scholarly journals Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Diego Javier Jiménez ◽  
Diego Chaves-Moreno ◽  
Jan Dirk van Elsas
Keyword(s):  
Wheat Straw ◽  
Microbial Consortia ◽  
Metabolic Potential

scholarly journals Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment

RSC Advances ◽  
2017 ◽  
Vol 7 (66) ◽  
pp. 41727-41737 ◽  
Author(s):  
Hebin Liang ◽  
Dongdong Ye ◽  
Lixin Luo
Keyword(s):  
Wastewater Treatment ◽  
Activated Sludge ◽  
Treatment Process ◽  
Sewage Treatment ◽  
Microbial Consortia ◽  
Biological Wastewater Treatment ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
Wastewater Treatment Process ◽  
System P

Activated sludge is essential for the biological wastewater treatment process and the identification of active microbes enlarges awareness of their ecological functions in this system.

scholarly journals Diversity of Active Viral Infections within the Sphagnum Microbiome

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Joshua M. A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Content Type ◽  
Virus Diversity

ABSTRACT Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome. IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.

scholarly journals Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

2014 ◽  
Vol 7 (1) ◽  
pp. 92 ◽  
Author(s):  
Diego Jiménez ◽  
Francisco Dini-Andreote ◽  
Jan van Elsas
Keyword(s):  
Wheat Straw ◽  
Microbial Consortia

scholarly journals Diversity of active viral infections within the Sphagnum microbiome

2018 ◽  
Author(s):  
Joshua M.A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Housekeeping Gene ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Virus Diversity

AbstractSphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced. Metatranscriptomes were assembled and contigs screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein, gp23, as a marker for phage diversity, we identified 33 contigs representing undocumented phage s that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) major capsid protein were used as markers for ssRNA viruses and NCLDV, respectively. In total 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent near-complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinto-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades, and suggest viruses may play a considerable role in the ecology of the Sphagnum microbiome.SignificanceSphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor its own growth over other plant species. This slows rates of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss’s growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome, and identifying new potential model systems to study virus-host interactions in the peatland ecosystem.

Microscopic analysis of wheat straw cell wall degradation by microbial consortia for hydrogen production

2015 ◽  
Vol 40 (1) ◽  
pp. 151-160 ◽  
Author(s):  
Marisol Pérez-Rangel ◽  
Francisco R. Quiroz-Figueroa ◽  
Jaquelina González-Castañeda ◽  
Idania Valdez-Vazquez
Keyword(s):  
Cell Wall ◽  
Hydrogen Production ◽  
Wheat Straw ◽  
Microscopic Analysis ◽  
Microbial Consortia ◽  
Cell Wall Degradation

Hydrogen and butanol production from native wheat straw by synthetic microbial consortia integrated by species of Enterococcus and Clostridium

Fuel ◽  
2015 ◽  
Vol 159 ◽  
pp. 214-222 ◽  
Author(s):  
Idania Valdez-Vazquez ◽  
Marisol Pérez-Rangel ◽  
Adán Tapia ◽  
Germán Buitrón ◽  
Carlos Molina ◽  
...  
Keyword(s):  
Wheat Straw ◽  
Microbial Consortia ◽  
Butanol Production ◽  
Synthetic Microbial Consortia

scholarly journals Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Diego Javier Jiménez ◽  
Yanfang Wang ◽  
Maryam Chaib de Mares ◽  
Larisa Cortes-Tolalpa ◽  
Jeffrey A Mertens ◽  
...  
Keyword(s):  
Wheat Straw ◽  
Microbial Consortium ◽  
Cellulose Degradation ◽  
Expression Profiles ◽  
Galactose Oxidase ◽  
Multidrug Transporter ◽  
Metabolic Potential ◽  
Great Capacity ◽  
Lignin Depolymerization

ABSTRACT Coniochaeta species are versatile ascomycetes that have great capacity to deconstruct lignocellulose. Here, we explore the transcriptome of Coniochaeta sp. strain 2T2.1 from wheat straw-driven cultures with the fungus growing alone or as a member of a synthetic microbial consortium with Sphingobacterium multivorum w15 and Citrobacter freundii so4. The differential expression profiles of carbohydrate-active enzymes indicated an onset of (hemi)cellulose degradation by 2T2.1 during the initial 24 hours of incubation. Within the tripartite consortium, 63 transcripts of strain 2T2.1 were differentially expressed at this time point. The presence of the two bacteria significantly upregulated the expression of one galactose oxidase, one GH79-like enzyme, one multidrug transporter, one laccase-like protein (AA1 family) and two bilirubin oxidases, suggesting that inter-kingdom interactions (e.g. amensalism) take place within this microbial consortium. Overexpression of multicopper oxidases indicated that strain 2T2.1 may be involved in lignin depolymerization (a trait of enzymatic synergism), while S. multivorum and C. freundii have the metabolic potential to deconstruct arabinoxylan. Under the conditions applied, 2T2.1 appears to be a better degrader of wheat straw when the two bacteria are absent. This conclusion is supported by the observed suppression of its (hemi)cellulolytic arsenal and lower degradation percentages within the microbial consortium.

scholarly journals Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities

2007 ◽  
Vol 73 (10) ◽  
pp. 3205-3214 ◽  
Author(s):  
Mircea Podar ◽  
Carl B. Abulencia ◽  
Marion Walcher ◽  
Don Hutchison ◽  
Karsten Zengler ◽  
...  
Keyword(s):  
Cell Separation ◽  
Genomic Dna ◽  
Microbial Consortia ◽  
Bacterial Cells ◽  
Metabolic Potential ◽  
Low Frequencies ◽  
Powerful Approach ◽  
Laboratory Cultures ◽  
First Time

ABSTRACT Current metagenomic approaches to the study of complex microbial consortia provide a glimpse into the community metabolism and occasionally allow genomic assemblies for the most abundant organisms. However, little information is gained for the members of the community present at low frequencies, especially those representing yet-uncultured taxa, which include the bulk of the diversity present in most environments. Here we used phylogenetically directed cell separation by fluorescence in situ hybridization and flow cytometry, followed by amplification and sequencing of a fraction of the genomic DNA of several bacterial cells that belong to the TM7 phylum. Partial genomic assembly allowed, for the first time, a look into the evolution and potential metabolism of a soil representative from this group of organisms for which there are no species in stable laboratory cultures. Genomic reconstruction from targeted cells of uncultured organisms isolated directly from the environment represents a powerful approach to access any specific members of a community and an alternative way to assess the community's metabolic potential.

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