{"entity": "journal", "iuid": "588129e9dfce481b854d00956b7d64e6", "timestamp": "2026-04-12T03:53:22.248Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Environ.%20Microbiol..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Environ.%20Microbiol."}}, "title": "Environ. Microbiol.", "issn": "1462-2920", "issn-l": "1462-2912", "publications_count": 13, "publications": [{"entity": "publication", "iuid": "0975152f3c0e48d89ba780a04681382b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b"}}, "title": "Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica.", "authors": [{"family": "Liao", "given": "Jingqiu", "initials": "J", "orcid": "0000-0002-2579-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac812840b9814e919ed1dca12a484c87.json"}}, {"family": "Orsi", "given": "Renato Hohl", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "22", "issue": "7", "pages": "2811-2828", "issn-l": "1462-2912"}, "abstract": "Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.", "doi": "10.1111/1462-2920.15014", "pmid": "32337816", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:25:39.817Z", "modified": "2025-03-18T17:25:39.889Z"}, {"entity": "publication", "iuid": "7a3f851c8c52495aaf0a1e133ab52985", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a3f851c8c52495aaf0a1e133ab52985.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a3f851c8c52495aaf0a1e133ab52985"}}, "title": "Life in the dark: far-red absorbing cyanobacteria extend photic zones deep into terrestrial caves.", "authors": [{"family": "Behrendt", "given": "Lars", "initials": "L", "orcid": "0000-0002-8988-2032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/037bb8f29ff24e95b3358ab1f0ff2ee6.json"}}, {"family": "Trampe", "given": "Erik L", "initials": "EL"}, {"family": "Nord", "given": "Nadia B", "initials": "NB"}, {"family": "Nguyen", "given": "Jen", "initials": "J"}, {"family": "K\u00fchl", "given": "Michael", "initials": "M"}, {"family": "Lonco", "given": "Danijela", "initials": "D"}, {"family": "Nyarko", "given": "Alex", "initials": "A"}, {"family": "Dhinojwala", "given": "Ali", "initials": "A"}, {"family": "Hershey", "given": "Olivia S", "initials": "OS"}, {"family": "Barton", "given": "Hazel", "initials": "H"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "issn-l": "1462-2912", "volume": "22", "issue": "3", "pages": "952-963"}, "abstract": "Chlorophyll (Chl) f and d are the most recently discovered chlorophylls, enabling cyanobacteria to harvest near-infrared radiation (NIR) at 700-780 nm for oxygenic photosynthesis. Little is known about the occurrence of these pigments in terrestrial habitats. Here, we provide first details on spectral photon irradiance within the photic zones of four terrestrial cave systems in concert with a detailed investigation of photopigmentation, light reflectance and microbial community composition. We frequently found Chl f and d along the photic zones of caves characterized by low light enriched in NIR and inhabited by cyanobacteria producing NIR-absorbing pigments. Surprisingly, deeper parts of caves still contained NIR, an effect likely attributable to the reflectance of specific wavelengths by the surface materials of cave walls. We argue that the stratification of microbial communities across the photic zones of cave entrances resembles the light-driven species distributions in forests and aquatic environments.", "doi": "10.1111/1462-2920.14774", "pmid": "31390129", "labels": {"Lars Behrendt": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-10-05T09:23:01.943Z", "modified": "2022-11-04T11:32:15.274Z"}, {"entity": "publication", "iuid": "18c617f0c4a54376bf2893e01d191ddd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/18c617f0c4a54376bf2893e01d191ddd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/18c617f0c4a54376bf2893e01d191ddd"}}, "title": "Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria.", "authors": [{"family": "Muthusamy", "given": "Saraladevi", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Mamede Branca", "given": "Rui Miguel", "initials": "RM"}, {"family": "Baltar", "given": "Federico", "initials": "F"}, {"family": "Gonz\u00e1lez", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "19", "issue": "6", "pages": "2301-2319", "issn-l": "1462-2912"}, "abstract": "Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.", "doi": "10.1111/1462-2920.13725", "pmid": "28371138", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T12:59:10.872Z", "modified": "2018-12-05T12:59:10.890Z"}, {"entity": "publication", "iuid": "a9e6ee0f98834d07bfc063774c0be432", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a9e6ee0f98834d07bfc063774c0be432.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a9e6ee0f98834d07bfc063774c0be432"}}, "title": "Mixing of water masses caused by a drifting iceberg affects bacterial activity, community composition and substrate utilization capability in the Southern Ocean.", "authors": [{"family": "Dinasquet", "given": "Julie", "initials": "J"}, {"family": "Richert", "given": "Inga", "initials": "I"}, {"family": "Logares", "given": "Ramiro", "initials": "R"}, {"family": "Yager", "given": "Patricia", "initials": "P"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "19", "issue": "6", "pages": "2453-2467", "issn-l": "1462-2912"}, "abstract": "The number of icebergs produced from ice-shelf disintegration has increased over the past decade in Antarctica. These drifting icebergs mix the water column, influence stratification and nutrient condition, and can affect local productivity and food web composition. Data on whether icebergs affect bacterioplankton function and composition are scarce, however. We assessed the influence of iceberg drift on bacterial community composition and on their ability to exploit carbon substrates during summer in the coastal Southern Ocean. An elevated bacterial production and a different community composition were observed in iceberg-influenced waters relative to the undisturbed water column nearby. These major differences were confirmed in short-term incubations with bromodeoxyuridine followed by CARD-FISH. Furthermore, one-week bottle incubations amended with inorganic nutrients and carbon substrates (a mix of substrates, glutamine, N-acetylglucosamine, or pyruvate) revealed contrasting capacity of bacterioplankton to utilize specific carbon substrates in the iceberg-influenced waters compared with the undisturbed site. Our study demonstrates that the hydrographical perturbations introduced by a drifting iceberg can affect activity, composition, and substrate utilization capability of marine bacterioplankton. Consequently, in a context of global warming, increased frequency of drifting icebergs in polar regions holds the potential to affect carbon and nutrient biogeochemistry at local and possibly regional scales.", "doi": "10.1111/1462-2920.13769", "pmid": "28429510", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T12:59:07.179Z", "modified": "2018-12-05T12:59:07.198Z"}, {"entity": "publication", "iuid": "5dd1b690eb724f25a6b7d6af56fa1815", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd1b690eb724f25a6b7d6af56fa1815.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5dd1b690eb724f25a6b7d6af56fa1815"}}, "title": "Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Ekstam", "given": "B\u00f6rje", "initials": "B"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/290a3bc9eb554620906b93d7f1d57184.json"}}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/28b77762086343048e74046a6486caff.json"}}], "type": "journal article", "published": "2017-03-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "19", "issue": "3", "pages": "1222-1236", "issn-l": "1462-2912"}, "abstract": "Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.", "doi": "10.1111/1462-2920.13650", "pmid": "28028880", "labels": {"Affiliated researcher": null, "Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-05T12:12:42.674Z", "modified": "2023-10-27T09:40:16.524Z"}, {"entity": "publication", "iuid": "f8c0737a0f5342ae96a101ef017b4578", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f8c0737a0f5342ae96a101ef017b4578.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f8c0737a0f5342ae96a101ef017b4578"}}, "title": "Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.", "authors": [{"family": "Celepli", "given": "Narin", "initials": "N"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Dupont", "given": "Chris L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}], "type": "journal article", "published": "2017-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "19", "issue": "2", "pages": "673-686", "issn-l": "1462-2912"}, "abstract": "Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16\u00a0psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.", "doi": "10.1111/1462-2920.13592", "pmid": "27871145", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T11:16:48.759Z", "modified": "2018-12-05T11:16:48.779Z"}, {"entity": "publication", "iuid": "5d11b6b4436d4a5e9f12b362311cc121", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5d11b6b4436d4a5e9f12b362311cc121.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5d11b6b4436d4a5e9f12b362311cc121"}}, "title": "Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.", "authors": [{"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2016-12-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "18", "issue": "12", "pages": "4442-4455", "issn-l": "1462-2912"}, "abstract": "Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from \u223c0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 \u03bcm), relative to the medium (0.8-3.0 \u03bcm) and large (>3.0 \u03bcm) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.", "doi": "10.1111/1462-2920.13407", "pmid": "27306515", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T12:14:05.406Z", "modified": "2018-12-05T12:14:05.425Z"}, {"entity": "publication", "iuid": "ea99c55797364c86854c8dc8e16fc91f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea99c55797364c86854c8dc8e16fc91f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea99c55797364c86854c8dc8e16fc91f"}}, "title": "A Rickettsiales symbiont of amoebae with ancient features.", "authors": [{"family": "Schulz", "given": "Frederik", "initials": "F"}, {"family": "Martijn", "given": "Joran", "initials": "J"}, {"family": "Wascher", "given": "Florian", "initials": "F"}, {"family": "Lagkouvardos", "given": "Ilias", "initials": "I"}, {"family": "Kostanj\u0161ek", "given": "Rok", "initials": "R"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}, {"family": "Horn", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2016-09-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "18", "issue": "8", "pages": "2326-2342", "issn-l": "1462-2912"}, "abstract": "The Rickettsiae comprise intracellular bacterial symbionts and pathogens infecting diverse eukaryotes. Here, we provide a detailed characterization of 'Candidatus\u2005Jidaibacter acanthamoeba', a rickettsial symbiont of Acanthamoeba. The bacterium establishes the infection in its amoeba host within 2\u2009h where it replicates within vacuoles. Higher bacterial loads and accelerated spread of infection at elevated temperatures were observed. The infection had a negative impact on host growth rate, although no increased levels of host cell lysis were seen. Phylogenomic analysis identified this bacterium as member of the Midichloriaceae. Its 2.4\u2009Mb genome represents the largest among Rickettsiales and is characterized by a moderate degree of pseudogenization and a high coding density. We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich repeats and tetratricopeptide repeats, which likely function in host interaction. There are a total of three divergent, independently acquired type IV secretion systems, and 35 flagellar genes representing the most complete set found in an obligate intracellular Alphaproteobacterium. The deeply branching phylogenetic position of 'Candidatus\u2005Jidaibacter acanthamoeba' together with its ancient features place it closely to the rickettsial ancestor and helps to better understand the transition from a free-living to an intracellular lifestyle.", "doi": "10.1111/1462-2920.12881", "pmid": "25908022", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T10:16:57.933Z", "modified": "2018-12-05T10:16:57.952Z"}, {"entity": "publication", "iuid": "9c3fb756407a4e84a2c74092a2e651ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3fb756407a4e84a2c74092a2e651ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3fb756407a4e84a2c74092a2e651ee"}}, "title": "Bacterial diversity along a 2600\u2009km river continuum.", "authors": [{"family": "Savio", "given": "Domenico", "initials": "D"}, {"family": "Sinclair", "given": "Lucas", "initials": "L"}, {"family": "Ijaz", "given": "Umer Z", "initials": "UZ"}, {"family": "Parajka", "given": "Juraj", "initials": "J"}, {"family": "Reischer", "given": "Georg H", "initials": "GH"}, {"family": "Stadler", "given": "Philipp", "initials": "P"}, {"family": "Blaschke", "given": "Alfred P", "initials": "AP"}, {"family": "Bl\u00f6schl", "given": "G\u00fcnter", "initials": "G"}, {"family": "Mach", "given": "Robert L", "initials": "RL"}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AK"}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2015-12-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "17", "issue": "12", "pages": "4994-5007", "issn-l": "1462-2912"}, "abstract": "The bacterioplankton diversity in large rivers has thus far been under-sampled despite the importance of streams and rivers as components of continental landscapes. Here, we present a comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries. Using 16S rRNA-gene amplicon sequencing, our analysis revealed that bacterial richness and evenness gradually declined downriver in both the free-living and particle-associated bacterial communities. These shifts were also supported by beta diversity analysis, where the effects of tributaries were negligible in regards to the overall variation. In addition, the river was largely dominated by bacteria that are commonly observed in freshwaters. Dominated by the acI lineage, the freshwater SAR11 (LD12) and the Polynucleobacter group, typical freshwater taxa increased in proportion downriver and were accompanied by a decrease in soil and groundwater-affiliated bacteria. Based on views of the meta-community and River Continuum Concept, we interpret the observed taxonomic patterns and accompanying changes in alpha and beta diversity with the intention of laying the foundation for a unified concept for river bacterioplankton diversity. ", "doi": "10.1111/1462-2920.12886", "pmid": "25922985", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC4918796"}, {"db": "mid", "key": "EMS68181"}], "notes": [], "created": "2018-12-05T08:57:32.183Z", "modified": "2018-12-05T08:57:32.213Z"}, {"entity": "publication", "iuid": "c90dd8628f7047bbb3295840d2cc5a75", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c90dd8628f7047bbb3295840d2cc5a75.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c90dd8628f7047bbb3295840d2cc5a75"}}, "title": "Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Baltar", "given": "Federico", "initials": "F"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Muthusamy", "given": "Saraladevi", "initials": "S"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2015-07-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "17", "issue": "7", "pages": "2459-2476", "issn-l": "1462-2912"}, "abstract": "Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.", "doi": "10.1111/1462-2920.12720", "pmid": "25403576", "labels": {"Affiliated researcher": null, "Luisa Hugerth": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2018-12-05T09:06:32.502Z", "modified": "2023-10-27T09:34:13.443Z"}, {"entity": "publication", "iuid": "1b139bf7da254b1caadcb1a8ddff07fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1b139bf7da254b1caadcb1a8ddff07fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1b139bf7da254b1caadcb1a8ddff07fe"}}, "title": "Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.", "authors": [{"family": "Leong", "given": "Su-Lin L", "initials": "SL"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV"}, {"family": "Frisvad", "given": "Jens C", "initials": "JC"}, {"family": "Thrane", "given": "Ulf", "initials": "U"}, {"family": "Heipieper", "given": "Hermann J", "initials": "HJ"}, {"family": "Dijksterhuis", "given": "Jan", "initials": "J"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Schn\u00fcrer", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2015-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "17", "issue": "2", "pages": "496-513", "issn-l": "1462-2912"}, "abstract": "Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22\u2009Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X.\u2009bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.\u2009bisporus. However, transcriptomes at optimal (\u223c\u20090.89) versus low aw (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.\u2009bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a 'chaophile', preferring solutes that disorder biomolecular structures. Both X.\u2009bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of 'chaophiles'. ", "doi": "10.1111/1462-2920.12596", "pmid": "25142400", "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T10:14:04.580Z", "modified": "2018-12-05T10:14:04.598Z"}, {"entity": "publication", "iuid": "687d95be22d94d56aecc14766943e3e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/687d95be22d94d56aecc14766943e3e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/687d95be22d94d56aecc14766943e3e2"}}, "title": "Distribution of acI-Actinorhodopsin genes in Baltic Sea salinity gradients indicates adaptation of facultative freshwater photoheterotrophs to brackish waters.", "authors": [{"family": "Salka", "given": "Ivette", "initials": "I"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Grossart", "given": "Hans-Peter", "initials": "HP"}], "type": "journal article", "published": "2014-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "16", "issue": "2", "pages": "586-597", "issn-l": "1462-2912"}, "abstract": "Knowledge on Actinobacteria rhodopsin gene (actR) diversity and spatial distribution is scarce. The Baltic Sea is characterized by strong salinity gradients leading to the coexistence of marine and freshwater bacteria and hence is an ideal study area to elucidate the dispersion and phylogenetic affiliation of actR in dependence on salinity. ActR DGGE fingerprints in summer 2008 revealed between 3 and 19 distinct bands within a salinity range of 2.4-27 PSU. Environmental actR clone sequences were obtained from stations distributed along the whole salinity gradient. Overall, 20 different actR sequence groups (operational taxonomic units) were found, with up to 11 different ones per station. Phylogenetically, the actR sequences were predominantly (80%) affiliated with freshwater acI-Actinobacteria whose 16S rRNA gene accounted for 2-33% of total 16S rRNA genes in both the Bothnian Sea and central Baltic Sea. However, at salinities above 14 PSU, acI-16S rRNA gene accounted for less than 1%. In contrast, the diversity of actR remained high. Changes in actR gene diversity were significantly correlated with salinity, oxygen, silica or abundance of Synechococcus sp. Our results demonstrate a wide distribution of freshwater actR along the Baltic Sea salinity gradient indicating that some freshwater Actinobacteria might have adapted to higher salinities.", "doi": "10.1111/1462-2920.12185", "pmid": "23841943", "labels": {"Sarahi Garcia": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2020-11-05T17:28:35.158Z", "modified": "2022-11-07T11:37:23.511Z"}, {"entity": "publication", "iuid": "94870a6cda6c4e2999c7cfe1f2f07fda", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/94870a6cda6c4e2999c7cfe1f2f07fda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/94870a6cda6c4e2999c7cfe1f2f07fda"}}, "title": "Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium.", "authors": [{"family": "Jonas", "given": "Kristina", "initials": "K"}, {"family": "Edwards", "given": "Adrianne N", "initials": "AN"}, {"family": "Ahmad", "given": "Irfan", "initials": "I"}, {"family": "Romeo", "given": "Tony", "initials": "T"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}, {"family": "Melefors", "given": "Ojar", "initials": "O"}], "type": "journal article", "published": "2010-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "12", "issue": "2", "pages": "524-540", "issn-l": "1462-2912"}, "abstract": "Bacterial survival depends on the ability to switch between sessile and motile lifestyles in response to changing environmental conditions. In many species, this switch is governed by (3'-5')-cyclic-diguanosine monophosphate (c-di-GMP), a signalling molecule, which is metabolized by proteins containing GGDEF and/or EAL domains. Salmonella Typhimurium contains 20 such proteins. Here, we show that the RNA-binding protein CsrA regulates the expression of eight genes encoding GGDEF, GGDEF-EAL and EAL domain proteins. CsrA bound directly to the mRNA leaders of five of these genes, suggesting that it may regulate these genes post-transcriptionally. The c-di-GMP-specific phosphodiesterase STM3611, which reciprocally controls flagella function and production of biofilm matrix components, was regulated by CsrA binding to the mRNA, but was also indirectly regulated by CsrA through the FlhDC/FliA flagella cascade and STM1344. STM1344 is an unconventional (c-di-GMP-inactive) EAL domain protein, recently identified as a negative regulator of flagella gene expression. Here, we demonstrate that CsrA directly downregulates expression of STM1344, which in turn regulates STM3611 through fliA and thus reciprocally controls motility and biofilm factors. Altogether, our data reveal that the concerted and complex regulation of several genes encoding GGDEF/EAL domain proteins allows CsrA to control the motility-sessility switch in S. Typhimurium at multiple levels.", "doi": "10.1111/j.1462-2920.2009.02097.x", "pmid": "19919539", "labels": {"Kristina Jonas": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "EMI2097"}, {"db": "pmc", "key": "PMC2888478"}, {"db": "mid", "key": "NIHMS194244"}], "notes": [], "created": "2018-12-03T14:30:25.734Z", "modified": "2022-11-07T11:33:47.254Z"}], "created": "2018-12-03T14:30:25.747Z", "modified": "2020-11-27T13:12:53.941Z"}