0000000000394680
AUTHOR
Francisco Rodriguez-valera
Ecological and genomic features of two widespread freshwater picocyanobacteria
We present two genomes of widespread freshwater picocyanobacteria isolated by extinction dilution from a Spanish oligotrophic reservoir. Based on microscopy and genomic properties, both picocyanobacteria were tentatively designated Synechococcus lacustris Tous, formerly described as a metagenome assembled genome (MAG) from the same habitat, and Cyanobium usitatum Tous, described here for the first time. Both strains were purified in unicyanobacterial cultures, and their genomes were sequenced. They are broadly distributed in freshwater systems; the first seems to be a specialist on temperate reservoirs (Tous, Amadorio, Dexter, Lake Lanier, Sparkling), and the second appears to also be abund…
Key roles for freshwater A ctinobacteria revealed by deep metagenomic sequencing
Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria.…
Metagenomics of the Mucosal Microbiota of European Eels
ABSTRACT European eels are an economically important and threatened species that are prone to rapid collapse in farm conditions. Using metagenomics, we show that the eel mucosal microbiota has specific features distinguishing it from the surrounding aquatic community. This is a first step in dissecting the resident microbiota of this critical barrier that may have implications for maintenance of healthy eel populations.
Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs
The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenomeassembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far. Some of the Opitutae family MAGs were small, cosmopolitan, with a general heterotrophic met…
Additional file 12 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 12: Fig. S3. Genomic context of the phoBR two-component system in different marine, brackish and freshwater cluster 5 picocyanobacteria. Each subunit is color coded accordingly. The right panel shows a phylogenomic tree with all those freshwater strains (colored red) possessing two copies of the phoB gene.
Additional file 20 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 20: Fig. S5. Total number (Y axis) of A) transposases and B) integrases found in freshwater, brackish and marine picocyanobacteria.
Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs
Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybri…
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…
Additional file 18 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 18: Fig. S4. Phylogenetic analysis of picocyanobacterial Ni/Cu/Zn/Fe/Mn superoxide dismutases. The Ni-type maturation protease from marine strains was used to root the tree. Bootstrap values >75 are shown and the habitat of each picocyanobacterial enzyme is color coded.
Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla)
In this work, we used the eel (Anguilla anguilla) as an animal model to test the hypothesis of Barr et al. (2013a,b) about the putative role of the epidermal mucosa as a phage enrichment layer. To this end, we analyzed the microbial content of the skin mucus of wild and farmed eels by using a metagenomic approach. We found a great abundance of replicating phage genomes (concatemers) in all the samples. They were assembled in four complete genomes of three Myovirus and one Podovirus. We also found evidences that ΦKZ and Podovirus phages could be part of the resident microbiota associated to the eel mucosal surface and persist on them over the time. Moreover, the viral abundance estimated by …
Microbiome of the Black Sea Water Column Analyzed by Genome Centric Metagenomics  
Abstract Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has simil…
Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
We describe a deep-branching lineage of marine Actinobacteria with very low GC content (33%) and the smallest free living cells described yet (cell volume ca. 0.013 μm(3)), even smaller than the cosmopolitan marine photoheterotroph, 'Candidatus Pelagibacter ubique'. These microbes are highly related to 16S rRNA sequences retrieved by PCR from the Pacific and Atlantic oceans 20 years ago. Metagenomic fosmids allowed a virtual genome reconstruction that also indicated very small genomes below 1 Mb. A new kind of rhodopsin was detected indicating a photoheterotrophic lifestyle. They are estimated to be ~4% of the total numbers of cells found at the site studied (the Mediterranean deep chloroph…
Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution
Background Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. Results Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibr…
Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Abstract Background Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. …
Additional file 2 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 2: Fig. S1. Average Nucleotide Identity (ANI) matrix between all 132 compared picocyanobacteria from SCs 5.1, 5.2 and 5.3.
Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax
Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-beta-hydroxybutyrate granules. The G + C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene seq…
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 4 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 4: Fig. S2. A) Cross-comparison of strict core, soft core, shell and cloud in all 132 picocyanobacteria from all habitats and SCs. B) Plots estimating the core genome (n° of genes) and pangenome (n° of genes) of all three SCs. C) Functionality of the meta-pangenome of picocyanobacteria assessed by SEED/KEGG. Each gene category is color coded for the shared (strict core, soft core) and flexible (shell and cloud) genome.
Metagenomes of Mediterranean Coastal Lagoons
Coastal lagoons, both hypersaline and freshwater, are common, but still understudied ecosystems. We describe, for the first time, using high throughput sequencing, the extant microbiota of two large and representative Mediterranean coastal lagoons, the hypersaline Mar Menor, and the freshwater Albufera de Valencia, both located on the south eastern coast of Spain. We show there are considerable differences in the microbiota of both lagoons, in comparison to other marine and freshwater habitats. Importantly, a novel uncultured sulfur oxidizing Alphaproteobacteria was found to dominate bacterioplankton in the hypersaline Mar Menor. Also, in the latter prokaryotic cyanobacteria were almost exc…
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 6 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 6: Additional Dataset 3. 5.1-5.2-5.3 meta-pangenome. Core, strict-core, shell and cloud annotated genes with Cyanorak clusters (CK) and SEED.
Additional file 15 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 15: Table S8. Compatible solutes and osmolytes. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 8 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 8: Additional Dataset 4. Non-clustered CK genes from all 132 analyzed picocyanobacteria. BLASTP results obtained with the closest taxon from the NCBI nr database.
Data from: Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing
Freshwaters ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria…
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 16 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 16: Table S9. Broad transporters, permeases, channels and uptake systems. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
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 21 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 21: Table S12. Mobile genetic elements. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 5 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 5: Additional Dataset 2. Pangenomic analysis between all picocyanobacterial isolates from SCs 5.1, 5.2 and 5.3. The total number of genes for each category (strict core, soft core, shell and cloud) and isolate are specified.
Additional file 11 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 11: Table S5. P metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 3 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 3: Additional Dataset 1. Average and standard deviation genome size, median intergenic spacers, coding density and %GC of all culture-derived picocyanobacteria. Single pair ANOVA tests for each origin and sub-cluster and for different genomic features.
Additional file 1 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 1: Table S1. Main genomic features of marine, brackish and freswhater culture-derived picocyanobacteria. An asterisk in the origin column indicates strains where euryhaline physiology is known.
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)
Additional file 14 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 14: Table S7. Amino acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 10 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 10: Table S4. N metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 19 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 19: Table S11. Reactive oxygen species (ROS). Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 13 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 13: Table S6. C fixation/photosynthesis. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 9 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 9: Table S3. S metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 17 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 17: Table S10. Glycerolipid/Fatty acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering >50 % of the protein.
Additional file 7 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
Additional file 7: Table S2. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters.