| 1. |
- Barnes, Paul W., et al.
(författare)
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Ozone depletion, ultraviolet radiation, climate change and prospects for a sustainable future
- 2019
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2:7, s. 569-579
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Forskningsöversikt (refereegranskat)abstract
- © 2019, Springer Nature Limited. Changes in stratospheric ozone and climate over the past 40-plus years have altered the solar ultraviolet (UV) radiation conditions at the Earth’s surface. Ozone depletion has also contributed to climate change across the Southern Hemisphere. These changes are interacting in complex ways to affect human health, food and water security, and ecosystem services. Many adverse effects of high UV exposure have been avoided thanks to the Montreal Protocol with its Amendments and Adjustments, which have effectively controlled the production and use of ozone-depleting substances. This international treaty has also played an important role in mitigating climate change. Climate change is modifying UV exposure and affecting how people and ecosystems respond to UV; these effects will become more pronounced in the future. The interactions between stratospheric ozone, climate and UV radiation will therefore shift over time; however, the Montreal Protocol will continue to have far-reaching benefits for human well-being and environmental sustainability.
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| 2. |
- Corcoll, Natàlia, 1981, et al.
(författare)
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Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing
- 2017
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 364:14
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput DNA sequencing technologies are increasingly used for the metagenomic characterization of microbial biodiversity. However, basic issues, such as the choice of an appropriate DNA extraction method, are still not resolved for non-model microbial communities. This study evaluates four commonly used DNA extraction methods for marine periphyton biofilms in terms of DNA yield, efficiency, purity, integrity and resulting 16S rRNA bacterial diversity. Among the tested methods, the Plant DNAzol® Reagent (PlantDNAzol) and the Fast DNATM SPIN Kit for Soil (FastDNA Soil) methods were best suited to extract high quantities of DNA (77 - 130 μg g wet wt-1). Lower amounts of DNA were obtained (
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| 3. |
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| 4. |
- Falster, Daniel, et al.
(författare)
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AusTraits, a curated plant trait database for the Australian flora
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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| 5. |
- Langenheder, Silke, et al.
(författare)
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Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin
- 2016
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 8:4, s. 479-485
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Tidskriftsartikel (refereegranskat)abstract
- Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140–8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.
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| 6. |
- Peura, Sari, et al.
(författare)
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Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Thousands of net-heterotrophic and strongly stratifying lakes dominate the boreal landscape. Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. Using shotgun metagenomics, we show that the functional potential differs among lake types, with humic lakes being particularly enriched in carbon degradation genes. Most of the metabolic pathways exhibit oxygen- and temperature-dependent stratification over depth, coinciding with shifts in bacterial community composition, implying that stratification is a major factor controlling lake metabolism. In the bottom waters, rare and poorly characterized taxa, such as epsilon-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. These oxygen-depleted layers exhibited high genetic potential for mineralization, but also for fixation of carbon and nitrogen, and genetic markers for both methane production and oxidation were present. Our study provides a first glimpse of the genetic versatility of freshwater anoxic zones, and demonstrates the potential for complete turnover of carbon compounds within the water column.
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| 7. |
- Savio, Domenico, et al.
(författare)
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Bacterial diversity along a 2600 km river continuum
- 2015
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 17:12, s. 4994-5007
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Tidskriftsartikel (refereegranskat)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.
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| 8. |
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| 9. |
- Sinclair, Lucas, et al.
(författare)
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Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons : Evaluating the Illumina Platform
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:2
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Tidskriftsartikel (refereegranskat)abstract
- As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences between individually barcodes samples. Using either a one-step or a two-step PCR preparation resulted in significantly different estimates in both alpha and beta diversity. Comparing with a previous method based on 454 pyrosequencing, we found that our Illumina protocol performed in a similar manner – with the exception for evenness estimates where correspondence between the methods was low. We further quantified the data loss at every processing step eventually accumulating to 50% of the raw reads. When evaluating different OTU clustering methods, we observed a stark contrast between the results of QIIME with default settings and the more recent UPARSE algorithm when it comes to the number of OTUs generated. Still, overall trends in alpha and beta diversity corresponded highly using both clustering methods. Our procedure performed well considering the precisions of alpha and beta diversity estimates, with insignificant effects of individual barcodes. Comparative analyses suggest that 454 and Illumina sequence data can be combined if the same PCR protocol and bioinformatic workflows are used for describing patterns in richness, beta-diversity and taxonomic composition.
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| 10. |
- Sinclair, Lucas, 1985-
(författare)
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Molecular methods for microbial ecology : Developments, applications and results
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Recent developments in DNA sequencing technology allow the study of microbial ecology at unmatched detail. To fully embrace this revolution, an important avenue of research is the development of bioinformatic tools that enable scientists to leverage and manipulate the exceedingly large amounts of data produced. In this thesis, several bioinformatic tools were developed in order to process and analyze metagenomic sequence data. Subsequently, the tools were applied to the study of microbial biogeography and microbial systems biology.A targeted metagenomics pipeline automating quality filtering, joining and taxonomic annotation was developed to assess the diversity of bacteria, archaea and eukaryotes permitting the study of biogeographic patterns in great detail. Next, a second software package which provides annotation based on environmental ontology terms was coded aiming to exploit the cornucopia of information available in public databases. It was applied to resource tracking, paleontology, and biogeography. Indeed, both these tools have already found broad applications in extending our understanding of microbial diversity in inland waters and have contributed to the development of conceptual frameworks for microbial biogeography in lotic systems. The programs were used for analyzing samples from several environments such as alkaline soda lakes and ancient sediment cores. These studies corroborated the view that the dispersal limitations of microbes are more or less non-existant as environmental properties dictating their distribution and that dormant microbes allow the reconstruction of the origin and history of the sampled community.Furthermore, a shotgun metagenomics analysis pipeline for the characterization of total DNA extraction from the environment was put in place. The pipeline included all essential steps from raw sequence processing to functional annotation and reconstruction of prokaryotic genomes. By applying this tool, we were able to reconstruct the biochemical processes in a selection of systems representative of the tens of millions of lakes and ponds of the boreal landscape. This revealed the genomic content of abundant and so far undescribed prokaryotes harboring important functions in these ecosystems. We could show the presence of organisms with the capacity for photoferrotrophy and anaerobic methanotrophy encoded in their genomes, traits not previously detected in these systems. In another study, we showed that microbes respond to alkaline conditions by adjusting their energy acquisition and carbon fixation strategies. To conclude, we demonstrated that the "reverse ecology" approach in which the role of microbes in elemental cycles is assessed by genomic tools is very powerful as we can identify novel pathways and obtain the partitioning of metabolic processes in natural environments.
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