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  • 1
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    Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates
    Springer Science and Business Media LLC ; 2022
    In:  BMC Biology Vol. 20, No. 1 ( 2022-08-08)
    Details
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2022-08-08)
    Abstract: 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. Results Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ ggp/gpg/gmg clusters and glycerolipids glpK / glpA ), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. Conclusions The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.
    Type of Medium: Online Resource
    ISSN: 1741-7007
    URL: Article
    DOI: 10.1186/s12915-022-01379-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2133020-7
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  • 2
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    α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats
    Springer Science and Business Media LLC ; 2022
    In:  The ISME Journal Vol. 16, No. 10 ( 2022-10), p. 2421-2432
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 16, No. 10 ( 2022-10), p. 2421-2432
    Abstract: RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO 2 and O 2 . To compensate, organisms have evolved convergent solutions to concentrate CO 2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet’s carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/s41396-022-01282-z
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2299378-2
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  • 3
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    Vertical niche occupation and potential metabolic interplay of microbial consortia in a deeply stratified meromictic model lake
    Wiley ; 2023
    In:  Limnology and Oceanography Vol. 68, No. 11 ( 2023-11), p. 2492-2511
    Details
    In: Limnology and Oceanography, Wiley, Vol. 68, No. 11 ( 2023-11), p. 2492-2511
    Abstract: The microbial ecology of meromictic lakes assessed with “omics” is still poorly studied compared to other aquatic systems. Here, a combination of metagenomics, high resolution sampling and detailed physical–chemical data gathering allowed to study the planktonic prokaryotic assemblages and metabolic capabilities in the crenogenic meromictic Lake El Tobar (Spain), a model lake for such purposes. This system presents a specific stratification comprising a freshwater layer and a halocline linked to the oxycline, driving to the euxinic hypersaline waters of the deep monimolimnion. The different strata showed a highly diverse and vertically distributed microbiome with their metabolic capacities fitting/influencing the physical–chemical environment. Overall, up to 338 novel genomes were found from metagenome assembled genomes. Picocyanobacteria and methanotrophs were abundant in the upper part of the oxycline. Anoxygenic phototrophs ( Chlorobium , Thiohalocapsa , Chromatiaceae, Rhodospirillum, and Rhodobacteraceae spp.) dominated the 12.5–14 m anoxic waters with dim light availability. Sulfate reducers (Desulfobacterota and Firmicutes) inhabited low redox horizons from 13.5 to the bottom (18 m). The potential microbial synergistic performance increases toward the monimolimnion. Among these, a microbial assemblage mostly composed of Spirochaetota, Cloacimonadota, Omitrophota, Firmicutes, Marinisomatota, Nanoarchaeota, and Patescibacteria in hypersaline waters of 14–18 m (conductivities of 118–213 mS cm −1 ), is potentially capable of performing mixed‐acid fermentations, even including hydrogen and butanol biosynthesis of biotechnological interest. This metagenomics study shows how microbial lifestyles may be determinant in the interplay of environmental gradients, and exemplifies the potential interactions between the microbial guilds thereby.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    URL: Article
    DOI: 10.1002/lno.v68.11
    DOI: 10.1002/lno.12437
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2033191-5
    detail.hit.zdb_id: 412737-7
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  • 4
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    The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics
    Springer Science and Business Media LLC ; 2021
    In:  Environmental Microbiome Vol. 16, No. 1 ( 2021-03-16)
    Details
    In: Environmental Microbiome, Springer Science and Business Media LLC, Vol. 16, No. 1 ( 2021-03-16)
    Abstract: 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 temperature. Despite its well-known hydrology and physicochemical features, 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 shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria ( Synechococcus but a conspicuously absent Prochlorococcus ), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism ( Thioglobus ) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of “dark matter” streamlined genomes of largely unpredictable ecology. Conclusions The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.
    Type of Medium: Online Resource
    ISSN: 2524-6372
    URL: Article
    DOI: 10.1186/s40793-021-00374-1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 3007163-X
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  • 5
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    Ecological and genomic features of two widespread freshwater picocyanobacteria
    Wiley ; 2018
    In:  Environmental Microbiology Vol. 20, No. 10 ( 2018-10), p. 3757-3771
    Details
    In: Environmental Microbiology, Wiley, Vol. 20, No. 10 ( 2018-10), p. 3757-3771
    Abstract: 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 abundant in cold environments including ice‐covered lakes such as Lake Baikal, Lake Erie or the brackish Baltic Sea. Having complete genomes provided access to the flexible genome that does not assemble in MAGs. We found several genomic islands in both genomes, within which there were genes for nitrogen acquisition, transporters for a wide set of compounds and biosynthesis of phycobilisomes in both strains. Some of these regions of low coverage in metagenomes also included antimicrobial compounds, transposases and phage defence systems, including a novel type III CRISPR‐Cas phage defence system that was only detected in Synechococcus lacustris Tous.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2018.20.issue-10
    DOI: 10.1111/1462-2920.14377
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020213-1
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  • 6
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    The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth
    Elsevier BV ; 2024
    In:  Environmental Pollution Vol. 342 ( 2024-02), p. 123065-
    Details
    In: Environmental Pollution, Elsevier BV, Vol. 342 ( 2024-02), p. 123065-
    Type of Medium: Online Resource
    ISSN: 0269-7491
    URL: Article
    DOI: 10.1016/j.envpol.2023.123065
    RVK:
    AR 10100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 280652-6
    detail.hit.zdb_id: 2013037-5
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  • 7
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    Antibiotic resistance genes correlate with metal resistances and accumulate in the deep water layers of the Black Sea
    Elsevier BV ; 2022
    In:  Environmental Pollution Vol. 312 ( 2022-11), p. 120033-
    Details
    In: Environmental Pollution, Elsevier BV, Vol. 312 ( 2022-11), p. 120033-
    Type of Medium: Online Resource
    ISSN: 0269-7491
    URL: Article
    DOI: 10.1016/j.envpol.2022.120033
    RVK:
    AR 10100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 280652-6
    detail.hit.zdb_id: 2013037-5
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  • 8
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    Polymicrobial Aggregates in Human Saliva Build the Oral Biofilm
    American Society for Microbiology ; 2022
    In:  mBio Vol. 13, No. 1 ( 2022-02-22)
    Details
    In: mBio, American Society for Microbiology, Vol. 13, No. 1 ( 2022-02-22)
    Abstract: Biofilm community development has been established as a sequential process starting from the attachment of single cells on a surface. However, microorganisms are often found as aggregates in the environment and in biological fluids. Here, we conduct a comprehensive analysis of the native structure and composition of aggregated microbial assemblages in human saliva and investigate their spatiotemporal attachment and biofilm community development. Using multiscale imaging, cell sorting, and computational approaches combined with sequencing analysis, a diverse mixture of aggregates varying in size, structure, and microbial composition, including bacteria associated with host epithelial cells, can be found in saliva in addition to a few single-cell forms. Phylogenetic analysis reveals a mixture of complex consortia of aerobes and anaerobes in which bacteria traditionally considered early and late colonizers are found mixed together. When individually tracked during colonization and biofilm initiation, aggregates rapidly proliferate and expand tridimensionally, modulating population growth, spatial organization, and community scaffolding. In contrast, most single cells remain static or are incorporated by actively growing aggregates. These results suggest an alternative biofilm development process whereby aggregates containing different species or associated with human cells collectively adhere to the surface as “growth nuclei” to build the biofilm and shape polymicrobial communities at various spatial and taxonomic scales. IMPORTANCE Microbes in biological fluids can be found as aggregates. How these multicellular structures bind to surfaces and initiate the biofilm life cycle remains understudied. Here, we investigate the structural organization of microbial aggregates in human saliva and their role in biofilm formation. We found diverse mixtures of aggregates with different sizes, structures, and compositions in addition to free-living cells. When individually tracked during binding and growth on tooth-like surfaces, most aggregates developed into structured biofilm communities, whereas most single cells remained static or were engulfed by the growing aggregates. Our results reveal that preformed microbial consortia adhere as “buds of growth,” governing biofilm initiation without specific taxonomic order or cell-by-cell succession, which provide new insights into spatial and population heterogeneity development in complex ecosystems.
    Type of Medium: Online Resource
    ISSN: 2150-7511
    URL: Article
    DOI: 10.1128/mbio.00131-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 2557172-2
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  • 9
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    Zooplankton as a Transitional Host for Escherichia coli in Freshwater
    American Society for Microbiology ; 2022
    In:  Applied and Environmental Microbiology Vol. 88, No. 9 ( 2022-05-10)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 88, No. 9 ( 2022-05-10)
    Abstract: This study shows that Escherichia coli can be temporarily enriched in zooplankton under natural conditions and that these bacteria can belong to different phylogroups and sequence types (STs), including environmental, clinical, and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically, the two isolates were closer to strains isolated from poultry meat than to freshwater E. coli , albeit their genomes were smaller than those of the poultry isolates. After isolation and fluorescent protein tagging of strains ED1 and ED157, we show that Daphnia sp. can take up these strains and release them alive again, thus becoming a temporary host for E. coli . In a chemostat experiment, we show that this association does not prolong bacterial long-term survival, but at low abundances it also does not significantly reduce bacterial numbers. We demonstrate that E. coli does not belong to the core microbiota of Daphnia , suffers from competition by the natural Daphnia microbiota, but can profit from its carapax to survive in water. All in all, this study suggests that the association of E. coli with Daphnia is only temporary, but the cells are viable therein, and this might allow encounters with other bacteria for genetic exchange and potential genomic adaptation to the freshwater environment. IMPORTANCE The contamination of freshwater with feces-derived bacteria is a major concern regarding drinking water acquisition and recreational activities. Ecological interactions promoting their persistence are still very scarcely studied. This study, which analyses the survival of E. coli in the presence of zooplankton, is thus of ecological and water safety relevance.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/aem.02522-21
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2022
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 10
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    The “Dark Side” of Picocyanobacteria: Life as We Do Not Know It (Yet)
    MDPI AG ; 2022
    In:  Microorganisms Vol. 10, No. 3 ( 2022-03-02), p. 546-
    Details
    In: Microorganisms, MDPI AG, Vol. 10, No. 3 ( 2022-03-02), p. 546-
    Abstract: Picocyanobacteria of the genus Synechococcus (together with Cyanobium and Prochlorococcus) have captured the attention of microbial ecologists since their description in the 1970s. These pico-sized microorganisms are ubiquitous in aquatic environments and are known to be some of the most ancient and adaptable primary producers. Yet, it was only recently, and thanks to developments in molecular biology and in the understanding of gene sequences and genomes, that we could shed light on the depth of the connection between their evolution and the history of life on the planet. Here, we briefly review the current understanding of these small prokaryotic cells, from their physiological features to their role and dynamics in different aquatic environments, focussing particularly on the still poorly understood ability of picocyanobacteria to adapt to dark conditions. While the recent discovery of Synechococcus strains able to survive in the deep Black Sea highlights how adaptable picocyanobacteria can be, it also raises more questions—showing how much we still do not know about microbial life. Using available information from brackish Black Sea strains able to perform and survive in dark (anoxic) conditions, we illustrate how adaptation to narrow ecological niches interacts with gene evolution and metabolic capacity.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms10030546
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2720891-6
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