| 1. |
- Alneberg, Johannes, et al.
(author)
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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
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Other publication (other academic/artistic)abstract
- The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.
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| 2. |
- Alneberg, Johannes, et al.
(author)
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Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning
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Other publication (other academic/artistic)abstract
- Aquatic microorganism are key drivers of global biogeochemical cycles and form the basis of aquatic food webs. However, there is still much left to be learned about these organisms and their interaction within specific environments, such as the Baltic Sea. Crucial information for such an understanding can be found within the genome sequences of organisms within the microbial community.In this study, the previous set of Baltic Sea clusters, constructed by Hugert et al., is greatly expanded using a large set of metagenomic samples, spanning the environmental gradients of the Baltic Sea. In total, 124 samples were individually assembled and binned to obtain 2,032 Metagenome Assembled Genomes (MAGs), clustered into 353 prokaryotic and 14 eukaryotic species- level clusters. The prokaryotic genomes were widely distributed over the prokaryotic tree of life, representing 20 different phyla, while the eukaryotic genomes were mostly limited to the division of Chlorophyta. The large number of reconstructed genomes allowed us to identify key factors determining the quality of the genome reconstructions.The Baltic Sea is heavily influenced of human activities of which we might not see the full implications. The genomes reported within this study will greatly aid further studies in our strive for an understanding of the Baltic Sea microbial ecosystem.
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| 3. |
- Andersson, Agneta, et al.
(author)
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The pelagic food web
- 2017
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In: Biological oceanography of the Baltic sea. - Dordrecht : Springer Netherlands. - 9789400706682 - 9789400706675 ; , s. 281-332
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Book chapter (peer-reviewed)abstract
- Environmental drivers and food web structure in the pelagic zone vary from south to north in the Baltic Sea. While nitrogen is generally the limiting nutrient for primary production in the Baltic Sea, phosphorus is the limiting nutrient in the Bothnian Bay. In the Gulf of Bothnia the food web is to a large extent driven by terrestrial allochthonous material, while autochthonous production dominates in the other parts of the Baltic Sea. Changes in bacterioplankton, protist and zooplankton community composition from south to north are mainly driven by salinity. Bacteria are crucial constituents of the pelagic food web (microbial loop) and in oxygen-poor and anoxic bottom waters where they mediate element transformations. Diatoms and dinoflagellates are the major primary producers in the pelagic zone. Summer blooms of diazotrophic (nitrogen-fixing) filamentous cyanobacteria are typical of the Baltic Sea, especially in the Baltic Sea proper and the Gulf of Finland. The mesozooplankton (mainly copepods and cladocerans) channel energy from primary producers and the microbial food web to fish and finally to the top predators in the pelagic system (waterbirds and mammals). Herring and sprat populations are affected by the foraging intensity of their main predator (cod), and therefore the environmental conditions that affect cod may also influence mesozooplankton due to food web effects "cascading down the food web". Anthropogenic pressures, such as overexploitation of fish stocks, eutrophication, climate change, introduction of non-indigenous species and contamination of top predators by hazardous substances, cause changes in the pelagic food web that may have consequences for the balance and stability of the whole ecosystem.
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| 4. |
- Bentzon-Tilia, Mikkel, et al.
(author)
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Cultivation and isolation of N2-fixing bacteria from suboxic waters in the Baltic Sea
- 2014
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In: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 88:2, s. 358-371
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Journal article (peer-reviewed)abstract
- Nitrogenase genes (nifH) from heterotrophic dinitrogen (N-2)-fixing bacteria appear ubiquitous in marine bacterioplankton, but the significance of these bacteria for N cycling is unknown. Quantitative data on the N-2-fixation potential of marine and estuarine heterotrophs are scarce, and the shortage of cultivated specimens currently precludes ecophysiological characterization of these bacteria. Through the cultivation of diazotrophs from suboxic (1.79molO(2)L(-1)) Baltic Sea water in an artificial seawater medium devoid of combined N, we report the cultivability of a considerable fraction of the diazotrophic community in the Gotland Deep. Two nifH clades were present both in situ and in enrichment cultures showing gene abundances of up to 4.6x10(5) and 5.8x10(5)nifH gene copies L-1 within two vertical profiles in the Baltic Sea. The distributions of the two clades suggested a relationship with the O-2 concentrations in the water column as abundances increased in the suboxic and anoxic waters. It was possible to cultivate and isolate representatives from one of these prevalent clades, and preliminary analysis of their ecophysiology demonstrated growth optima at 0.5-15molO(2)L(-1) and 186-194molO(2)L(-1) in the absence of combined N.
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| 5. |
- Berglund, Johnny, et al.
(author)
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Use of group-specific PCR primers for identification of chrysophytes by denaturing gradient gel electrophoresis
- 2005
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In: Aquatic Microbial Ecology. - Olendorf/Luhe : Inter-Research. - 0948-3055 .- 1616-1564. ; 39:2, s. 171-182
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Journal article (peer-reviewed)abstract
- The chrysophytes Chrysophyceae and Synurophyceae are ecologically important groups of autotrophic, mixotrophic and heterotrophic flagellates. The smallest forms are difficult to identify by classical microscopy but have important functions both as primary producers and as consumers of bacteria in the aquatic food chain. Group-specific primers for amplification of the 18S small sub-unit rRNA gene were developed for analysis of chrysophyte diversity by denaturing gradient gel electrophoresis (DGGE). Two different primer pairs were tested. The first primer pair (EukC1-F–Chryso-R) primarily targeted Paraphysomonadaceae and Ochromonadales, which generally have heterotrophic or mixotrophic nutrition. The second primer pair (EukC2-F–Chryso-R) targeted both Chrysophyceae and Synurophyceae. The primer pairs were tested for PCR amplification of the 18S rRNA gene of 25 cultured chrysophyte species and 6 other closely related nanoplanktonic species. Both primer pairs performed well, since PCR products were obtained for the corresponding chrysophyte cultures. None of the non-chrysophyte species were amplified with these primers. PCR products of chrysophyte cultures could be separated by DGGE in a denaturing gradient from 40 to 60%. In order to test this PCR-DGGE system for natural planktonic systems, we used field samples from a brackish water area (Baltic Sea) and a freshwater lake. The most intense DGGE bands were excised, sequenced and compared to sequences in GenBank. All obtained sequences grouped within the chrysophytes. Thus, the method seems to be promising for examining chrysophyte diversity in planktonic systems.
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| 6. |
- Eriksson, Karolina I. A., 1991-
(author)
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Bacteria that escape predation : waterborne pathogens and their relatives
- 2023
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Doctoral thesis (other academic/artistic)abstract
- The hidden presence of opportunistic bacterial pathogens in the environment evokes concerns about emerging diseases, especially in the light of climate change. The co-evolution of bacteria and their predators (protozoa) has led to bacterial defence strategies of which some contribute to the ability of bacteria to cause disease. To increase our understanding of the interplay between bacteria, protozoa, land use, and climate scenarios in Nordic brackish and freshwater, four studies were designed. The first study explored the co-occurrence patterns between predation resistant bacteria (PRB) and bacterivorous protozoa in a coastal area in the northern Baltic Sea. The results showed higher PRB diversity in the bays and freshwater inlets, than in the offshore waters. Further, genotype specific interactions between protozoa and bacteria were identified. The second study focused on Legionella species diversity and their association with humic substances and low salinity, potentially facilitated through the promotion of the heterotrophic microbial food web or by iron availability. The third study examined the impact of intensified land use on bacterial taxa abundance and community composition in lake inflows, demonstrating indirect downstream effects on water quality. Factors such as pastures, fields, farms, aluminium, iron, and humic substances were linked to increased Legionella abundance. The fourth study exposed aquatic organisms to climate change scenarios, causing eutrophication or brownification with elevated iron levels. Pseudomonas aeruginosa were found to be especially persistent to iron, likely linked to the same mechanism that enables survival in protozoan cells. This trait was shared with other observed intracellular pathogens and uncultured species, who showed elevated resilience to brownification and ability to survive outside host cells. These findings identified complex relationships, which improve our understanding of the intricate dynamics that shape aquatic ecosystems, and highlight the importance of considering multiple factors in managing water resources and maintaining ecosystem health. Human activities including intensified land use can have far-reaching consequences, jeopardizing the pristine nature of water bodies and escalate the presence of environmental and opportunistic bacterial pathogens.
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| 7. |
- Herlemann, Daniel P. R., et al.
(author)
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Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria
- 2013
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In: mBio. - 2161-2129 .- 2150-7511. ; 4:3, s. e00569-12-
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Journal article (peer-reviewed)abstract
- The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype's distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates. IMPORTANCE The ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the class Spartobacteria within the Verrucomicrobia that, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquatic Verrucomicrobia by applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able to in silico isolate genome fragments belonging to a phylotype of the Spartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs with Cyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.
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| 8. |
- Izabel-Shen, Dandan, et al.
(author)
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Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles
- 2021
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 12
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Journal article (peer-reviewed)abstract
- Abundance-occupancy relationships (AORs) are an important determinant of biotic community dynamics and habitat suitability. However, little is known about their role in complex bacterial communities, either within a phylogenetic framework or as a function of niche breadth. Based on data obtained in a field study in the St. Lawrence Estuary, we used 16S rRNA gene sequencing to examine the vertical patterns, strength, and character of AORs for particle-attached and free-living bacterial assemblages. Free-living communities were phylogenetically more diverse than particle-attached communities. The dominant taxa were consistent in terms of their presence/absence but population abundances differed in surface water vs. the cold intermediate layer. Significant, positive AORs characterized all of the surveyed communities across all taxonomic ranks of bacteria, thus demonstrating an ecologically conserved trend for both free-living and particle-attached bacteria. The strength of the AORs was low at the species level but higher at and above the genus level. These results demonstrate that an assessment of the distributions and population densities of finely resolved taxa does not necessarily improve determinations of apparent niche differences in marine bacterioplankton communities at regional scales compared with the information inferred from a broad taxonomic classification.
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| 9. |
- Jürgens, Klaus, et al.
(author)
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[Indirect parameters: Ecosystem] Microbial community and processes
- 2021
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In: Climate change in the baltic sea. - Helsinki : Helsinki Commission (HELCOM). ; , s. 39-39
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Book chapter (peer-reviewed)abstract
- This overview focuses on bacterioplankton, comprising single-celled prokaryotes, i.e.,small organisms that lack a nucleus (Bacteriaand Archaea), in the water column, consuming organic carbon as an energy and carbonsource. Benthic prokaryotes and protozoa (i.e., unicellular zooplankton and zoobenthos) are also important but not included here. Bacteria are the major transformers of carbon, nitrogen, sulphur, and trace metalcycles in aquatic environments. The supply of organic carbon mainly controls bacterial biomass production. The bacterial community composition changes along the salinity andoxygen gradients of the Baltic Sea. Shifts in, e.g., food sources, temperature, and oxygen concentration result in rapid bacterioplankton community changes, with potential impact also on overall ecosystem functions, such as respiration, carbon consumption, and biomass production.
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| 10. |
- Kuliński, Karol, et al.
(author)
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Biogeochemical functioning of the Baltic Sea
- 2022
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In: Earth System Dynamics. - : Copernicus GmbH. - 2190-4979 .- 2190-4987. ; 13, s. 633-685
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Research review (peer-reviewed)abstract
- Location, specific topography, and hydrographic setting together with climate change and strong anthropogenic pressure are the main factors shaping the biogeochemical functioning and thus also the ecological status of the Baltic Sea. The recent decades have brought significant changes in the Baltic Sea. First, the rising nutrient loads from land in the second half of the 20th century led to eutrophication and spreading of hypoxic and anoxic areas, for which permanent stratification of the water column and limited ventilation of deep-water layers made favourable conditions. Since the 1980s the nutrient loads to the Baltic Sea have been continuously decreasing. This, however, has so far not resulted in significant improvements in oxygen availability in the deep regions, which has revealed a slow response time of the system to the reduction of the land-derived nutrient loads. Responsible for that is the low burial efficiency of phosphorus at anoxic conditions and its remobilization from sediments when conditions change from oxic to anoxic. This results in a stoichiometric excess of phosphorus available for organic-matter production, which promotes the growth of N2-fixing cyanobacteria and in turn supports eutrophication. This assessment reviews the available and published knowledge on the biogeochemical functioning of the Baltic Sea. In its content, the paper covers the aspects related to changes in carbon, nitrogen, and phosphorus (C, N, and P) external loads, their transformations in the coastal zone, changes in organic-matter production (eutrophication) and remineralization (oxygen availability), and the role of sediments in burial and turnover of C, N, and P. In addition to that, this paper focuses also on changes in the marine CO2 system, the structure and functioning of the microbial community, and the role of contaminants for biogeochemical processes. This comprehensive assessment allowed also for identifying knowledge gaps and future research needs in the field of marine biogeochemistry in the Baltic Sea. Copyright:
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