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Microorganisms
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Biomass Deconstruction
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Biomass Deconstruction

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 17391

Special Issue Editor

Prof. Dr. Renaud Berlemont

E-Mail Website
Guest Editor
Department of Biological Sciences, California StateUniversity-Long Beach, 1250 Bellflower Blvd., Long Beach, CA 90840-9502, USA
Interests: microbial genomics; microbiome; plant biomass deconstruction; glycoside hydrolase; nutrient cycling; bioinformatics

Special Issue Information

Dear Colleagues,

Biomass Deconstruction by microbes, across environments, is essential to support ecosystem functioning. In the gut, in the soil, in aquatic ecosystems, and in extreme environments, microbes produce enzymatic systems for efficient biomass deconstruction. The precise understanding of how microbes deconstruct biomass is a prerequisite (i) to elucidate the functioning of the dynamic and changing Earth ecosystems and (ii) to develop new sustainable biotechnologies.

Understanding biomass deconstruction by microbes is a complex task and requires combined effort from many fields, including structural biology, enzymology, (meta)genomics, and microbial ecology, among others. In this context, I believe it is the right to publish a Special Issue on Biomass Deconstruction to include cutting-edge research papers and review manuscripts in this scientifically exciting and challenging field.

Prof. Dr. Renaud Berlemont
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (5 papers)

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Research

18 pages, 6891 KiB  
Article
Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics
by Bruno Weiss, Anna Carolina Oliveira Souza, Milena Tavares Lima Constancio, Danillo Oliveira Alvarenga, Victor S. Pylro, Lucia M. Carareto Alves and Alessandro M. Varani
Microorganisms 2021, 9(5), 995; https://doi.org/10.3390/microorganisms9050995 - 05 May 2021
Cited by 12 | Viewed by 3179
Abstract
Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in [...] Read more.
Second-generation biofuel production is in high demand, but lignocellulosic biomass’ complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber’s appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium. Full article
(This article belongs to the Special Issue Biomass Deconstruction)
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13 pages, 1451 KiB  
Article
Characterizing Fungal Decay of Beech Wood: Potential for Biotechnological Applications
by Ehsan Bari, Katie Ohno, Nural Yilgor, Adya P. Singh, Jeffrey J. Morrell, Antonio Pizzi, Mohammad Ali Tajick Ghanbary and Javier Ribera
Microorganisms 2021, 9(2), 247; https://doi.org/10.3390/microorganisms9020247 - 26 Jan 2021
Cited by 15 | Viewed by 2674
Abstract
The biotechnological potential of nine decay fungi collected from stored beech logs at a pulp and paper factory yard in Northern Iran was investigated. Beech blocks exposed to the fungi in a laboratory decay test were used to study changes in cell wall [...] Read more.
The biotechnological potential of nine decay fungi collected from stored beech logs at a pulp and paper factory yard in Northern Iran was investigated. Beech blocks exposed to the fungi in a laboratory decay test were used to study changes in cell wall chemistry using both wet chemistry and spectroscopic methods. Pleurotus ostreatus, P. pulmonarius, and Lentinus sajor-caju caused greater lignin breakdown compared to other white-rot fungi, which led to a 28% reduction in refining energy. Trametesversicolor caused the greatest glucan loss, while P. ostreatus and L. sajor-caju were associated with the lowest losses of this sugar. Fourier transform infrared spectroscopy (FTIR) analyses indicated that white-rot fungi caused greater lignin degradation in the cell walls via the oxidation aromatic rings, confirming the chemical analysis. The rate of cellulose and lignin degradation by the T.versicolor and Pleurotus species was high compared to the other decay fungi analyzed in this study. Based on the above information, we propose that, among the fungi tested, P. ostreatus (27.42% lignin loss and 1.58% cellulose loss) and L. sajor-caju (29.92% lignin loss and 5.95% cellulose loss) have the greatest potential for biopulping. Full article
(This article belongs to the Special Issue Biomass Deconstruction)
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20 pages, 7469 KiB  
Article
Comparison of the Decay Behavior of Two White-Rot Fungi in Relation to Wood Type and Exposure Conditions
by Ehsan Bari, Geoffrey Daniel, Nural Yilgor, Jong Sik Kim, Mohammad Ali Tajick-Ghanbary, Adya P. Singh and Javier Ribera
Microorganisms 2020, 8(12), 1931; https://doi.org/10.3390/microorganisms8121931 - 04 Dec 2020
Cited by 39 | Viewed by 4231
Abstract
Fungal wood decay strategies are influenced by several factors, such as wood species, moisture content, and temperature. This study aims to evaluate wood degradation characteristics of spruce, beech, and oak after exposure to the white-rot fungi Pleurotusostreatus and Trametesversicolor. Both [...] Read more.
Fungal wood decay strategies are influenced by several factors, such as wood species, moisture content, and temperature. This study aims to evaluate wood degradation characteristics of spruce, beech, and oak after exposure to the white-rot fungi Pleurotusostreatus and Trametesversicolor. Both fungi caused high mass losses in beech wood, while spruce and oak wood were more resistant to decay. The moisture content values of the decayed wood correlated with the mass losses for all three wood species and incubation periods. Combined microscopic and chemical studies indicated that the two fungi differed in their decay behavior. While T. versicolor produced a decay pattern (cell wall erosion) typical of white-rot fungi in all wood species, P. ostreatus caused cell wall erosion in spruce and beech and soft-rot type I (cavity formation) decay in oak wood. These observations suggest that P. ostreatus may have the capacity to produce a wider range of enzymes/radicals triggered by the chemical composition of wood cell walls and/or local compositional variability within the cell wall. Full article
(This article belongs to the Special Issue Biomass Deconstruction)
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27 pages, 4626 KiB  
Article
Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides
by Kristin E. Low, Xiaohui Xing, Paul E. Moote, G. Douglas Inglis, Sivasankari Venketachalam, Michael G. Hahn, Marissa L. King, Catherine Y. Tétard-Jones, Darryl R. Jones, William G. T. Willats, Bogdan A. Slominski and D. Wade Abbott
Microorganisms 2020, 8(12), 1888; https://doi.org/10.3390/microorganisms8121888 - 29 Nov 2020
Cited by 13 | Viewed by 3037
Abstract
Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and [...] Read more.
Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and lignin. The addition of exogenous enzymes to promote the digestion of CM NSP in chickens has potential to increase the metabolizable energy of CM. We isolated chicken cecal bacteria from a continuous-flow mini-bioreactor system and selected for those with the ability to metabolize CM NSP. Of 100 isolates identified, Bacteroides spp. and Enterococcus spp. were the most common species with these capabilities. To identify enzymes specifically for the digestion of CM NSP, we used a combination of glycomics techniques, including enzyme-linked immunosorbent assay characterization of the plant cell wall fractions, glycosidic linkage analysis (methylation-GC-MS analysis) of CM NSP and their fractions, bacterial growth profiles using minimal media supplemented with CM NSP, and the sequencing and de novo annotation of bacterial genomes of high-efficiency CM NSP utilizing bacteria. The SACCHARIS pipeline was used to select plant cell wall active enzymes for recombinant production and characterization. This approach represents a multidisciplinary innovation platform to bioprospect endogenous CAZymes from the intestinal microbiota of herbivorous and omnivorous animals which is adaptable to a variety of applications and dietary polysaccharides. Full article
(This article belongs to the Special Issue Biomass Deconstruction)
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22 pages, 2037 KiB  
Article
Role of Leaf Litter in Above-Ground Wood Decay
by Grant T. Kirker, Amy Bishell, Jed Cappellazzi, Jonathan Palmer, Nathan Bechle, Patricia Lebow and Stan Lebow
Microorganisms 2020, 8(5), 696; https://doi.org/10.3390/microorganisms8050696 - 09 May 2020
Cited by 5 | Viewed by 3198
Abstract
The effects of leaf litter on moisture content and fungal decay development in above-ground wood specimens were assessed. Untreated southern pine specimens were exposed with or without leaf litter contact. Two types of leaf litter were evaluated; aged (decomposed) and young (early stages [...] Read more.
The effects of leaf litter on moisture content and fungal decay development in above-ground wood specimens were assessed. Untreated southern pine specimens were exposed with or without leaf litter contact. Two types of leaf litter were evaluated; aged (decomposed) and young (early stages of decomposition). The moisture content of specimens was monitored, and specimens were periodically removed for visual evaluation of decay development. In addition, amplicon-based sequencing analysis of specimens and associated leaf litter was conducted at two time points. Contact with either type of leaf litter resulted in consistently higher moisture contents than those not in contact with leaf litter. Visually, evident decay developed most rapidly in specimens in contact with the aged leaf litter. Analysis of amplicon-based sequencing revealed that leaf litter contributes a significant amount of the available wood decay fungal community with similar communities found in the litter exposed wood and litter itself, but dissimilar community profiles from unexposed wood. Dominant species and guild composition shifted over time, beginning initially with more leaf saprophytes (ascomycetes) and over time shifting to more wood rotting fungi (basidiomycetes). These results highlight the importance of the contributions of leaf litter to fungal colonization and subsequent decay hazard for above-ground wood. Full article
(This article belongs to the Special Issue Biomass Deconstruction)
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