4.8 Article

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

Related references

Note: Only part of the references are listed.
Review Chemistry, Multidisciplinary

Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels

Lee R. Lynd et al.

Summary: This article identifies the technology challenges and opportunities for developing economically viable, scalable, and sustainable technologies for converting lignocellulosic polysaccharides to liquid fuels. The overview of feedstocks, processes, and products highlights the potential of anaerobic processing for fuel production and the distinctive challenges associated with microbial processing of cellulosic biomass. The article also discusses opportunities to increase product tolerance and decrease the cost of product recovery, as well as pathways for converting anaerobic fermentation products to larger fuel molecules using chemo-catalysis.

ENERGY & ENVIRONMENTAL SCIENCE (2022)

Article Biotechnology & Applied Microbiology

Declining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic tests

Matthew R. Kubis et al.

Summary: Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum-mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum, which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture.

BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS (2022)

Article Engineering, Environmental

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers

Chenjing Jiang et al.

Summary: This study investigated the microbial ecology of anaerobic digestion (AD) in 46 digesters at 22 wastewater treatment plants in Denmark. High-resolution bacterial and archaeal community analyses revealed the characteristics and drivers of community composition in AD systems. The comprehensive insight into community structure at species level provides a foundation for future studies on the ecological significance, characteristics, and function of novel or poorly described taxa.

WATER RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Effect of solid loading on the behaviour of pectin-degrading enzymes

Fan Li et al.

Summary: The study focused on the behavior of pectin-degrading enzymes in lemon peel with varying solid loading. Pectin lyase was less affected by low water content compared to other enzymes, leading to different impacts on pectin solubilisation. At similar pectin concentrations, pectin solutions hindered the diffusion of hydrolases more than the solid substrate did, suggesting potential benefits for biorefinery processing.

BIOTECHNOLOGY FOR BIOFUELS (2021)

Article Multidisciplinary Sciences

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

Bridget B. McGivern et al.

Summary: This study provides experimental evidence that some soil microbiota can degrade polyphenols under anoxic conditions, contrary to the assumption that polyphenols inhibit organic matter decomposition in oxygen-deprived soils. The researchers used metabolomics and metaproteomics to show the biodegradation of polyphenols and maintenance of soil microbial community metabolism under anoxia.

NATURE COMMUNICATIONS (2021)

Article Microbiology

The Termite Fungal Cultivar Termitomyces Combines Diverse Enzymes and Oxidative Reactions for Plant Biomass Conversion

Felix Schalk et al.

Summary: Macrotermitine termites utilize a combination of carbohydrate-active enzymes and oxidizing enzymes, as well as Fenton chemistry, to degrade lignin-rich plant biomass in their symbiotic relationship with Termitomyces fungi.
Article Biology

A microbial gene catalog of anaerobic digestion from full-scale biogas plants

Shichun Ma et al.

Summary: This study provides insights into the microbial composition and function in anaerobic digestion (AD), showing the influence of feedstock type on carbohydrate hydrolysis and methanogenesis. Additionally, a large number of reference genome and gene resources were identified for analysis of anaerobic microbiota.

GIGASCIENCE (2021)

Article Biotechnology & Applied Microbiology

Understanding and Eliminating the Detrimental Effect o Thiamine Deficiency on the Oleaginous Yeast Yarrowia lipolytica

Caleb Walker et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

Evert K. Holwerda et al.

BIOTECHNOLOGY FOR BIOFUELS (2020)

Review Biochemical Research Methods

Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction

Stephen P. Lillington et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

Review Biotechnology & Applied Microbiology

Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives

Heidi Ostby et al.

JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY (2020)

Article Biochemical Research Methods

Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation

Tanveer S. Batth et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Review Microbiology

The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge

Lachlan B. M. Speirs et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Biotechnology & Applied Microbiology

Mechanism of Tolerance to the Lignin-Derived Inhibitor p-Benzoquinone and Metabolic Modification of Biorefinery Fermentation Strains

Zhao Yan et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2019)

Review Biotechnology & Applied Microbiology

An update on enzymatic cocktails for lignocellulose breakdown

A. M. Lopes et al.

JOURNAL OF APPLIED MICROBIOLOGY (2018)

Article Biotechnology & Applied Microbiology

Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis

Ajaya K. Biswal et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Green & Sustainable Science & Technology

Inhibitory effects of lignin on enzymatic hydrolysis: The role of lignin chemistry and molecular weight

Xiang Li et al.

RENEWABLE ENERGY (2018)

Article Biotechnology & Applied Microbiology

Quantitative Metaproteomics Highlight the Metabolic Contributions of Uncultured Phylotypes in a Thermophilic Anaerobic Digester

Live H. Hagen et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2017)

Article Biotechnology & Applied Microbiology

The grand challenge of cellulosic biofuels

Lee R. Lynd

NATURE BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells

Alexandru Dumitrache et al.

SCIENTIFIC REPORTS (2017)

Article Biotechnology & Applied Microbiology

The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum

Tobin J. Verbeke et al.

BIOTECHNOLOGY FOR BIOFUELS (2017)

Article Biotechnology & Applied Microbiology

Inhibition of lignin-derived phenolic compounds to cellulase

Lei Qin et al.

BIOTECHNOLOGY FOR BIOFUELS (2016)

Review Biochemistry & Molecular Biology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

Minoru Kanehisa et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Strategies to reduce end-product inhibition in family 48 glycoside hydrolases

Mo Chen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)

Review Agricultural Engineering

Anaerobic digestion of lignocellulosic biomass: Challenges and opportunities

Chayanon Sawatdeenarunat et al.

BIORESOURCE TECHNOLOGY (2015)

Article Environmental Sciences

Modified Anaerobic Digestion Model No.1 for dry and semi-dry anaerobic digestion of solid organic waste

Flavia Liotta et al.

ENVIRONMENTAL TECHNOLOGY (2015)

Article Biotechnology & Applied Microbiology

Enzymatic liquefaction and saccharification of pretreated corn stover at high-solids concentrations in a horizontal rotating bioreactor

Jian Du et al.

BIOPROCESS AND BIOSYSTEMS ENGINEERING (2014)

Article Biotechnology & Applied Microbiology

Strong cellulase inhibition by Mannan polysaccharides in cellulose conversion to sugars

Rajeev Kumar et al.

BIOTECHNOLOGY AND BIOENGINEERING (2014)

Article Biotechnology & Applied Microbiology

The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading

Evert K. Holwerda et al.

BIOTECHNOLOGY FOR BIOFUELS (2014)

Article Biochemistry & Molecular Biology

The carbohydrate-active enzymes database (CAZy) in 2013

Vincent Lombard et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Engineering, Environmental

Effect of total solids content on methane and volatile fatty acid production in anaerobic digestion of food waste

Flavia Liotta et al.

WASTE MANAGEMENT & RESEARCH (2014)

Review Microbiology

Thermophilic lignocellulose deconstruction

Sara E. Blumer-Schuette et al.

FEMS MICROBIOLOGY REVIEWS (2014)

Review Agricultural Engineering

Enzymatic hydrolysis of biomass at high-solids loadings - A review

Alicia A. Modenbach et al.

BIOMASS & BIOENERGY (2013)

Article Agricultural Engineering

Microbial community signature of high-solid content methanogenic ecosystems

Amel Abbassi-Guendouz et al.

BIORESOURCE TECHNOLOGY (2013)

Article Biotechnology & Applied Microbiology

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

Anthony Levasseur et al.

BIOTECHNOLOGY FOR BIOFUELS (2013)

Article Biotechnology & Applied Microbiology

Total solids content: a key parameter of metabolic pathways in dry anaerobic digestion

Jean-Charles Motte et al.

BIOTECHNOLOGY FOR BIOFUELS (2013)

Article Microbiology

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

Carina Sundberg et al.

FEMS MICROBIOLOGY ECOLOGY (2013)

Article Multidisciplinary Sciences

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

Patrik D'haeseleer et al.

PLOS ONE (2013)

Review Plant Sciences

Roles of pectin in biomass yield and processing for biofuels

Chaowen Xiao et al.

FRONTIERS IN PLANT SCIENCE (2013)

Review Biotechnology & Applied Microbiology

Peculiarities of brown-rot fungi and biochemical Fenton reaction with regard to their potential as a model for bioprocessing biomass

Valdeir Arantes et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)

Article Agricultural Engineering

Enzymatic accessibility of fiber hemp is enhanced by enzymatic or chemical removal of pectin

A. Pakarinen et al.

BIORESOURCE TECHNOLOGY (2012)

Article Agricultural Engineering

Total solids content drives high solid anaerobic digestion via mass transfer limitation

Amel Abbassi-Guendouz et al.

BIORESOURCE TECHNOLOGY (2012)

Article Multidisciplinary Sciences

The Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips

Daniel van der Lelie et al.

PLOS ONE (2012)

Article Agricultural Engineering

A meta-analysis of the microbial diversity observed in anaerobic digesters

Michael C. Nelson et al.

BIORESOURCE TECHNOLOGY (2011)

Review Biochemistry & Molecular Biology

Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes

Dylan Dodd et al.

MOLECULAR MICROBIOLOGY (2011)

Review Biochemistry & Molecular Biology

Pathways for degradation of lignin in bacteria and fungi

Timothy D. H. Bugg et al.

NATURAL PRODUCT REPORTS (2011)

Article Agricultural Engineering

Chemical profiles of switchgrass

Zhoujian Hu et al.

BIORESOURCE TECHNOLOGY (2010)

Article Agricultural Engineering

Xylooligomers are strong inhibitors of cellulose hydrolysis by enzymes

Qing Qing et al.

BIORESOURCE TECHNOLOGY (2010)

Article Multidisciplinary Sciences

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

Martin Allgaier et al.

PLOS ONE (2010)

Article Biochemistry & Molecular Biology

Model-Based Fed-Batch for High-Solids Enzymatic Cellulose Hydrolysis

David B. Hodge et al.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY (2009)

Article Biotechnology & Applied Microbiology

Yield-determining factors in high-solids enzymatic hydrolysis of lignocellulose

Jan B. Kristensen et al.

BIOTECHNOLOGY FOR BIOFUELS (2009)

Article Biochemistry & Molecular Biology

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

Brandi L. Cantarel et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Biochemical Research Methods

The potential of cellulases and cellulosomes for cellulosic waste management

Edward A. Bayer et al.

CURRENT OPINION IN BIOTECHNOLOGY (2007)

Article Biotechnology & Applied Microbiology

Liquefaction of lignocellulose at high-solids concentrations

Henning Jorgensen et al.

BIOTECHNOLOGY AND BIOENGINEERING (2007)

Review Genetics & Heredity

Extracellular oxidative systems of the lignin-degrading Basidiomycete Phanerochaete chrysosporium

Phil Kersten et al.

FUNGAL GENETICS AND BIOLOGY (2007)

Article Biotechnology & Applied Microbiology

Inhibition of the Trichoderma reesei cellulases by cellobiose is strongly dependent on the nature of the substrate

M Gruno et al.

BIOTECHNOLOGY AND BIOENGINEERING (2004)

Correction Microbiology

Microbial cellulose utilization: Fundamentals and biotechnology (vol 66, pg 506, 2002)

LR Lynd et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2002)

Article Biotechnology & Applied Microbiology

Pathways for extracellular fenton chemistry in the brown rot basidiomycete Gloeophyllum trabeum

KA Jensen et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2001)