RESUMO
Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
RESUMO
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.
Assuntos
Ascomicetos/metabolismo , Lignina/metabolismo , Consórcios Microbianos , Ascomicetos/enzimologia , Ascomicetos/genética , Citrobacter freundii/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Perfilação da Expressão Gênica , Regulação Fúngica da Expressão Gênica , Sphingobacterium/metabolismo , Triticum/metabolismoRESUMO
Se realizó un estudio con el fin de determinar la estructura demográfica de Emilia sonchifolia (L.) DC en una finca cafetera del Municipio de Armenia, Quindío, Colombia, donde se recolectaron datos durante cuatro semanas, en tres sitios: exterior, borde e interior del cultivo. Usando parámetros calculados a partir de los datos de campo, se construyó un modelo logístico para describir el comportamiento poblacional de E. sonchifolia en el tiempo. Se encontraron diferencias significativas en las variables: número de individuos por estado etario en el tiempo, porcentaje de mortalidad, tiempo de cambio del estado plántula a juvenil y de juvenil a adulto, número de hojas y de ramas; no se encontraron diferencias significativas en la densidad poblacional, número de inflorescencias e infrutescencias en los sitios de estudio. En general, se puede atribuir este comportamiento a la estrategia de reproducción r que sigue E. sonchifolia. Finalmente, las simulaciones hechas a partir del modelo logístico sugieren que la especie tiende a desaparecer si alguno de los estados etarios no está presente inicialmente; así, una alternativa plausible para el control sería su eliminación en el estado juvenil. Los resultados ofrecen alternativas con respecto al manejo de poblaciones de arvenses.
A research study was conducted to determine the demographic structure of Emilia sonchifolia L. in a coffee plantation in Armenia, Quindío, Colombia. Data were collected over a period of four weeks on three sites: inside, at the border and outside a coffee farm. A logistic population model was built to describe the population behavior of E. sonchifolia over time. Statiscally significant differences were found between: number of individuals per life stage in time, mortality rate, transition time from seedling to juvenile and from juvenile to adult; and number of leaves and branches. There was no evidence for statistically significant differences in population density or in number of inflorescences and fruits between study sites. In general, the observed behavior may be attributed to the r strategy used by this species. Finally, our results suggest the survival of the species is conditioned by the presence of all life stages at the beginning of each simulation based on the logistic model; so, a potential strategy for its controlling would require the removal during the juvenile stage. The considerations offer alternatives regarding weed population management.