Project description:Kelp are the largest photosynthetic organisms in the ocean with tissue differentiation and complex life cycles. Other multicellular organisms with similar complexity such as plants and animals are well known to posses epigenetic mechanisms such as DNA methylation to control development and morphogenesis. Despite plant-like body plans and the presence of different life-cycle stages, the kelp species Saccharina japonica has only a very low level of DNA methylation, yet we have found strong evidence for differential methylation of regulatory elements and protein-coding genes which seem to contribute to the formation of life-cycle stages, tissue differentiation, growth and halogen metabolism. Thus, DNA methylation seems to play an important role in kelp, which has not been reported before.
Project description:Polylactic acid (PLA) is a promising biodegradable material used in various fields, such as mulching films and disposable packaging materials. Biological approaches for completely degrading biodegradable polymers can provide environmentally friendly solutions. However, to our knowledge, no studies have performed transcriptome profiling to analyze PLA-degrading genes of PLA-degrading bacteria. Therefore, this study reports for the first time an RNA sequence approach for tracing genes involved in PLA biodegradation in the PLA-degrading bacterium Brevibacillus brevis. In the interpretation results of the differentially expressed genes, the hydrolase genes mhqD and nap and the serine protease gene besA were up-regulated by a fold change of 7.97, 4.89, and 4.09, respectively. This result suggests that hydrolases play a key role in PLA biodegradation by B. brevis. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes implicated in biofilm formation were upregulated. The biodegradation of PLA starts with bacteria attaching to the surface of PLA and forming a biofilm. Therefore, it could be confirmed that the above genes were up-regulated for access to PLA and biodegradation. Our results provide transcriptome-based insights into PLA biodegradation, which pitch a better understanding of microbial biodegradation of plastics.
Project description:We performed a laboratory experiment with vegetative gametophytes of the kelp Saccharina latissima and exposed the gametophytes to three temperatures (4°C, 12°C and 20°C) by sex (female, male) for 14 days.
Project description:The use of carbon labelled PBAT units allowed us to follow biodegradation of all PBAT building blocks. The presented workflow is a novel approach to study the fundamental steps in polymer biodegradation in complex systems.
Project description:Petroleum hydrocarbons are recalcitrant contaminants, which has caused most serious environmental problems. Acinetobacter calcoaceticus Aca13 was isolated from petroleum polluted soil for petroleum biodegradation. Hexadecane and naphthalene were used to incubate with Acinetobacter calcoaceticus Aca13. After incubation, the whole transcriptome was obtained from treated groups and control groups, and then used for RNA sequence and analysis. Obtained data in this project will help us understand the biodegradation mechanism of hexadecane and naphthalene, and will be helpful for the bioremediation of petroleum hydrocarbons.
Project description:Understanding the bacterial community structure, and their functional analysis for active bioremediation process is essential to design better and cost effective strategies. Microarray analysis enables us to simultaneously study the functional and phylogenetic markers of hundreds of microorganisms which are involved in active bioremediation process in an environment. We have previously described development of a hybrid 60-mer multibacterial microarray platform (BiodegPhyloChip) for profiling the bacterial communities and functional genes simultaneously in environments undergoing active bioremediation process (Pathak et al; Appl Microbiol Biotechnol,Vol. 90, 1739-1754). The present study involved profiling the status of bacterial communities and functional (biodegradation) genes using the developed 60-mer oligonucleotide microarray BiodegPhyloChip at five contaminated hotspots in the state of Gujarat, in western India. The expression pattern of functional genes (coding for key enzymes in active bioremediation process) at these sites was studied to understand the dynamics of biodegradation in the presence of diverse group of chemicals. The results indicated that the nature of pollutants and their abundance greatly influence the structure of bacterial communities and the extent of expression of genes involved in various biodegradation pathways. In addition, site specific factors also play a pivotal role to affect the microbial community structure as was evident from results of 16S rRNA gene profiling of the five contaminated sites, where the community structure varied from one site to another drastically.