| 1. |
- Schönfeld, Joachim, et al.
(författare)
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Benthic foraminiferal patchiness revisited
- 2023
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Ingår i: Journal of Micropalaeontology. - : Copernicus Publications. - 0262-821X .- 2041-4978. ; 42:2, s. 171-192
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Tidskriftsartikel (refereegranskat)abstract
- Many benthic organisms show aggregated distribution patterns due to the spatial heterogeneity of niches or food availability. In particular, high-abundance patches of benthic foraminifera have been reported that extend from centimetres to metres in diameter in salt marshes or shallow waters. The dimensions of spatial variations of shelf or deep-sea foraminiferal abundances have not yet been identified. Therefore, we studied the distribution of Globobulimina turgida dwelling in the 0–3cm surface sediment at 118m water depth in the Alsbäck Deep, Gullmar Fjord, Sweden. Standing stock data from 58 randomly replicated samples depicted a log-normal distribution of G. turgida with weak evidence for an aggregated distribution on a decimetre scale. A model simulation with different patch sizes, outlines, and impedances yielded no significant correlation with the observed variability of G. turgida standing stocks. Instead, a perfect match with a random log-normal distribution of population densities was obtained. The data–model comparison revealed that foraminiferal populations in the Gullmar Fjord were not moulded by any underlying spatial structure beyond 10cm diameter. Log-normal population densities also characterise data from contiguous, gridded, or random sample replicates reported in the literature. Here, a centimetre-scale heterogeneity was found and interpreted to be a result of asexual reproduction events and restricted mobility of juveniles. Standing stocks of G. turgida from the Alsbäck Deep temporal data series from 1994 to 2021 showed two distinct cohorts of samples of either high or low densities. These cohorts are considered to represent two distinct ecological settings: hypoxic and well-ventilated conditions in the Gullmar Fjord. Environmental forcing is therefore considered to impact the population structure of benthic foraminifera rather than their reproduction dynamics.
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| 2. |
- Carlson, Michael. C. G., et al.
(författare)
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Viruses affect picocyanobacterial abundance and biogeography in the North Pacific Ocean
- 2022
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 7:4, s. 570-580
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Tidskriftsartikel (refereegranskat)abstract
- The photosynthetic picocyanobacteria Prochlorococcus and Synechococcus are models for dissecting how ecological niches are defined by environmental conditions, but how interactions with bacteriophages affect picocyanobacterial biogeography in open ocean biomes has rarely been assessed. We applied single-virus and single-cell infection approaches to quantify cyanophage abundance and infected picocyanobacteria in 87 surface water samples from five transects that traversed approximately 2,200 km in the North Pacific Ocean on three cruises, with a duration of 2–4 weeks, between 2015 and 2017. We detected a 550-km-wide hotspot of cyanophages and virus-infected picocyanobacteria in the transition zone between the North Pacific Subtropical and Subpolar gyres that was present in each transect. Notably, the hotspot occurred at a consistent temperature and displayed distinct cyanophage-lineage composition on all transects. On two of these transects, the levels of infection in the hotspot were estimated to be sufficient to substantially limit the geographical range of Prochlorococcus. Coincident with the detection of high levels of virally infected picocyanobacteria, we measured an increase of 10–100-fold in the Synechococcus populations in samples that are usually dominated by Prochlorococcus. We developed a multiple regression model of cyanophages, temperature and chlorophyll concentrations that inferred that the hotspot extended across the North Pacific Ocean, creating a biological boundary between gyres, with the potential to release organic matter comparable to that of the sevenfold-larger North Pacific Subtropical Gyre. Our results highlight the probable impact of viruses on large-scale phytoplankton biogeography and biogeochemistry in distinct regions of the oceans.
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| 3. |
- Glock, N., et al.
(författare)
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A hidden sedimentary phosphate pool inside benthic foraminifera from the Peruvian upwelling region might nucleate phosphogenesis
- 2020
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier. - 0016-7037 .- 1872-9533. ; 289, s. 14-32
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Tidskriftsartikel (refereegranskat)abstract
- Phosphorus is essential for all living organisms, being a component of DNA and RNA and the energy carrier ATP. Phosphogenesis is a main sink of reactive phosphorus in the oceans. The present study reports the presence of intracellular dissolved inorganic phosphate (DIP) in benthic foraminifera from the Peruvian oxygen minimum zone (OMZ). The mean intracellular DIP concentration was 28 ± 3 mM; two to three orders-of-magnitude higher than in the ambient pore waters. The biological implications of the high intracellular phosphate enrichment may be related to the synthesis of polyphosphates or phospholipids for cell-membranes. The comparative genomics analysis of multiple species of foraminifera from different environments reveals that foraminifers encode the genes required for both phospholipid and polyphosphate metabolism. Rapid phosphogenesis and phosphorite formation associated with foraminiferal tests is hypothesized due to the pre-concentration of intracellular phosphate in these organisms. The results indicate that foraminifera may play a key and previously overlooked role in the global phosphorus cycle.
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| 4. |
- Glock, Nicolaas, et al.
(författare)
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Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:8, s. 2860-2865
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Tidskriftsartikel (refereegranskat)abstract
- Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors—nitrate (NO3 − ) or oxygen (O2 )—makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2 respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2 respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2 respiration than for denitrification, indicating that NO3− metabolism during denitrification is more efficient than O 2 metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2 respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3− storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3− availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2 but rather by NO3 − availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3− is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3− and O2.
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| 5. |
- Heinrichs, Mara Elena, et al.
(författare)
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Breaking the Ice : A Review of Phages in Polar Ecosystems
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges like restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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| 6. |
- Heinrichs, Mara Elena, et al.
(författare)
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Breaking the Ice : A Review of Phages in Polar Ecosystems
- 2024
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Ingår i: Bacteriophages. - New York, NY : Humana Press. - 9781071635490 - 9781071635483 - 9781071635513 ; , s. 31-71
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Bokkapitel (refereegranskat)abstract
- Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage–host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.
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| 7. |
- Springstein, Benjamin L., et al.
(författare)
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Identification and characterization of novel filament-forming proteins in cyanobacteria
- 2020
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Filament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymers in vitro and three proteins that formed polymers in vivo. Fm7001 from Fischerella muscicola PCC 7414 polymerized in vitro and formed filaments in vivo in several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - in Anabaena sp. PCC 7120 that polymerized into filaments in vitro and in vivo. All4981 interacts with known cytoskeletal proteins and is indispensable for Anabaena viability. Although it did not form filaments in vitro, Syc2039 from Synechococcus elongatus PCC 7942 assembled into filaments in vivo and a Delta syc2039 mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.
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| 8. |
- Springstein, Benjamin L., et al.
(författare)
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Two novel heteropolymer‐forming proteins maintain the multicellular shape of the cyanobacterium Anabaena sp. PCC 7120
- 2020
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Ingår i: The FEBS Journal. - : John Wiley & Sons. - 1742-464X .- 1742-4658. ; 288:10, s. 3197-3216
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Tidskriftsartikel (refereegranskat)abstract
- olymerizing and filament-forming proteins are instrumental for numerous cellular processes such as cell division and growth. Their function in stabilization and localization of protein complexes and replicons is achieved by a filamentous structure. Known filamentous proteins assemble into homopolymers consisting of single subunits – for example, MreB and FtsZ in bacteria – or heteropolymers that are composed of two subunits, for example, keratin and α/β tubulin in eukaryotes. Here, we describe two novel coiled-coil-rich proteins (CCRPs) in the filament-forming cyanobacterium Anabaena sp. PCC 7120 (hereafter Anabaena) that assemble into a heteropolymer and function in the maintenance of the Anabaena multicellular shape (termed trichome). The two CCRPs – Alr4504 and Alr4505 (named ZicK and ZacK) – are strictly interdependent for the assembly of protein filaments in vivo and polymerize nucleotide independently in vitro, similar to known intermediate filament (IF) proteins. A ΔzicKΔzacK double mutant is characterized by a zigzagged cell arrangement and hence a loss of the typical linear Anabaena trichome shape. ZicK and ZacK interact with themselves, with each other, with the elongasome protein MreB, the septal junction protein SepJ and the divisome associate septal protein SepI. Our results suggest that ZicK and ZacK function in cooperation with SepJ and MreB to stabilize the Anabaena trichome and are likely essential for the manifestation of the multicellular shape in Anabaena. Our study reveals the presence of filament-forming IF-like proteins whose function is achieved through the formation of heteropolymers in cyanobacteria.
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| 9. |
- Weissenbach, Julia, et al.
(författare)
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Evolution of Chaperonin Gene Duplication in Stigonematalean Cyanobacteria (Subsection V)
- 2017
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 9:1, s. 241-252
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Tidskriftsartikel (refereegranskat)abstract
- Chaperonins promote protein folding and areknown to play a role in themaintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a single-copy bicistronic operon, whereas in cyanobacteria up to three groES/groEL paralogs have been documented. Here we study the evolution and functional diversification of chaperonin paralogs in the heterocystous, multi-seriate filament forming cyanobacterium Chlorogloeopsis fritschii PCC 6912. The genome of C. fritschii encodes two groES/groEL operons (groESL1, groESL1.2) and amonocistronic groEL gene (groEL2). A phylogenetic reconstruction reveals that the groEL2 duplication is as ancient as cyanobacteria, whereas the groESL1.2 duplication occurred at the ancestor of heterocystous cyanobacteria. A comparison of the groEL paralogs transcription levels under different growth conditions shows that they have adapted distinct transcriptional regulation. Our results reveal that groEL1 and groEL1.2 are upregulated during diazotrophic conditions and the localization of their promoter activity points towards a role in heterocyst differentiation. Furthermore, protein-protein interaction assays suggest that paralogs encoded in the two operons assemble into hybrid complexes. The monocistronic encoded GroEL2 is not forming oligomers nor does it interact with the co-chaperonins. Interaction between GroES1.2 and GroEL1.2 could not be documented, suggesting that the groESL1.2 operon does not encode a functional chaperonin complex. Functional complementation experiments in Escherichia coli show that only GroES1/GroEL1 and GroES1/GroEL1.2 can substitute the native operon. In summary, the evolutionary consequences of chaperonin duplication in cyanobacteria include the retention of groESL1 as a housekeeping gene, subfunctionalization of groESL1.2 and neofunctionalization of the monocistronic groEL2 paralog.
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| 10. |
- Woehle, Christian, et al.
(författare)
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A Novel Eukaryotic Denitrification Pathway in Foraminifera
- 2018
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Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 28:16, s. 2536-2543.e5
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Tidskriftsartikel (refereegranskat)abstract
- Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes’ evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period. Woehle, Roy, et al. report a novel eukaryotic denitrification pathway in foraminiferal genomes. The enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) are encoded in Globobulimina. A phylogenetic analysis provides insights into the genetic capacity for denitrification in foraminifera and its evolutionary origin in prokaryotes.
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| 11. |
- Woehle, Christian, et al.
(författare)
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Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Science. - 0027-8424 .- 1091-6490. ; 119:25
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Tidskriftsartikel (refereegranskat)abstract
- Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.
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