| 1. |
- Thompson, Luke R., et al.
(författare)
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A communal catalogue reveals Earth's multiscale microbial diversity
- 2017
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 551:7681, s. 457-463
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
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| 2. |
- Alsterberg, Christian, 1982, et al.
(författare)
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Habitat diversity and ecosystem multifunctionality-The importance of direct and indirect effects
- 2017
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 3:2
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Tidskriftsartikel (refereegranskat)abstract
- Ecosystems worldwide are facing habitat homogenization due to human activities. Although it is commonly proposed that such habitat homogenization can have negative repercussions for ecosystem functioning, this question has yet to receive explicit scientific attention. We expand on the framework for evaluating the functional consequences of bio-diversity loss by scaling up from the level of species to the level of the entire habitats. Just as species diversity generally fosters ecosystem functioning through positive interspecies interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and through exchange of material and energy across habitats. We show that experimental ecosystems comprised of a diversity of habitats show higher levels of multiple ecosystem functions than ecosystems with low habitat diversity. Our results demonstrate that the effect of habitat diversity on multifunctionality varies with season; it has direct effects on ecosystem functioning in summer and indirect effects, via changes in species diversity, in autumn, but no effect in spring. We propose that joint consideration of habitat diversity and species diversity will prove valuable for both environmental management and basic research.
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| 3. |
- Eilola, Kari, et al.
(författare)
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SMHI reportsSMHI rep., Oceanogr : Swedish Meteorological and Hydrological Institute reports. OceanographySMHISMHI report. Oceanography 2007:37OceanographyROSMHI RO
- 2017
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This report is related to the BONUS project “Nutrient Cocktails in COAstal zones of the Baltic Sea” alias COCOA. The aim of BONUS COCOA is to investigate physical, biogeochemical and biological processes in a combined and coordinated fashion to improve the understanding of the interaction of these processes on the removal of nutrients along the land -sea interface. The report is especially related to BONUS COCOA WP 6 in which the main objective is extrapolation of results from the BONUS COCOA learning sites to coastal sites around the Baltic Sea in general. Specific objectives of this deliverable (D6.4) were to connect observed process rates with modelling data and ecosystem characteristics.In the report we made statistical analyses of observations from BONUS COCOA study sites together with results from the Swedish Coastal zone Model (SCM). Eight structural variables (water depth, temperature, salinity, bottom water concentrations of oxygen, ammonium, nitrate and phosphate, as well as nitrogen content in sediment) were found common to both the experimentally determined and the model data sets. The observed process rate evaluated in this report was denitrification. In addition regressions were tested between observed denitrification rates and several structural variables (lat itude, longitude, depth, light, temperature, salinity, grain class, porosity, loss of ignition, sediment organic carbon, total nitrogen content in the sediment, sediment carbon/nitrogen-ratio, sediment chlorphyll-a as well as bottom water concentrations of oxygen, ammonium, nitrate, and dissolved inorganic phosphorus and silicate) for pooled data from all learning sites.The statistical results showed that experimentally determined multivariate data set from the shallow, illuminated stations was mainly found to be similar to the multivariate data set produced by the SCM model. Generally, no strong correlations of simple relations between observed denitrification and available structural variables were found for data collected from all the learning sites. We found some non-significant correlation between denitrification rates and bottom water dissolved inorganic phosphorous and dissolved silica but the reason behind the correlations is not clear.We also developed and evaluated a theory to relate process rates to monitoring data and nutrient retention. The theoretical analysis included nutrient retention due to denitrification as well as burial of phosphorus and nitrogen. The theory of nutrient retention showed good correlations with model results. It was found that area-specific nitrogen and phosphorus retention capacity in a sub-basin depend much on mean water depth, water residence time, basin area and the mean nutrient concentrations in the active sediment layer and in the water column.
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| 4. |
- Gilbert, F., et al.
(författare)
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Redox oscillation and benthic nitrogen mineralization within burrowed sediments: An experimental simulation at low frequency
- 2016
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Ingår i: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 482, s. 75-84
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Tidskriftsartikel (refereegranskat)abstract
- Possible effects of sediment ventilation by benthic organisms on the nitrogen cycle were investigated using an experimental setup that mimicked stable or relatively low frequency oscillating redox conditions potentially found in bioturbated deposits. Three different conditions inside burrowed sediments were simulated using 2 mm thick sediment layers: 1) continuously oxic sediment exposed to oxygenated overlying bottom water (e.g., burrow walls, surface sediment), 2) continuously anoxic sediment out of reach from either O-2 or NO3- diffusion and 3) the lining/boundary of burrow structures or sediment pockets (e.g., excavated during feeding) subject to intermittent irrigation and redox fluctuations over several day timescales. Results demonstrated that intermittent redox fluctuations allowed sustained denitrification and episodic nitrification, whereas significant denitrification and both nitrification and denitrification were absent after similar to 5-10 days from continuously oxidized and anoxic zones respectively. Intermittent redox oscillations enhance metabolic diversity, magnify loss of dissolved inorganic N to solution, and permit sustained coupling between ammonification, nitrification, and denitrification despite lack of a stable stratified oxic-anoxic redox structure. Even relatively low frequency redox oscillations induce greater N loss compared to sediment that is continuously exposed to oxic and anoxic conditions.
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| 5. |
- Karlsson, R., et al.
(författare)
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Proteotyping: Proteomic characterization, classification and identification of microorganisms - A prospectus
- 2015
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 38:4, s. 246-257
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Forskningsöversikt (refereegranskat)abstract
- Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels. (C) 2015 Elsevier GmbH. All rights reserved.
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| 6. |
- Wittorf, Lea, et al.
(författare)
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Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability
- 2016
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 8:4, s. 486-492
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Tidskriftsartikel (refereegranskat)abstract
- Denitrification is of global significance for the marine nitrogen budget and the main process for nitrogen loss in coastal sediments. This facultative anaerobic respiratory pathway is modular in nature and the final step, the reduction of nitrous oxide (N2O), is performed by microorganisms with a complete denitrification pathway as well as those only capable of N2O reduction. Fluctuating oxygen availability is a significant driver of denitrification in sediments, but the effects on the overall N2O-reducing community that ultimately controls the emission of N2O from marine sediments is not well known. To investigate the effects of different oxygen regimes on N2O reducing communities, coastal marine surface sediment was incubated in microcosms under oxic, anoxic or oscillating oxygen conditions in the overlying water for 137 days. Quantification of the genetic potential for denitrification, anammox and respiratory ammonification indicated that denitrification supported nitrogen removal in these sediments. Furthermore, denitrifiers with a complete pathway were identified as the dominant community involved in N2O reduction, rather than organisms that are only N2O reducers. Specific lineages within each group were associated with different oxygen regimes suggesting that oxygen availability in the overlying water is associated with habitat partitioning of N2O reducers in coastal marine surface sediments.
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