scholarly journals Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

2021 ◽  
Vol 9 (2) ◽  
pp. 321
Author(s):  
Jessica A. Lee ◽  
Alyssa C. Baugh ◽  
Nicholas J. Shevalier ◽  
Brandi Strand ◽  
Sergey Stolyar ◽  
...  
Keyword(s):  
Resource Competition ◽  
Plant Biomass ◽  
Lignocellulose Degradation ◽  
Toxic Metabolite ◽  
Growth Requirements ◽  
Mutualistic Interaction ◽  
Metabolite Exchange ◽  
Future Work ◽  
Biomass Transformation ◽  
Complex Organic

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

scholarly journals Properties of Thermobifida fusca peroxidase Tfu-1649 and its combined synergistic effects with xylanase on lignocellulose degradation

BioResources ◽  
2020 ◽  
Vol 16 (1) ◽  
pp. 942-953
Author(s):  
Wan-Yu Liao ◽  
Yu-Chun Huang ◽  
Wei-Lin Chen ◽  
Cheng-Yu Chen ◽  
Chao-Hsun Yang
Keyword(s):  
Reducing Sugars ◽  
Plant Biomass ◽  
Synergistic Effects ◽  
Culture Broth ◽  
Lignocellulose Degradation ◽  
Total Phenolic ◽  
Thermobifida Fusca ◽  
Zizania Latifolia ◽  
Thermophilic Actinomycetes ◽  
Biomass Decomposition

Lignocelluloses are comprised of cellulose, hemicellulose, and lignins, which constitute plant biomass. Since peroxidases can degrade lignins, the authors examined peroxidase Tfu-1649, which is secreted from the thermophilic actinomycetes, Thermobifida fusca BCRC 19214. After cultivating for 48 h, the culture broth accumulated 43.66 U/mL of peroxidase activity. The treatment of four types of lignocellulolytic byproducts, i.e., bagasse, corncob, pin sawdust, and Zizania latifolia Turcz husk, with Tfu-1649 alone increased the total phenolic compounds, with limited reducing sugars, but treatment with xylanase, Tfu-11, and peroxidase Tfu-1649 showed synergistic effects. Hence, the co-operative degradation of lignocelluloses by both peroxidase and xylanase could contribute to biomass decomposition and further applications in the agricultural and environmental industries.

scholarly journals Soil-Derived Microbial Consortia Enriched with Different Plant Biomass Reveal Distinct Players Acting in Lignocellulose Degradation

2015 ◽  
Vol 71 (3) ◽  
pp. 616-627 ◽  
Author(s):  
Maria Julia de Lima Brossi ◽  
Diego Javier Jiménez ◽  
Larisa Cortes-Tolalpa ◽  
Jan Dirk van Elsas
Keyword(s):  
Plant Biomass ◽  
Microbial Consortia ◽  
Lignocellulose Degradation

scholarly journals The termite fungal cultivar Termitomyces combines diverse enzymes and oxidative reactions for plant biomass conversion

2021 ◽  
Author(s):  
Felix Schalk ◽  
Cene Gostinčar ◽  
Nina B. Kreuzenbeck ◽  
Benjamin H. Conlon ◽  
Elisabeth Sommerwerk ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Biomass Conversion ◽  
Degradation Mechanism ◽  
Oxidative Degradation ◽  
Ligninolytic Enzymes ◽  
Brown Rot ◽  
Dicarboxylic Acids ◽  
Lignocellulose Degradation ◽  
Redox Shuttle ◽  
Phenolic Polymer

AbstractMacrotermitine termites have domesticated fungi in the genus Termitomyces as their primary food source using pre-digested plant biomass. To access the full nutritional value of lignin-enriched plant biomass, the termite-fungus symbiosis requires the depolymerization of this complex phenolic polymer. While most previous work suggests that lignocellulose degradation is accomplished predominantly by the fungal cultivar, our current understanding of the underlying biomolecular mechanisms remains rudimentary. Here, we provide conclusive OMICs and activity-based evidence that Termitomyces partially depolymerizes lignocellulose through the combined actions of high-redox potential oxidizing enzymes (laccases, aryl-alcohol oxidases and a manganese peroxidase), the production of extracellular H2O2 and Fenton-based oxidative degradation, which is catalyzed by a newly described 2-methoxybenzoquinone/hydroquinone redox shuttle system and mediated by secreted chelating dicarboxylic acids. In combination, our approaches reveal a comprehensive depiction of how the efficient biomass degradation mechanism in this ancient insect agricultural symbiosis is accomplished through a combination of white- and brown-rot mechanisms.ImportanceFungus-growing termites have perfected the decomposition of recalcitrant plant biomass to access valuable nutrients by engaging in a tripartite symbiosis with complementary contributions from a fungal mutualist and a co-diversified gut microbiome. This complex symbiotic interplay makes them one of the most successful and important decomposers for carbon cycling in Old World ecosystems. To date, most research has focused on the enzymatic contributions of microbial partners to carbohydrate decomposition. Here we provide genomic, transcriptomic and enzymatic evidence that Termitomyces also employs redox mechanisms, including diverse ligninolytic enzymes and a Fenton-based hydroquinone-catalyzed lignin-degradation mechanism, to break down lignin-rich plant material. Insights into these efficient decomposition mechanisms open new sources of efficient ligninolytic agents applicable for energy generation from renewable sources.

scholarly journals Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production

2021 ◽  
Vol 12 ◽  
Author(s):  
Caio Augusto Yoshiura ◽  
Andressa Monteiro Venturini ◽  
Lucas Palma Perez Braga ◽  
Aline Giovana da França ◽  
Maria do Carmo Catanho Pereira de Lyra ◽  
...  
Keyword(s):  
Greenhouse Gas ◽  
Biomass Production ◽  
Plant Biomass ◽  
Control Plant ◽  
Ghg Emissions ◽  
Control Treatment ◽  
Lignocellulose Degradation ◽  
Microbial Composition ◽  
Maize Stover ◽  
Plant Biomass Production

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.

scholarly journals Physiological Characteristics and Comparative Secretome Analysis of Morchella importuna Grown on Glucose, Rice Straw, Sawdust, Wheat Grain, and MIX Substrates

2021 ◽  
Vol 12 ◽  
Author(s):  
YingLi Cai ◽  
XiaoLong Ma ◽  
QianQian Zhang ◽  
FuQiang Yu ◽  
Qi Zhao ◽  
...  
Keyword(s):  
Rice Straw ◽  
Lignin Degradation ◽  
Extracellular Enzymes ◽  
Plant Biomass ◽  
Growth Potential ◽  
Glycoside Hydrolases ◽  
Lignocellulose Degradation ◽  
Wheat Grain ◽  
Predominant Component ◽  
Morchella Importuna

Morels (Morchella sp.) are economically important edible macro-fungi, which can grow on various synthetic or semi-synthetic media. However, the complex nutritional metabolism and requirements of these fungi remain ill-defined. This study, based on the plant biomass commonly used in the artificial cultivation of morels, assessed and compared the growth characteristics and extracellular enzymes of Morchella importuna cultivated on glucose, rice straw, sawdust, wheat grain, and a mixture of equal proportions of the three latter plant substrates (MIX). M. importuna could grow on all five tested media but displayed significant variations in mycelial growth rate, biomass, and sclerotium yield on the different media. The most suitable medium for M. importuna was wheat and wheat-containing medium, followed by glucose, while rice straw and sawdust were the least suitable. A total of 268 secretory proteins were identified by liquid chromatography coupled with tandem mass spectrometry detection. Functional classification and label-free comparative analysis of these proteins revealed that carbohydrate-active enzyme (CAZYme) proteins were the predominant component of the secretome of M. importuna, followed by protease, peptidase, and other proteins. The abundances of CAZYme proteins differed among the tested media, ranging from 64% on glucose to 88% on rice straw. The CAZYme classes of glycoside hydrolases and carbohydrate-binding module were enriched in the five secretomes. Furthermore, the enzyme activities of CMCase, lignase, amylase, xylase, pNPCase, and pNPGase were detected during the continuous culture of M. importuna in MIX medium, and the relative expression of the corresponding genes were detected by quantitative real-time PCR. The combined data of growth potential, secretome, extracellular enzyme activity, and gene expression on different substrates inferred that M. importuna was weak in lignocellulose degradation but a good starch decomposer. Specifically, in terms of the degradation of cellulose, the ability to degrade cellulose into oligosaccharides was weaker compared with further degradation into monosaccharides, and this might be the speed-limiting step of cellulose utilization in M. importuna. In addition, M. importuna had a strong ability to decompose various hemicellulose glycosidic bonds, especially α- and β-galactosidase. Only a very few lignin-degradation-related proteins were detected, and these were in low abundance, consistent with the presence of weak lignin degradation ability. Furthermore, the presence of lipase and chitinase implied that M. importuna was capable of decomposition of its own mycelia in vitro. The study provides key data that facilitates a further understanding of the complex nutritional metabolism of M. importuna.

scholarly journals Microbial and Phenyl Acid Dynamics during the Start-up Phase of Anaerobic Straw Degradation in Meso- and Thermophilic Batch Reactors

2019 ◽  
Vol 7 (12) ◽  
pp. 657 ◽  
Author(s):  
Eva Maria Prem ◽  
Rudolf Markt ◽  
Nina Lackner ◽  
Paul Illmer ◽  
Andreas Otto Wagner
Keyword(s):  
Anaerobic Degradation ◽  
Volatile Fatty Acids ◽  
Biogas Production ◽  
Lignocellulose Degradation ◽  
Batch Reactors ◽  
Highly Active ◽  
Start Up ◽  
Negative Effect ◽  
Complex Organic ◽  
Generation Sequencing

Aromatic compounds like phenyl acids derived from lignocellulose degradation have been suspected to negatively influence biogas production processes. However, results on this topic are still inconclusive. To study phenyl acid formation in batch reactors during the start-up phase of anaerobic degradation, different amounts of straw from grain were mixed with mesophilic and thermophilic sludge, respectively. Molecular biological parameters were assessed using next-generation sequencing and qPCR analyses. Metagenomic predictions were done via the program, piphillin. Methane production, concentrations of phenylacetate, phenylpropionate, phenylbutyrate, and volatile fatty acids were monitored chromatographically. Methanosarcina spp. was the dominant methanogen when high straw loads were effectively degraded, and thus confirmed its robustness towards overload conditions. Several microorganisms correlated negatively with phenyl acids; however, a negative effect, specifically on methanogens, could not be proven. A cascade-like increase/decrease from phenylacetate to phenylpropionate, and then to phenylbutyrate could be observed when methanogenesis was highly active. Due to these results, phenylacetate was shown to be an early sign for overload conditions, whereas an increase in phenylbutyrate possibly indicated a switch from degradation of easily available to more complex substrates. These dynamics during the start-up phase might be relevant for biogas plant operators using complex organic wastes for energy exploitation.

scholarly journals Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic GenusCaldicellulosiruptorby Genomic, Pangenomic, and Metagenomic Analyses

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Laura L. Lee ◽  
Sara E. Blumer-Schuette ◽  
Javier A. Izquierdo ◽  
Jeffrey V. Zurawski ◽  
Andrew J. Loder ◽  
...  
Keyword(s):  
Microcrystalline Cellulose ◽  
Plant Biomass ◽  
Thermophilic Bacteria ◽  
Cellulose Degradation ◽  
Glycoside Hydrolases ◽  
Metagenomic Data ◽  
Lignocellulose Degradation ◽  
Sequence Information ◽  
Metagenomic Sequence ◽  
Content Type

ABSTRACTMetagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilicCaldicellulosiruptor. The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species,Caldicellulosiruptorsp. strain Rt8.B8 (renamed hereCaldicellulosiruptor morganii),Thermoanaerobacter cellulolyticusstrain NA10 (renamed hereCaldicellulosiruptor naganoensis), andCaldicellulosiruptorsp. strain Wai35.B1 (renamed hereCaldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass).C. morganiiwas more efficient thanCaldicellulosiruptor besciiin this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that ofCaldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter,Fervidobacterium,Caloramator, andClostridium). One enrichment, containing 89.8%Caldicellulosiruptorand 9.7%Caloramator, had a capacity for switchgrass solubilization comparable to that ofC. bescii. These results refine the known biodiversity ofCaldicellulosiruptorand indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCEThe genusCaldicellulosiruptorcontains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.

scholarly journals Genome-centric metagenomics revealed the spatial distribution and the diverse metabolic functions of lignocellulose degrading uncultured bacteria

2018 ◽  
Author(s):  
Panagiotis G. Kougias ◽  
Stefano Campanaro ◽  
Laura Treu ◽  
Panagiotis Tsapekos ◽  
Andrea Armani ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Lignocellulose Degradation ◽  
Pig Manure ◽  
Carbohydrate Binding ◽  
Lignocellulosic Substrate ◽  
Polysaccharide Degradation ◽  
Carbohydrate Binding Modules ◽  
Metabolic Strategies

AbstractThe mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material allowing them to efficiently decompose the organic matter are far to be elucidated. To circumvent this issue, the microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads followed by binning process recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution into the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes can vary depending on the number and functional roles of carbohydrate-binding modules. On contrary, members of Bacteroidetes are able to adhere and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics allowing a functional and taxonomical exploration of the biogas microbiome.ImportanceThis work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales. Even though structural elements of cellulosome were restricted to Clostridiales, our study identified in Bacteroidetes a putative mechanism for biomass decomposition based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose and transport to cytoplasm.

Plant zonation in a brackish tidal marsh: descriptive verification of resource-based competition and community structure

1990 ◽  
Vol 68 (8) ◽  
pp. 1689-1697 ◽  
Author(s):  
Michael J. Pidwirny
Keyword(s):  
Soil Nitrogen ◽  
Tidal Marsh ◽  
Resource Competition ◽  
Plant Biomass ◽  
Soil Surface ◽  
Tidal Marshes ◽  
High Marsh ◽  
Plant Zonation ◽  
Total Species ◽  
Total Soil Nitrogen

This study examined the hypothesis that the zonal patterns of dominant species in brackish tidal marshes may be explained by resource competition for soil nitrogen and light. This hypothesis was tested by analyzing abiotic and biotic field data collected from a brackish tidal marsh located at Brunswick Point, British Columbia. Biotic data revealed that this tidal marsh is dominated by two species that occupy distinct separate zones correlated to marsh elevation. In particular, sites whose elevation was from −0.80 to 0.20 m (geodetic datum) were dominated by Scirpus americanus, while sites with an elevation 0.20 m were dominated by Carex lyngbyei. Analysis of the relationships between measured variables indicated that total species biomass, species height, and total soil nitrogen were all positively correlated to sample site elevation. Further, the availability of light at the soil surface was found to be negatively correlated to plant biomass and site elevation. These results may suggest that S. americanus is dominant in the low marsh because it is a better competitor for soil nitrogen. Carex lyngbyei may be competitively dominant in the high marsh because its greater biomass and height make it a superior competitor for light. Key words: competition, light, nitrogen, tidal marshes, zonation.

scholarly journals The transcription factor Roc1 is a regulator of cellulose degradation in the wood-decaying mushroom Schizophyllum commune

2021 ◽  
Author(s):  
Ioana M Marian ◽  
Peter Jan Vonk ◽  
Ivan D Valdes ◽  
Kerrie Barry ◽  
Benedict Bostock ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Schizophyllum Commune ◽  
Building Blocks ◽  
Lignocellulose Degradation ◽  
Transcriptional Level ◽  
Wide Range

Wood-decaying fungi of the class Agaricomycetes (phylum Basidiomycota) are saprotrophs that break down lignocellulose and play an important role in the nutrient recycling. They secrete a wide range of extracellular plant cell wall degrading enzymes that break down cellulose, hemicellulose and lignin, the main building blocks of plant biomass. Although the production of these enzymes is regulated mainly at the transcriptional level, no activating regulators have been identified in any wood-decaying fungus in the class Agaricomycetes. We studied the regulation of cellulase expression in the wood-decaying fungus Schizophyllum commune. Comparative genomics and transcriptomics on two wild isolates revealed a Zn2Cys6-type transcription factor gene (roc1) that was highly up-regulated during growth on cellulose, when compared to glucose. It is only conserved in the class Agaricomycetes. A roc1 knockout strain showed an inability to grow on medium with cellulose as sole carbon source, and growth on cellobiose and xylan (other components of wood) was inhibited. Growth on non-wood-related carbon sources was not inhibited. Cellulase activity was reduced in the growth medium of the Δroc1 strain. ChIP-Seq identified 1474 binding sites of the Roc1 transcription factor. Promoters of genes involved in lignocellulose degradation were enriched with these binding sites, especially those of LPMO (lytic polysaccharide monooxygenase) CAZymes, indicating that Roc1 directly regulates these genes. A GC-rich motif was identified as the binding site of Roc1, which was confirmed by a functional promoter analysis. Together, Roc1 is a key regulator of cellulose degradation and the first identified in wood-decaying fungi in the phylum Basidiomycota.

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