Draft Genome Sequence of
            <i>Coniochaeta ligniaria</i>
            NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates

Jiménez, Diego Javier; Hector, Ronald E.; Riley, Robert; Lipzen, Anna; Kuo, Rita C.; Amirebrahimi, Mojgan; Barry, Kerrie; Grigoriev, Igor V.; Elsas, Jan Dirk van; Nichols, Nancy N.

doi:10.1128/genomea.01476-16

Cited by 18 publications

(10 citation statements)

References 16 publications

(15 reference statements)

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“…Overall, the three isolated Coniochaeta species were among the best enzyme producers in this study, producing relatively high levels of all four enzymes. Recent draft genome sequences of several of these wood rot fungi have revealed their large arsenal of genes for biomassdegradation, including genes encoding novel lignindegrading enzymes [82,83]. The cultured strains are now a resource for mining new lignocellulosic modifying enzymes.…”

Section: Discussionmentioning

confidence: 99%

“…In the selective culturing some isolates of the same species were cultured under more than one condition (Additional file 1). For example, strains most similar to Thielavia terrestris (RP40, 41,43,44,45,54,76,77,78,80,81,83) were cultured at 50°C, on CMC, xylan and guaiacol. While most of the partial 16S or ITS sequences of the cultured strains were 99-100% identical to a sequence of a known species in the databases, some showed slightly less similarity (Additional file 1).…”

Section: Bagasse Sampling and Analysismentioning

confidence: 99%

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A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

et al. 2020

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Background: Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. Results: Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. Conclusions: A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.

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Section: Discussionmentioning

confidence: 99%

Section: Bagasse Sampling and Analysismentioning

confidence: 99%

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

et al. 2020

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“…Recently, the first genome sequence of C. ligniaria 30616 was revealed that contained 1070 oxidoreductase, 926 dehydrogenases, 227 decarboxylases, and 23 genes related to oxidative stress. These findings have a strong potential to be applied to genetic and metabolic engineering [ 153 ].…”

Section: Strategies To Cope With Inhibition Issuesmentioning

confidence: 99%

Physico-Chemical Conversion of Lignocellulose: Inhibitor Effects and Detoxification Strategies: A Mini Review

2018

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A pretreatment of lignocellulosic biomass to produce biofuels, polymers, and other chemicals plays a vital role in the biochemical conversion process toward disrupting the closely associated structures of the cellulose-hemicellulose-lignin molecules. Various pretreatment steps alter the chemical/physical structure of lignocellulosic materials by solubilizing hemicellulose and/or lignin, decreasing the particle sizes of substrate and the crystalline portions of cellulose, and increasing the surface area of biomass. These modifications enhance the hydrolysis of cellulose by increasing accessibilities of acids or enzymes onto the surface of cellulose. However, lignocellulose-derived byproducts, which can inhibit and/or deactivate enzyme and microbial biocatalysts, are formed, including furan derivatives, lignin-derived phenolics, and carboxylic acids. These generation of compounds during pretreatment with inhibitory effects can lead to negative effects on subsequent steps in sugar flat-form processes. A number of physico-chemical pretreatment methods such as steam explosion, ammonia fiber explosion (AFEX), and liquid hot water (LHW) have been suggested and developed for minimizing formation of inhibitory compounds and alleviating their effects on ethanol production processes. This work reviews the physico-chemical pretreatment methods used for various biomass sources, formation of lignocellulose-derived inhibitors, and their contributions to enzymatic hydrolysis and microbial activities. Furthermore, we provide an overview of the current strategies to alleviate inhibitory compounds present in the hydrolysates or slurries.

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“…There are many fungi present in the upper layer, like Tetraploa (HdV-89), a mold on plant leaves, Coniochaeta cf. lignaria (HdV-172), an ascomycete that can decompose lignocellulosic material [59], Microthyrium (HdV-8b), another ascomycete, and further fungal remains (EMA-160, HdV-124). Probably, the fungi in this (periodically) oxic layer are instrumental in decomposing the aboveground litter, including leaf sheaths.…”

Section: Site Developmentmentioning

confidence: 99%

Roots, Tissues, Cells and Fragments—How to Characterize Peat from Drained and Rewetted Fens

2020

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We present analyses of macroscopic and microscopic remains as a tool to characterise sedge fen peats. We use it to describe peat composition and stages of peat decomposition, to assess the success of rewetting of a formerly drained fen, and to understand the workings of these novel ecosystems. We studied two percolation fen sites, one drained and one drained and rewetted 20 years ago. Years of deep drainage have resulted in a layer of strongly decomposed peat which lacks recognizable macro-remains. We could associate micro-remains with macro-remains, and thus still characterise the peat and the plants that once formed it. We show that the strongly decomposed peat is of the same origin as the slightly decomposed peat below, and that is was ploughed. We present descriptions of eight types of the main constituent of sedge peat: plant roots, including Carex rostrata type, C. lasiocarpa/rostrata type, C. limosa type, C. acutiformis type, C. echinata type, Phragmites australis type, Cladium type, Equisetum type. We describe three new non-pollen palynomorph types (microscopic remains) and five new subtypes. The rewetted fen provides insights into plant succession after rewetting and the formation of peat that predominantly consists of roots. Results indicate that leaf sheaths may be a consistent component of the peat.

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Draft Genome Sequence of Coniochaeta ligniaria NRRL 30616, a Lignocellulolytic Fungus for Bioabatement of Inhibitors in Plant Biomass Hydrolysates

Cited by 18 publications

References 16 publications

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

Physico-Chemical Conversion of Lignocellulose: Inhibitor Effects and Detoxification Strategies: A Mini Review

Roots, Tissues, Cells and Fragments—How to Characterize Peat from Drained and Rewetted Fens

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