0000000001295711
AUTHOR
Mario López-pérez
Functional and Pharmacological Analyses of the Role of Penicillium digitatum Proteases on Virulence
© The Author(s).
Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability
AbstractThe increasing demand for products for human consumption is leading to the fast-growing expansion of numerous food sectors such as marine aquaculture (mariculture). However, excessive input of nutrients and pollutants modifies marine ecosystems. Here, we applied a metagenomic approach to investigate these perturbations in samples from marine farms of gilthead seabream cultures. Results revealed dysbiosis and functional imbalance within the net cage with a unique structure, with little interference with samples from the fish microbiota or those collected far away from the coast. Remarkably, below the cage the prokaryotic community was highly similar to the marine microbiome of photic…
Fine stratification of microbial communities through a metagenomic profile of the photic zone
ABSTRACTMost marine metagenomic studies of the marine photic zone analyze only samples taken at one or two depths. However, when the water column is stratified, physicochemical parameters change dramatically over relatively short depth intervals. We sampled the photic water column every 15m depth at a single point of an off-shore Mediterranean site during a period of strong stratification (early autumn) to evaluate the effects of small depth increases on the microbiome. Using genomic assembly and metagenomic read recruitment, we found major shifts in the community structure over small variations of depth, with most microbes showing a distribution limited to layers approximately 30 meters th…
Development of a green fluorescent tagged strain of Aspergillus carbonarius to monitor fungal colonization in grapes.
An enhanced green fluorescent protein has been used to tag an OTA-producing strain of Aspergillus carbonarius (W04-40) isolated from naturally infected grape berries. Transformation of the fungus was mediated by Agrobacterium tumefaciens. The most efficient transformation occurred when the co-cultivation was done with 104 conidia due to higher frequency of resistance colonies (894 per 104 conidia) and lower background obtained. To confirm the presence of the hph gene in hygromycin resistant colonies, 20 putative transformants were screened by PCR analysis. The hph gene was identified in all the transformants. Variation on the expression levels of the eGFP was detected among the transformant…
Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Background: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment. Results: Our results showed significant differences in the microbial composition of different layers within th…
Additional file 1: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Figure S1. Method used for sampling. Water was pumped through a hose directly on to the filters instead of using the Niskin bottles rosette. Figure S2. Bar plot showing the concentration of inorganic nutrients in both stratified (blue) and mixed (red) samples. Figure S3. Simpson Diversity Index versus depth. Figure S4. Assembled contigs. A) Size of individual contigs to the left and total assembled size to the right for each phylum. Proteobacteria was divided into its class-level taxonomy. The number of contigs longer than 10 Kb that were taxonomically classified is indicated within brackets. B) Individual contribution of each metagenome to the total assembled size. Figure S5. Phylogenetic …
Additional file 2: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Table S1. Relative abundance of 16S rRNA reads. (XLSX 25 kb)
Additional file 4: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Table S3. Relative abundance of functional gene categories related to motility and chemotaxis at subsystem level 3 (SEED database). The highest value for each one has been highlighted in red. (XLSX 13 kb)
Additional file 4: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Table S3. Relative abundance of functional gene categories related to motility and chemotaxis at subsystem level 3 (SEED database). The highest value for each one has been highlighted in red. (XLSX 13 kb)
Additional file 3: of Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment
Table S2. Summary statistics of the reconstructed genomes obtained from metagenomes. (XLSX 16 kb)