scholarly journals Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes

2021 ◽  
Author(s):  
Xuefeng Peng ◽  
St. Elmo Wilken ◽  
Thomas S. Lankiewicz ◽  
Sean P. Gilmore ◽  
Jennifer L. Brown ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Cellulose Degradation ◽  
Anaerobic Bacteria ◽  
Short Chain Fatty Acids ◽  
Division Of Labour ◽  
Microbial Consortia ◽  
Bacterial Consortia ◽  
Green Biotechnology ◽  
Enrichment Experiments ◽  
Bacteria And Fungi

AbstractThe herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.

scholarly journals Gut microbiome of capybara, the Amazon master of the grasses, harbors unprecedented enzymatic strategies for plant glycans breakdown

2021 ◽  
Author(s):  
Lucelia Cabral ◽  
Gabriela F. Persinoti ◽  
Douglas A. A. Paixao ◽  
Marcele P. Martins ◽  
Mariana Chinaglia ◽  
...  
Keyword(s):  
Amazon Basin ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Short Chain Fatty Acids ◽  
Ecological Niches ◽  
Metabolic Reconstruction ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Fermentation Products ◽  
Plant Polysaccharides

Abstract Background: Plant biomass is a promising feedstock to replace fossil-based products including fuels, chemicals and materials. However, the high resistance of plant biomass to either physicochemical or biological deconstruction has been hampering its broad industrial utilization and, consequently, the transition to a sustainable bioeconomy. The gut system from herbivores are formidable bioreactors in nature for lignocellulose breakdown and the diverse ecological niches where herbivores are found have led to the rise of a myriad of molecular strategies to cope with the sheer complexity of plant polysaccharides. This study illuminates how the underexplored microbiota of the largest living rodent, capybara, found in Pantanal wetlands and the Amazon basin, can efficiently depolymerize and utilize lignocellulosic biomass.Results: Here, we have elucidated the gut microbial structure and composition of the semiaquatic herbivorous capybara through multi-omics approaches. Metabolic reconstruction of this microbiota showed that cellulose degradation is likely performed by Fibrobacter bacteria, whereas hemicelluloses and pectins are processed by a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) identified in the multiple metagenome-assembled genomes from the phylum Bacteroidetes. Furthermore, metabolomics analysis showed short chain fatty acids as major fermentation products, which are key markers of digestion performance of plant polysaccharides. Exploring the genomic dark matter of this gut microbial community, two novel CAZymes families were unveiled including a glycoside hydrolase family of β-galactosidases (GHXXX) and a carbohydrate-binding module family (CBMXX) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. Conclusions: Our results reveal how the capybara gut microbiota orchestrates the depolymerization and utilization of dietary plant polysaccharides, representing an untapped reservoir of new and intricate enzymatic strategies to overcome the recalcitrance of plant polysaccharides, a central challenge toward a circular and sustainable economy.

Gut Microbiome of the Amazon Master of the Grasses Harbors Unprecedented Enzymatic Strategies for Plant Glycans Breakdown

2020 ◽  
Author(s):  
Lucelia Cabral ◽  
Gabriela F Persinoti ◽  
Douglas A Paixao ◽  
Marcele P Martins ◽  
Mariana Chinaglia ◽  
...  
Keyword(s):  
Amazon Basin ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Short Chain Fatty Acids ◽  
Ecological Niches ◽  
Metabolic Reconstruction ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Binding ◽  
Fermentation Products ◽  
Plant Polysaccharides

Abstract BackgroundPlant biomass is a promising feedstock to replace fossil-based products including fuels, chemicals and materials. However, the high resistance of plant biomass to either physicochemical or biological deconstruction has been hampering its broad industrial utilization and, consequently, the transition to a sustainable bioeconomy. The gut system from herbivores are formidable bioreactors in nature for lignocellulose breakdown and the diverse ecological niches where herbivores are found have led to the rise of a myriad of molecular strategies to cope with the sheer complexity of plant polysaccharides. This study illuminates how the unexplored microbiota of the largest living rodent, capybara, found in Pantanal wetlands and the Amazon basin, can efficiently depolymerize and utilize lignocellulosic biomass. ResultsHere, we have elucidated the gut microbial structure and composition of the semiaquatic herbivorous capybara through multi-omics approaches. Metabolic reconstruction of this microbiota showed that cellulose degradation is chiefly performed by Fibrobacter bacteria, whereas hemicelluloses and pectins are processed by a broad arsenal of Carbohydrate-Active enZymes (CAZymes) organized in polysaccharide utilization loci (PULs) identified in multiple metagenome-assembled genomes from the phylum Bacteroidetes. Furthermore, metabolomics analysis showed short chain fatty acids as major fermentation products, which are key markers of digestion performance of plant polysaccharides. Exploring the genomic dark matter of this gut microbial community, two novel CAZymes families were unveiled including a glycoside hydrolase family of β-galactosidases and a carbohydrate-binding module family involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to CAZymes. ConclusionsOur results unveil how the capybara gut microbiota orchestrates the depolymerization and utilization of dietary plant polysaccharides, representing an untapped reservoir of new and intricate enzymatic strategies to overcome the recalcitrance of plant polysaccharides, a central challenge toward a circular and sustainable economy.

scholarly journals Effect of Microbial Inoculants on Plant Attributes and Nutrients Uptake by Soybean in Vertisols

2021 ◽  
pp. 102-109
Author(s):  
Sanjeet Kumar ◽  
R. K. Sahu ◽  
R. K. Thakur ◽  
Bablu Yaduwanshi ◽  
N. G. Mitra
Keyword(s):  
Crop Production ◽  
Plant Biomass ◽  
Block Design ◽  
Soil Health ◽  
Microbial Consortia ◽  
Microbial Inoculants ◽  
Randomized Block Design ◽  
Nutrients Uptake ◽  
Agricultural Chemistry ◽  
Plant Attributes

The present study was carried out during kharif season 2019-20 at the Research Farm, Department of Soil Science & Agricultural Chemistry, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh (INDIA), to assess the effect of microbial inoculants on plant attributes and nutrients uptake by soybean in Vertisols. The experiment was laid out under randomized block design (RBD) with three replications. The 15 treatments comprised of different beneficial microbial consortia in possible combinations applied as seed treatments. The crop was supplemented with recommended dose of fertilizers 20 N : 80 P2O5 : 20 K2O kg ha-1. Besides these, two control plots were maintained as fertilized un-inoculated control (FUI) and unfertilized un-inoculated control (UFUI). The findings revealed that the significant improvement were noticed by the application of consortia NPK+EM+PGPR in plant growth attributes of nodulation at 25, 45 & 65 DAS (71, 70 & 59% respectively), over control (9.5, 33.4 & 34.7 nodule plant-1) and its biomass, (62, 69 & 74% respectively),over the control  (0.58, 1.16 & 0.99 g plant-1),  plant height at 25, 45 & 65DAS were increased 61, 40, 41% respectively, over the control (16.20, 34.90 and 44.30 cm) and plant biomass, (48, 62 & 53%), over the control 1.67, 4.73 and 6.1 g plant-1. Similarly, nutrient uptake (seed & stover) were also increased at 25, 45 and 65 stages of crop growth, with 36.6, 34.8 & 51.3% in seed and 66.7, 98.2 & 67.2% in straw respectively over the control (98.5, 63.8, 5.2, and 7.4, 24.9 and 44.4 kg ha-1 respectively). Thus, it may be concluded that the consortium of NPK + EM + PGPR was superior for sustainable crop production and soil health.

scholarly journals A light tunable differentiation system for the creation and control of consortia in yeast

2021 ◽  
Author(s):  
Chetan Aditya ◽  
François Bertaux ◽  
Gregory Batt ◽  
Jakob Ruess
Keyword(s):  
Dynamic Control ◽  
Division Of Labour ◽  
Microbial Consortia ◽  
Continuous Cultures ◽  
Straightforward Manner ◽  
Single Strain ◽  
Differentiation Strategy ◽  
The Creation ◽  
And Control ◽  
Immense Potential

Artificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.

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 ABC Transporters Required for Hexose Uptake byClostridium phytofermentans

2019 ◽  
Vol 201 (15) ◽  
Author(s):  
Tristan Cerisy ◽  
Alba Iglesias ◽  
William Rostain ◽  
Magali Boutard ◽  
Christine Pelle ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Extracellular Enzymes ◽  
Plant Biomass ◽  
Carbon Sources ◽  
Anaerobic Bacteria ◽  
Model Organism ◽  
Industrial Transformation ◽  
Content Type ◽  
Plant Matter

ABSTRACTThe mechanisms by which bacteria uptake solutes across the cell membrane broadly impact their cellular energetics. Here, we use functional genomic, genetic, and biophysical approaches to reveal howClostridium(Lachnoclostridium)phytofermentans, a model bacterium that ferments lignocellulosic biomass, uptakes plant hexoses using highly specific, nonredundant ATP-binding cassette (ABC) transporters. We analyze the transcription patterns of its 173 annotated sugar transporter genes to find those upregulated on specific carbon sources. Inactivation of these genes reveals that individual ABC transporters are required for uptake of hexoses and hexo-oligosaccharides and that distinct ABC transporters are used for oligosaccharides versus their constituent monomers. The thermodynamics of sugar binding shows that substrate specificity of these transporters is encoded by the extracellular solute-binding subunit. As sugars are not phosphorylated during ABC transport, we identify intracellular hexokinases based onin vitroactivities. These mechanisms used byClostridiato uptake plant hexoses are key to understanding soil and intestinal microbiomes and to engineer strains for industrial transformation of lignocellulose.IMPORTANCEPlant-fermentingClostridiaare anaerobic bacteria that recycle plant matter in soil and promote human health by fermenting dietary fiber in the intestine.Clostridiadegrade plant biomass using extracellular enzymes and then uptake the liberated sugars for fermentation. The main sugars in plant biomass are hexoses, and here, we identify how hexoses are taken in to the cell by the model organismClostridium phytofermentans. We show that this bacterium uptakes hexoses using a set of highly specific, nonredundant ABC transporters. Once in the cell, the hexoses are phosphorylated by intracellular hexokinases. This study provides insight into the functioning of abundant members of soil and intestinal microbiomes and identifies gene targets to engineer strains for industrial lignocellulosic fermentation.

scholarly journals Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass

2014 ◽  
Vol 80 (23) ◽  
pp. 7423-7432 ◽  
Author(s):  
Stephanie A. Eichorst ◽  
Chijioke Joshua ◽  
Noppadon Sathitsuksanoh ◽  
Seema Singh ◽  
Blake A. Simmons ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Plant Biomass ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Gravimetric Analysis ◽  
Content Type ◽  
Biomass Deconstruction ◽  
Bacterial Consortia ◽  
Residual Biomass ◽  
Chemical Pretreatments

ABSTRACTMicrobial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of theFirmicutes, theBacteroidetes, andDeinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction.

Isolation and Genetic Identification of Dibenzothiophene Degrading Bacteria from Contaminated Soil

2012 ◽  
Vol 610-613 ◽  
pp. 292-295 ◽  
Author(s):  
Lin Li ◽  
Chao Cheng Zhao ◽  
Qi You Liu ◽  
Yun Bo Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Contaminated Soil ◽  
Bacterial Strain ◽  
Degradation Efficiency ◽  
Genetic Identification ◽  
Microbial Consortia ◽  
Bacterial Strains ◽  
Bacterial Consortia ◽  
Degrading Bacteria

The biodegradation abilities of 10 dibenzothiophene degrading microbial consortia isolated from contaminated soil were investigated. 5 highly efficient dibenzothiophene degrading bacterial strains were obtained from the consortium LKY10 by screening on LB-agar plates.The bacterial strain LKY10-5 reduced more than 90% of dibenzothiophene with 40 mg•L-1concentration, and had higher degradation efficiency than enriched bacterial consortia in 7 days of cultivation. According to species identification and phylogenetic analysis, strain LKY10-1 and LKY10-3 belonged to Actinobacteria and could be included in Rhodococcus and Cellulosimicrobium genus, LKY10-5 and LKY10-6 belonged to Proteobacteria and could be included in Pseudomonas and Devosia genus, and LKY10-13 could be included in Lysinibacillus genus and belonged to Firmicutes.

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