| 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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BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
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In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
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Journal article (peer-reviewed)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. [GRAPHICS] .
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| 3. |
- Capo, Eric, et al.
(author)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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In: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Research review (peer-reviewed)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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| 4. |
- Hötzinger, Matthias, et al.
(author)
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Dynamics of Baltic Sea phages driven by environmental changes
- 2022
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In: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:8, s. 4576-4594
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Journal article (peer-reviewed)abstract
- Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.
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| 5. |
- Ismagilova, Alina, et al.
(author)
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Ecotoxicity of isosorbide acrylate and methacrylate monomers and corresponding polymers
- 2023
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In: Green Chemistry. - 1463-9270. ; 25:4, s. 1626-1634
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Journal article (peer-reviewed)abstract
- Isosorbide is a well-investigated and accessible biomass-derived compound that has found wide use in medicine, cosmetics, and material sciences. The efforts to employ this rigid bicyclic diol as a sustainable building block in high-performance biobased plastics for, e.g., the engineering, coating, and packaging sectors have grown sharply in recent years. Due to the biomass origin, there is an implicit assumption of a low toxicity and an environmentally benign nature of isosorbide-derived plastics. In the present work, the ecotoxicity of isosorbide acrylate and methacrylate monomers and the corresponding poly(meth)acrylates, as well as industrially produced latexes from these monomers, were evaluated towards bacteria (Escherichia coli, Aliivibrio fischeri), vascular plants (Spirodela polyrhiza) and invertebrates (Thamnocephalus platyurus) using widely acknowledged test assays. The measured half maximal effective concentration (EC50) values indicate that the chemically reactive isosorbide acrylate monomers are toxic towards higher multicellular organisms (S. polyrhiza and T. platyurus, EC50 ~9 mg L-1) and moderately toxic towards bacteria (E. coli), whereas the corresponding methacrylate monomers can be considered as practically harmless or harmless on the same test assays. Corresponding isosorbide polyacrylate and polymethacrylate polymers are harmless towards the tested organisms (EC50 > 1000 mg L-1), except towards E. coli, where two polymers are classified as practically harmless (EC50 = 374 and 514 mg L-1). Moreover, industrially produced isosorbide methacrylate derived latexes can be classified as harmless based on this study.
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| 6. |
- Karlsson, Christofer M. G., et al.
(author)
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Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings
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Other publication (other academic/artistic)abstract
- Climate change is predicted to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture- influenced catchment areas were added to Baltic Sea Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment (before the phytoplankton bloom), but expression patterns diverged significantly upon bloom senescence.Notably, transcripts associated with phosphate metabolism were significantly enriched , whereas transcripts related to nitrogen metabolism were significantly lower in the agriculture river treatment compared to the boreal forest river treatment. The opposite pattern was observed in the boreal forest river water treatment. Overall, our results showed that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. This suggests that bacterial transformations of organic matter and nutrient cycling in coastal waters and estuarine environments are sensitive to changes in precipitation patterns in a catchment area-dependent manner.
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| 7. |
- Kisand, Veljo, et al.
(author)
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Bacterial freshwater species successfully immigrate to the brackish water environment in the northern Baltic
- 2005
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In: Limnology and Oceanography. - : American Society of Limnology and Oceanography. - 0024-3590 .- 1939-5590. ; 50:3, s. 945-956
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Journal article (peer-reviewed)abstract
- We studied the distribution and seasonal dynamics of five species from the genus Flavobacterium and one species from the genus Marinomonas over the course of a year along a northern Baltic Sea river-marine transect. All of the species had been previously demonstrated as important consumers of riverine dissolved organic carbon. Quantitative DNA-DNA hybridization data showed that two of the Flavobacterium spp. and the Marinomonas sp. had highest abundance in the river water (maximum 20,000 cells ml-1), with maximum relative abundance of 0.5-2.5% of the bacterial community. These species declined in abundance from the river to the estuary and the offshore site. Abundance and dynamics in the estuarine environment suggested successful immigration of freshwater bacteria, accompanied by growth in the brackish water environment. Two of the three abundant species showed high cell numbers also during late autumn to early spring in the estuary, indicating a selective advantage when riverine dissolved organic carbon was the main carbon source. The remaining three species showed more episodic abundance close to the detection limit of the method, providing weaker evidence of occurrence in the freshwater environment. Some bacterioplankton consuming riverine organic carbon in the brackish water environment in the northern Baltic are therefore freshwater species, with a selective advantage during winter.
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| 8. |
- Kisand, Veljo, et al.
(author)
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Combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter
- 2003
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In: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 69:6, s. 3607-3616
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Journal article (peer-reviewed)abstract
- Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated beta-proteobacteria to be RDOM consumers.
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| 9. |
- Kisand, Veljo, et al.
(author)
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Genome sequencing of bacteria : sequencing, de novo assembly and rapid analysis using open source tools
- 2013
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In: BMC Genomics. - : BIOMED CENTRAL LTD. - 1471-2164. ; 14
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Journal article (peer-reviewed)abstract
- Background: De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads(<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. Results: The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (similar to 30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Conclusions: Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.
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| 10. |
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