Metagenome-assembled genome of a Chitinophaga sp. and its potential in plant biomass degradation, as well of affiliated Pandoraea and Labrys species

2021 ◽  
Vol 37 (9) ◽  
Author(s):  
Michelli Inácio Gonçalves Funnicelli ◽  
Daniel Guariz Pinheiro ◽  
Elisângela Soares Gomes-Pepe ◽  
Lucas Amoroso Lopes de Carvalho ◽  
João Carlos Campanharo ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Biomass Degradation ◽  
Plant Biomass Degradation

scholarly journals Inter- and intra-domain functional redundancy in the rumen microbiome during plant biomass degradation

2018 ◽  
Author(s):  
Andrea Söllinger ◽  
Alexander Tøsdal Tveit ◽  
Morten Poulsen ◽  
Samantha Joan Noel ◽  
Mia Bengtsson ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Plant Biomass ◽  
Expression Profiles ◽  
Functional Redundancy ◽  
Mitigation Strategies ◽  
Biomass Degradation ◽  
Strong Response ◽  
Plant Biomass Degradation ◽  
Rumen Microbiome ◽  
Domain Functional

AbstractBackgroundRuminant livestock is a major source of the potent greenhouse gas methane (CH4), produced by the complex rumen microbiome. Using an integrated approach, combining quantitative metatranscriptomics with gas- and volatile fatty acid (VFA) profiling, we gained fundamental insights into temporal dynamics of the cow rumen microbiome during feed degradation.ResultsThe microbiome composition was highly individual and remarkably stable within each cow, despite similar gas emission and VFA profiles between cows. Gene expression profiles revealed a fast microbial growth response to feeding, reflected by drastic increases in microbial biomass, CH4emissions and VFA concentrations. Microbiome individuality was accompanied by high inter- and intra-domain functional redundancy among pro- and eukaryotic microbiome members in the key steps of anaerobic feed degradation. Methyl-reducing but not CO2-reducing methanogens were correlated with increased CH4emissions during plant biomass degradation.ConclusionsThe major response of the rumen microbiome to feed intake was a general growth of the whole community. The high functional redundancy of the cow-individual microbiomes was possibly linked to the robust performance of the anaerobic degradation process. Furthermore, the strong response of methylotrophic methanogens is suggesting that they might play a more important role in ruminant CH4emissions than previously assumed, making them potential targets for CH4mitigation strategies.

scholarly journals “Integrative Genomic Analysis for the Bioprospection of Regulators and Accessory Enzymes Associated with Cellulose Degradation in a Filamentous Fungus (Trichoderma harzianum)”

2019 ◽  
Author(s):  
Jaire A. Ferreira Filho ◽  
Maria Augusta C. Horta ◽  
Clelton A. dos Santos ◽  
Deborah A. Almeida ◽  
Natália F. Murad ◽  
...  
Keyword(s):  
Trichoderma Harzianum ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Genome Structure ◽  
Hydrolytic Enzyme ◽  
Differentially Expressed ◽  
Fungal Genome ◽  
Biomass Degradation ◽  
Plant Biomass Degradation ◽  
Genomic Regions

AbstractBackgroundUnveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters.ResultsWe used bioinformatics tools to mine the T. harzianum genome for potential genomics, transcriptomics, and exoproteomics data and coexpression networks. The DNA was sequenced by PacBio SMRT technology for multi-omics data analysis and integration. In total, 1676 genes were annotated in the genomic regions analyzed; 222 were identified as CAZymes in T. harzianum IOC3844. When comparing transcriptome data under cellulose or glucose conditions, 114 genes were differentially expressed in cellulose, with 51 CAZymes. CLR2, a transcription factor physically and phylogenetically conserved in T. harzianum spp., was differentially expressed under cellulose conditions. The genes induced/repressed under cellulose conditions included those important for plant biomass degradation, including CIP2 of the CE15 family and a copper-dependent LPMO of the AA9 family.ConclusionsOur results provide new insights into the relationship between genomic organization and hydrolytic enzyme expression and regulation in T. harzianum IOC3844. Our results can improve plant biomass degradation, which is fundamental for developing more efficient strains and/or enzymatic cocktails for the production of hydrolytic enzymes.

scholarly journals Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation

2020 ◽  
Vol 8 ◽  
Author(s):  
Camila L. Corrêa ◽  
Glaucia E. O. Midorikawa ◽  
Edivaldo Ximenes Ferreira Filho ◽  
Eliane Ferreira Noronha ◽  
Gabriel S. C. Alves ◽  
...  
Keyword(s):  
Aspergillus Terreus ◽  
Plant Biomass ◽  
Transcriptome Profiling ◽  
Biomass Degradation ◽  
Carbohydrate Active Enzymes ◽  
Plant Biomass Degradation

The FibRumBa Database: A Resource for Biologists with Interests in Gastrointestinal Microbial Ecology, Plant Biomass Degradation, and Anaerobic Microbiology

2009 ◽  
Vol 59 (2) ◽  
pp. 212-213 ◽  
Author(s):  
Mark Morrison ◽  
◽  
Sean C. Daugherty ◽  
William C. Nelson ◽  
Tanja Davidsen ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Plant Biomass ◽  
Biomass Degradation ◽  
Plant Biomass Degradation

scholarly journals Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

2018 ◽  
Vol 91 ◽  
pp. 79-99 ◽  
Author(s):  
M.R. Mäkelä ◽  
M. DiFalco ◽  
E. McDonnell ◽  
T.T.M. Nguyen ◽  
A. Wiebenga ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Biomass Degradation ◽  
Plant Biomass Degradation

scholarly journals De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

2013 ◽  
Vol 6 (1) ◽  
pp. 24 ◽  
Author(s):  
Aaron Weimann ◽  
Yulia Trukhina ◽  
Phillip B Pope ◽  
Sebastian GA Konietzny ◽  
Alice C McHardy
Keyword(s):  
De Novo ◽  
Plant Biomass ◽  
Biomass Degradation ◽  
Plant Biomass Degradation

scholarly journals Complete Genome Sequence of a New Firmicutes Species Isolated from Anaerobic Biomass Hydrolysis

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Christian Abendroth ◽  
Sarah Hahnke ◽  
Francisco M. Codoñer ◽  
Michael Klocke ◽  
Olaf Luschnig ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Bacterial Isolate ◽  
Plant Biomass ◽  
Biomass Degradation ◽  
Biomass Hydrolysis ◽  
Two Stage ◽  
Plant Biomass Degradation ◽  
Anaerobic Biomass

ABSTRACT A new Firmicutes isolate, strain HV4-6-A5C, was obtained from the hydrolysis stage of a mesophilic and anaerobic two-stage lab-scale leach-bed system for biomethanation of fresh grass. It is assumed that the bacterial isolate contributes to plant biomass degradation. Here, we report a draft annotated genome sequence of this organism.

scholarly journals Screening of anaerobic gut fungi for effective plant biomass degradation using gas production

1997 ◽  
Vol 37 (Suppl. 1) ◽  
pp. 41-42
Author(s):  
W-Y Zhu ◽  
MK Theodorou ◽  
BB Nielsen ◽  
APJ Trinci
Keyword(s):  
Plant Biomass ◽  
Gas Production ◽  
Biomass Degradation ◽  
Plant Biomass Degradation

scholarly journals The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation

2020 ◽  
Author(s):  
Déborah Aires Almeida ◽  
Maria Augusta Crivelente Horta ◽  
Jaire Alves Ferreira Filho ◽  
Natália Faraj Murad ◽  
Anete Pereira de Souza
Keyword(s):  
Trichoderma Harzianum ◽  
Plant Biomass ◽  
Cellulose Degradation ◽  
Differentially Expressed ◽  
Secreted Proteins ◽  
Enzymatic Reactions ◽  
Potential Candidate ◽  
Biomass Degradation ◽  
Plant Biomass Degradation ◽  
Coexpression Networks

AbstractBioprospecting genes and proteins related to plant biomass degradation is an attractive approach for the identification of target genes for biotechnological purposes, especially genes with potential applications in the biorefinery industry that can enhance second-generation ethanol production technology. Trichoderma harzianum is a potential candidate for cellulolytic enzyme prospection and production. Herein, the enzymatic activities, transcriptome, exoproteome, and coexpression networks of the T. harzianum strain CBMAI-0179 were examined under biomass degradation conditions. We used RNA-Seq to identify differentially expressed genes (DEGs) and carbohydrate-active enzyme (CAZyme) genes related to plant biomass degradation and compared them with the genes of strains from congeneric species (T. harzianum IOC-3844 and T. atroviride CBMAI-0020). T. harzianum CBMAI-0179 harbors strain- and treatment-specific CAZyme genes and transcription factors. We detected important proteins related to biomass degradation, including β-glucosidases, endoglucanases, cellobiohydrolases, lytic polysaccharide monooxygenases, endo-1,4-β-xylanases and β-mannanases, in the exoproteome under cellulose growth conditions. Coexpression networks were constructed to explore the relationships among the genes and corresponding secreted proteins that act synergistically for cellulose degradation. An enriched cluster with degradative enzymes was described, and the subnetwork of CAZymes revealed strong correlations among the secreted proteins (AA9, GH6, GH10, GH11 and CBM1) and differentially expressed CAZyme genes (GH45, GH7, AA7 and GH1). Our results provide valuable information for future studies on the genetic regulation of plant cell wall-degrading enzymes. This knowledge can be exploited for the improvement of enzymatic reactions in biomass degradation for bioethanol production.Key pointsDifferent biotechnological approaches were used to understand the mechanism of cellulose degradation of Trichoderma spp.T. harzianum CBMAI-0179 is a potential candidate for the production of cellulolytic enzymes.Coexpression networks revealed genes and proteins acting synergistically for cellulose hydrolysis.

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