotechnol Biofuels

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BackgroundMixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures.ResultsIn order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith’s phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions.ConclusionIn an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass.

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Section: Introductionmentioning

confidence: 99%

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

Jiménez

Dini‐Andreote

Elsas

2014

Biotechnol Biofuels

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“…Different techniques, including functional-based and sequence-based gene identification and direct highthroughput pyrosequencing have been used to explore environmental metagenomes and reveal complex structures of microbial assemblages in various ecosystems related to plant biomass decomposition (8,9). These approaches have been used to identify a number of genes encoding various novel lignocellulose degrading enzymes from termite gut (10,11), cow rumen (12), compost (13), and symbiotic microbial consortia (14). A number of them show desirable properties for industrial applications such as alkaliphilic xylanases for pulp bio-bleaching (10).…”

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Identification of glycosyl hydrolases from a metagenomic library of microflora in sugarcane bagasse collection site and their cooperative action on cellulose degradation

Kanokratana

Eurwilaichitr

Pootanakit

et al. 2015

Journal of Bioscience and Bioengineering

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“…8 Enzyme activity proles and specicities of the cellulolytic consortia were found to be inuenced by the physical and chemical nature of the target substrates. 9 The use of lignocellulolytic microbial consortia (LMCs) to enhance the digestibility of lignocelluloses in the AD of ber-rich cellulosic substrates (such as cassava residues, swine manure and paper wastes), has been reported. [10][11][12] This resulted in a varying degree of enhancement on the rate and yield of biogas production, which were related to the higher removal efficiencies of cellulose and hemicelluloses in the substrates.…”

Section: -7mentioning

confidence: 99%

“…29 The enrichment of Clostridium has been reported in various LMCs isolated from cellulolytic seed cultures from different sources. 9 Tepidimicrobium sp. has been reported for the production of a xylanolytic multi-enzyme complex with efficient capability regarding the degradation of hemicelluloses.…”

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Structural and metabolic adaptation of cellulolytic microcosm in co-digested Napier grass-swine manure and its application in enhancing thermophilic biogas production

et al. 2018

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Biogas production from cellulosic wastes has received increasing attention. However, its efficiency is limited by the recalcitrant nature of plant cell wall materials. In this study, an active and structurally stable lignocellulolytic microcosm (PLMC) was isolated from seed culture in sugarcane bagasse compost by successive enrichment on Napier grass supplemented with swine manure, which is a mixture of highly fibrous co-digested waste under septic conditions. Tagged 16S rRNA gene sequencing on an Ion PGM platform revealed the adaptive merging of microorganisms in the co-digested substrates resulting in a stable symbiotic consortium comprising anaerobic cellulolytic clostridia stably co-existing with facultative (hemi)cellulolytic bacteria in the background of native microflora in the substrates.Ethanoligenens, Tepidimicrobium, Clostridium, Coprococcus, and Ruminococcus were the most predominant taxonomic groups comprising 72.82% of the total community. The remarkable enrichment of catabolic genes encoding for endo-cellulases and hemicellulases, both of which are key accessory enzymes in PLMC, was predicted by PICRUSt. PLMC was capable of degrading 43.6% g VS and 36.8% g VSS of the co-digested substrates within 7 days at 55 C. Inoculation of the microcosm to batch thermophilic anaerobic digestion containing both substrates led to a 36.6% increase in methane yield along with an increase in cellulose removal efficiency. This study demonstrated structural and metabolic adaptation of the cellulolytic microcosms isolated in the background of native microflora from the codigested wastes and its potent application in the enhancement of anaerobic digestion efficiency.

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Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia

Cited by 62 publications

References 39 publications

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

Identification of glycosyl hydrolases from a metagenomic library of microflora in sugarcane bagasse collection site and their cooperative action on cellulose degradation

Structural and metabolic adaptation of cellulolytic microcosm in co-digested Napier grass-swine manure and its application in enhancing thermophilic biogas production

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