| 1. |
- Alneberg, Johannes, et al.
(författare)
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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes
- 2020
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 3:1, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
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| 2. |
- Holmfeldt, Karin, 1980-, et al.
(författare)
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles
- 2021
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.
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| 3. |
- Sourav, Suddha, et al.
(författare)
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Sound suppresses earliest visual cortical processing after sight recovery in congenitally blind humans
- 2024
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Neuroscientific research has consistently shown more extensive non-visual activity in the visual cortex of congenitally blind humans compared to sighted controls; a phenomenon known as crossmodal plasticity. Whether or not crossmodal activation of the visual cortex retracts if sight can be restored is still unknown. The present study, involving a rare group of sight-recovery individuals who were born pattern vision blind, employed visual event-related potentials to investigate persisting crossmodal modulation of the initial visual cortical processing stages. Here we report that the earliest, stimulus-driven retinotopic visual cortical activity (<100 ms) was suppressed in a spatially specific manner in sight-recovery individuals when concomitant sounds accompanied visual stimulation. In contrast, sounds did not modulate the earliest visual cortical response in two groups of typically sighted controls, nor in a third control group of sight-recovery individuals who had suffered a transient phase of later (rather than congenital) visual impairment. These results provide strong evidence for persisting crossmodal activity in the visual cortex after sight recovery following a period of congenital visual deprivation. Based on the time course of this modulation, we speculate on a role of exuberant crossmodal thalamic input which may arise during a sensitive phase of brain development.
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| 4. |
- Sunde, Johanna, et al.
(författare)
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Century-long butterfly range expansions in northern Europe depend on climate, land use and species traits
- 2023
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is an important driver of range shifts and community composition changes. Still, little is known about how the responses are influenced by the combination of land use, species interactions and species traits. We integrate climate and distributional data for 131 butterfly species in Sweden and Finland and show that cumulative species richness has increased with increasing temperature over the past 120 years. Average provincial species richness increased by 64% (range 15-229%), from 46 to 70. The rate and direction of range expansions have not matched the temperature changes, in part because colonisations have been modified by other climatic variables, land use and vary according to species characteristics representing ecological generalisation and species interactions. Results emphasise the role of a broad ecological filtering, whereby a mismatch between environmental conditions and species preferences limit the ability to disperse and establish populations in emerging climates and novel areas, with potentially widespread implications for ecosystem functioning. Century-long data on climate and butterfly distribution show that species richness has increased with increasing temperature, and that the rate and direction of range expansions are influenced by land use, species interactions and species traits.
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| 5. |
- Ušaj, Marko, et al.
(författare)
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Single molecule turnover of fluorescent ATP by myosin and actomyosin unveil elusive enzymatic mechanisms
- 2021
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 4:1, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, results from recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies. We found that key reasons are complexities due to dye photophysics and fluorescent contaminants. After eliminating these, through surface cleaning and use of triple state quenchers and redox agents, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, with and without actin, and with and without the inhibitor para-aminoblebbistatin. Two processes are attributable to ATP turnover by myosin and actomyosin respectively, whereas the remaining process (rate constant 0.2-0.5 s(-1)) is consistent with non-specific ATP binding to myosin, possibly accelerating ATP transport to the active site. Finally, our study of actin-activated myosin ATP turnover without sliding between actin and myosin reveals heterogeneity in the ATP turnover kinetics consistent with models of isometric contraction.
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| 6. |
- Westmeijer, George, et al.
(författare)
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Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities
- 2022
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Ingår i: Communications Biology. - : Nature Publishing Group. - 2399-3642. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the Äspö Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.
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