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…

Influence of the conservation status on carbon balances of semiarid coastal Mediterranean wetlands

Permanent freshwater and brackish marshes are the typical wetland type of the Mediterranean Spanish coast. Historically, alterations to the original morphological and hydrological characteristics o...

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.…

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…

Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments

Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most …

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…

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.

Functional ecological patterns and the effect of anthropogenic disturbances on a recently restored Mediterranean coastal lagoon. Needs for a sustainable restoration

Abstract We present here a detailed case study on the lessons learned after a restoration process of a natural ecosystem, which can be considered as an ecological experiment. Senillar de Moraira is a brackish water small coastal lagoon located in the Spanish Mediterranean coast. It is separated from the sea by a sand bar and a beach, and is regularly fed by groundwater. Mostly due to the strong anthropogenic pressure this lagoon was degraded, and a restoration process, consisting mostly on the rebuilt of hydrogeomorphological features, was accomplished about a decade ago. After the restoration project, ecological monitoring was performed to reveal the recovery of the ecological integrity of…

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.

A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins

Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The Europea…

Stratification strength and light climate explain variation in chlorophyll a at the continental scale in a European multilake survey in a heatwave summer

The authors acknowledge COST Action ES 1105 "CYANOCOST Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management" and COST Action Global Change Biology ES 1201 NETLAKE -Networking Lake Observatories in Europe" for contributing to this study through networking and knowledge sharing with European experts in the field. We acknowledge the members of the Global Lake Ecological Observatory Network (GLEON) for their collaborative spirit and enthusiasm that inspired the grassroots effort of the EMLS. E.M. was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation to Bas Ibelings and by supplementary funding from University of Geneva…

Effect of wastewater management on phosphorus content and sedimentary fractionation in Mediterranean saline lakes

The La Mancha Húmeda Biosphere Reserve is the largest wetland district in the Iberian Peninsula, containing many temporary saline lakes undergoing different anthropogenic pressures. Eleven of these lakes were selected to assess phosphorus (P) burial, fractionation and mobilization in their sediments. Wastewater inputs, wherever they occurred, favored accumulation of all P sedimentary fractions, which took place mainly via precipitation with divalent cations (i.e. calcium or magnesium) and as buried organic matter, both representing relatively occluded P forms, although they can also be involved in P release. P immobilization would be partially restrained in the volcanic lakes of the region,…

Effect of experimentally increased nutrient availability on the structure, metabolic activities, and potential microbial functions of a maritime Antarctic microbial mat.

The role of competitive interactions based on resource utilisation was explored in a phototrophic microbial mat from Byers Peninsula (Maritime Antarctica). Shotgun metagenomic profiling of the mat showed a taxonomic and functionally diverse microbial community. The heterotrophic bacterial community was dominated by Proteobacteria, where genera typically found in polar habitats, such as Janthinobacterium, Pseudomonas, and Polaromonas, were highly prevalent. Cyanobacteria played the main role as primary producers, accompanied by diatoms and chlorophytes. To test the potential effects of the inorganic nutrient (N and P) availability on this community, a fully factorial nitrate and phosphorus a…

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…

Carbon metabolic rates and GHG emissions in different wetland types of the Ebro Delta

Deltaic wetlands are highly productive ecosystems, which characteristically can act as C-sinks. However, they are among the most threatened ecosystems, being very vulnerable to global change, and require special attention towards its conservation. Knowing their climate change mitigating potential, conservation measures should also be oriented with a climatic approach, to strengthen their regulatory services. In this work we studied the carbon biogeochemistry and the specific relevance of certain microbial guilds on carbon metabolisms of the three main types of deltaic wetlands located in the Ebro Delta, north-eastern Spain, as well as how they deal with human pressures and climate change ef…

Environmental and Human Drivers of Carbon Sequestration and Greenhouse Gas Emissions in the Ebro Delta, Spain

Metacommunities from bacteria to birds: stronger environmental selection in mediterranean than in tropical ponds

AbstractThe metacommunity concept provides a theoretical framework that aims at explaining organism distributions by a combination of environmental filtering, dispersal and drift. With the development of statistical tools to quantify and partially isolate the role of each of these processes, empirical metacommunity studies have multiplied worldwide. However, few works attempt a multi-taxon approach and even fewer compare two distant biogeographical regions using the same methodology. Under this framework, we tested the expectation that temperate (mediterranean-climate) pond metacommunities would be more influenced by environmental and spatial processes than tropical ones, because of stronge…

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.

Functional Metabolic Diversity of Bacterioplankton in Maritime Antarctic Lakes

A summer survey was conducted on the bacterioplankton communities of seven lakes from Byers Peninsula (Maritime Antarctica), differing in trophic and morphological characteristics. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The versatility for metabolizing carbon sources was also assessed in three of the lakes using Biolog Ecoplates. Relevant differences among lakes and within lake depths were observed. A total of 23 metabolic activities associated to the main biogeochemical cycles were foreseen, namely, carbon (11), nitrogen (4), sulfur (5), iron (2), and hydrogen (1). The aerobic metabolisms dominated, althou…

Bacterioplankton Community Composition Along Environmental Gradients in Lakes From Byers Peninsula (Maritime Antarctica) as Determined by Next-Generation Sequencing

This study comprises the first attempt to describe the planktonic bacterial communities of lakes from Byers Peninsula, one of the most significant limnological districts in the Maritime Antarctica, leveraging next-generation sequencing (NGS) technologies. For the survey, we selected 7 lakes covering the environmental gradient from inland to coastal lakes, some of them sampled both in surface and deep waters. Analysis provided just over 85,000 high quality sequences that were clustered into 864 unique Zero-radius Operational Taxonomic Units (ZOTUs) (i.e., 100% sequence similarity). Yet, several taxonomic uncertainties remained in the analysis likely suggesting the occurrence of local bacteri…

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…

Diversity of freshwater Epsilonproteobacteria and dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake.

Sulfidic redoxclines are a suitable niche for the growth and activity of different chemo- and photolithotrophic sulphide-oxidizing microbial groups such as the Epsilonproteobacteria and the green sulfur bacteria (GSB). We have investigated the diversity, abundance and contribution to inorganic carbon uptake of Epsilonproteobacteria in a meromictic basin of Lake Banyoles. CARD-FISH counts revealed that Epsilonproteobacteria were prevalent at the redoxcline in winter (maximum abundance of 2 × 10(6) cells mL(-1), ≈60% of total cells) but they were nearly absent in summer, when GSB bloomed. This seasonal trend was supported by 16S rRNA gene pyrotag datasets, which revealed that the epsilonprote…

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.

Lake La Cruz, an Iron-Rich Karstic Meromictic Lake in Central Spain

Laguna de la Cruz (Lake La Cruz ) is a small karstic meromictic lake located in Central-Eastern Spain. Its biogenic meromixis (originated ca.1660) is favoured by the high relative depth and the steep doline walls. Calcium and magnesium bicarbonate are the main salts. The monimolimnion permanently spans from 18 m to the lake bottom (ca.21 m), whereas thermal stratification occurs above from April to October. Steep chemical gradients appear both at the bottom of the metalimnion (seasonally) and, permanently, at the permanent chemocline (16–18 m). Nutrients in surface waters decay as stratification advances, but deeper they are abundant. Linked to physical and chemical gradients, sharply strat…

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…

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants

© The Author(s).

Temperature effects explain continental scale distribution of cyanobacterial toxins

Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect…

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.

Structure of planktonic microbial communities along a trophic gradient in lakes of Byers Peninsula, South Shetland Islands

AbstractA systematic limnological survey of water bodies of Byers Peninsula (Livingston Island, South Shetland Islands) was carried out during the summer of 2001/02. Abundances of microbial plankton were determined which allowed a delineation of the pelagic food web structure. We also report the nutrient status of these lakes. We demonstrate the occurrence of a trophic gradient that extended from upland lakes (oligotrophic) to the coastal ones (eutrophic). The study shows that a lake's morphology regulates the relative importance of the pelagic and benthic habitats, whereas nutrient loads mainly determine its trophic status. Yet, some of the variability observed could be also a legacy of th…

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.

Influence of the conservation status on carbon balances of semiarid coastal Mediterranean wetlands

Permanent freshwater and brackish marshes are the typical wetland type of the Mediterranean Spanish coast. Historically, alterations to the original morphological and hydrological characteristics of some these ecosystems have increased their trophic status, which could influence the carbon (C) balance, while other ecosystems remain close to their natural condition. In this work, the main processes related to the C cycle were studied in several Mediterranean coastal marshes with different degrees of alteration and in sites restored and managed in different ways. Carbon associated with greenhouse gases (CO2 and CH4) was determined using gas exchange methods for plankton, benthos, and sediment…

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.