| 1. |
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| 2. |
- Alneberg, Johannes, et al.
(författare)
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Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
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Ingår i: Microbiome. - : BioMed Central. - 2049-2618. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 3. |
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| 4. |
- Capo, Eric, et al.
(författare)
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A consensus protocol for the recovery of mercury methylation genes from metagenomes
- 2023
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 23:1, s. 190-204
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Tidskriftsartikel (refereegranskat)abstract
- Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
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| 5. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)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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| 6. |
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| 7. |
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| 8. |
- Garcia, Sarahi L, et al.
(författare)
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Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
- 2018
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 12:3, s. 742-755
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Tidskriftsartikel (refereegranskat)abstract
- To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.
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| 9. |
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| 10. |
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| 11. |
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| 12. |
- Hellberg, C., et al.
(författare)
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Evidence and evidence gaps in assessments and interventions in areas related to social work research and practice - an overview of four evidence maps
- 2023
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Ingår i: European Journal of Social Work. - : Informa UK Limited. - 1369-1457 .- 1468-2664. ; 26:5
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Tidskriftsartikel (refereegranskat)abstract
- This overview of four evidence maps is based on systematic reviews of assessment and interventions in social work practice. The aim was to investigate the evidence and evidence gaps within four important areas for social work research and practice. Descriptive data on search strategies and domains were collected from four evidence maps, on Social Assistance, Substance Dependence, Care for older adults respectively for persons with disabilities. The scientific quality and scientific evidence were assessed. Key findings were summarised by analyzing and discussing common and specific elements in the evidence maps. The overview was undertaken in close collaboration between researchers with expertise in the field and a government agency. The overview identified both evidence and evidence gaps with respect to effects and experiences of interventions and assessment methods in four evidence maps. Evidence maps provide a comprehensive picture of the state of social services research and can thereby be of use to both researchers and practitioners, and in the production of evidence based social work.
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Yager, P. L., et al.
(författare)
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A carbon budget for the Amundsen Sea Polynya, Antarctica: Estimating net community production and export in a highly productive polar ecosystem
- 2016
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Ingår i: Elementa-Science of the Anthropocene. - : University of California Press. - 2325-1026. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- Polynyas, or recurring areas of seasonally open water surrounded by sea ice, are foci for energy and material transfer between the atmosphere and the polar ocean. They are also climate sensitive, with both sea ice extent and glacial melt influencing their productivity. The Amundsen Sea Polynya (ASP) is the greenest polynya in the Southern Ocean, with summertime chlorophyll a concentrations exceeding 20 mu g L-1. During the Amundsen Sea Polynya International Research Expedition (ASPIRE) in austral summer 2010-11, we aimed to determine the fate of this high algal productivity. We collected water column profiles for total dissolved inorganic carbon (DIC) and nutrients, particulate and dissolved organic matter, chlorophyll a, mesozoo-plankton, and microbial biomass to make a carbon budget for this ecosystem. We also measured primary and secondary production, community respiration rates, vertical particle flux and fecal pellet production and grazing. With observations arranged along a gradient of increasing integrated dissolved inorganic nitrogen drawdown (Delta DIN; 0.027-0.74 mol N m(-2)), changes in DIC in the upper water column (ranging from 0.2 to 4.7 mol C m(-2)) and gas exchange (0-1.7 mol C m(-2)) were combined to estimate early season net community production (sNCP; 0.2-5.9 mol C m(-2)) and then compared to organic matter inventories to estimate export. From a phytoplankton bloom dominated by Phaeocystis antarctica, a high fraction (up to similar to 60%) of sNCP was exported to sub-euphotic depths. Microbial respiration remineralized much of this export in the mid waters. Comparisons to short-term (2-3 days) drifting traps and a year-long moored sediment trap capturing the downward flux confirmed that a relatively high fraction (3-6%) of the export from similar to 100 m made it through the mid waters to depth. We discuss the climate-sensitive nature of these carbon fluxes, in light of the changing sea ice cover and melting ice sheets in the region.
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| 17. |
- Alneberg, Johannes, et al.
(författare)
-
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 18. |
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| 19. |
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| 20. |
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| 21. |
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| 22. |
- Beier, Sara, et al.
(författare)
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Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing
- 2012
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 14:9, s. 2467-2479
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Tidskriftsartikel (refereegranskat)abstract
- Seasonal variation in activity of enzymes involved in polymer degradation, including chitinases, has been observed previously in freshwater environments. However, it is not known whether the seasonal dynamics are due to shifts in the activity of bacteria already present, or shifts in community structure towards emergence or disappearance of chitinolytic organisms. We traced seasonal shifts in the chitinase gene assemblage in a temperate lake and linked these communities to variation in chitinase activity. Chitinase genes from 20 samples collected over a full yearly cycle were characterized by pyrosequencing. Pronounced temporal shifts in composition of the chitinase gene pool (beta diversity) occurred along with distinct shifts in richness (alpha diversity) as well as chitin processing. Changes in the chitinase gene pool correlated mainly with temperature, abundance of crustacean zooplankton and phytoplankton blooms. Also changes in the physical structure of the lake, e.g. stratification and mixing were associated with changes in the chitinolytic community, while differences were minor between surface and suboxic hypolimnetic water. The lake characteristics influencing the chitinolytic community are all linked to changes in organic particles and we suggest that seasonal changes in particle quality and availability foster microbial communities adapted to efficiently degrade them.
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| 23. |
- Bendall, Matthew L, et al.
(författare)
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Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
- 2016
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Ingår i: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 10:7, s. 1589-1601
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Tidskriftsartikel (refereegranskat)abstract
- Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the /`ecotype model/' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.
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| 24. |
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| 25. |
- Bertilsson, Erik, et al.
(författare)
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A Modular Base Station Architecture for Massive MIMO with Antenna and User Scalability per Processing Node
- 2018
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Ingår i: 2018 CONFERENCE RECORD OF 52ND ASILOMAR CONFERENCE ON SIGNALS, SYSTEMS, AND COMPUTERS. - : IEEE. - 9781538692189 ; , s. 1649-1653
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Konferensbidrag (refereegranskat)abstract
- Massive MIMO is key technology for the upcoming fifth generation cellular networks (5G), promising high spectral efficiency, low power consumption, and the use of cheap hardware to reduce costs. Previous work has shown how to create a distributed processing architecture, where each node in a network performs the computations related to one or more antennas. The required total number of antennas, M, at the base station depends on the number of simultaneously operating terminals, K. In this work, a flexible node architecture is presented, where the number of terminals can he traded for additional antennas at the same node. This means that the same node can be used with a wide range of system configurations. The computational complexity, along with the order in which to compute incoming and outgoing symbols is explored.
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| 26. |
- Bertilsson, Erik, et al.
(författare)
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A Scalable Architecture for Massive MIMO Base Stations Using Distributed Processing
- 2016
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Ingår i: 2016 50TH ASILOMAR CONFERENCE ON SIGNALS, SYSTEMS AND COMPUTERS. - Washington : IEEE COMPUTER SOC. - 9781538639542 ; , s. 864-868
-
Konferensbidrag (refereegranskat)abstract
- Massive MIMO-systems have received considerable attention in recent years as an enabler in future wireless communication systems. As the idea is based on having a large number of antennas at the base station it is important to have both a scalable and distributed realization of such a system to ease deployment. Most work so far have focused on the theoretical aspects although a few demonstrators have been reported. In this work, we propose a base station architecture based on connecting the processing nodes in a K-ary tree, allowing simple scalability. Furthermore, it is shown that most of the processing can be performed locally in each node. Further analysis of the node processing shows that it should be enough that each node contains one or two complex multipliers and a few complex adders/subtracters operating at some hundred MHz. It is also shown that a communication link of some Gbps is required between the nodes, and, hence, it is fully feasible to have one or a few links between the nodes to cope with the communication requirements.
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| 27. |
- Bertilsson, Erik, 1990-, et al.
(författare)
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Computation Limited Matrix Inversion Using Neumann Series Expansion for Massive MIMO
- 2017
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Ingår i: 2017 FIFTY-FIRST ASILOMAR CONFERENCE ON SIGNALS, SYSTEMS, AND COMPUTERS. - 9781538618233 ; , s. 466-469
-
Konferensbidrag (refereegranskat)abstract
- Neumann series expansion is a method for performing matrix inversion that has received a lot of interest in the context of massive MIMO systems. However, the computational complexity of the Neumann methods is higher than for the lowest complexity exact matrix inversion algorithms, such as LDL, when the number of terms in the series is three or more. In this paper, the Neumann series expansion is analyzed from a computational perspective for cases when the complexity of performing exact matrix inversion is too high. By partially computing the third term of the Neumann series, the computational complexity can be reduced. Three different preconditioning matrices are considered. Simulation results show that when limiting the total number of operations performed, the BER performance of the tree different preconditioning matrices is the same.
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| 28. |
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| 29. |
- Bertilsson, G, et al.
(författare)
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Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction
- 1998
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Ingår i: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 95:21, s. 12208-12213
-
Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nuclear receptors regulate metabolic pathways in response to changes in the environment by appropriate alterations in gene expression of key metabolic enzymes, Here, a computational search approach based on iteratively built hidden Markov models of nuclea
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| 30. |
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| 31. |
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| 32. |
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| 33. |
- Bertilsson, Stefan, et al.
(författare)
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Links between bacterial production, amino acid utilization and community composition in productive lakes
- 2007
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Ingår i: ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 1:6, s. 532-544
-
Tidskriftsartikel (refereegranskat)abstract
- Influence of distribution and abundance of bacterial taxa on ecosystem function are poorly understood for natural microbial communities. We related 16S rRNA-based terminal restriction fragment length polymorphism to bacterial production and arginine uptake kinetics to test if functional features of bacterioplankton in four lakes could be predicted from community composition. Maximum arginine uptake rate (arginine Vmax) ranged from 10% to 100% of bacterial production. Owing to high growth efficiencies on arginine (63–77%), the bacterial community could potentially saturate its carbon demand using this single organic substrate, for example, during sudden surges of free amino acids. However, due to low in situ concentrations of arginine in these lakes (<0.9 g l-1), actual uptake rates at ambient concentrations rarely exceeded 10% of Vmax. Bacterial production and arginine Vmax could be predicted from a subset of bacterial ribotypes, tentatively affiliated with several bacterial divisions (Cyanobacteria, Actinobacteria, Bacteroidetes and Proteobacteria). Multivariate statistical analysis indicates that there were both highly important and less important ribotypes for the prediction of bacterial production and arginine Vmax. These populations were either negatively or positively related to the respective functional feature, indicating contrasting ecological roles. Our study provides a statistically robust demonstration that, apart from environmental conditions, patterns in bacterial community composition can also be used to predict lake ecosystem function.
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| 34. |
- Bertilsson, Stefan, et al.
(författare)
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The under-ice microbiome of seasonally frozen lakes
- 2013
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 58:6, s. 1998-2012
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Forskningsöversikt (refereegranskat)abstract
- Compared to the well-studied open water of the ‘‘growing’’ season, under-ice conditions in lakes are characterized by low and rather constant temperature, slow water movements, limited light availability, and reduced exchange with the surrounding landscape. These conditions interact with ice-cover duration to shape microbial processes in temperate lakes and ultimately influence the phenology of community and ecosystem processes. We review the current knowledge on microorganisms in seasonally frozen lakes. Specifically, we highlight how under-ice conditions alter lake physics and the ways that this can affect the distribution and metabolism of auto- and heterotrophic microorganisms. We identify functional traits that we hypothesize are important for understanding under-ice dynamics and discuss how these traits influence species interactions. As ice coverage duration has already been seen to reduce as air temperatures have warmed, the dynamics of the under- ice microbiome are important for understanding and predicting the dynamics and functioning of seasonally frozen lakes in the near future.
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| 35. |
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| 36. |
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| 37. |
- Bravo, Andrea G., et al.
(författare)
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Methanogens and iron-reducing bacteria : the overlooked members of mercury-methylating microbial communities in boreal lakes
- 2018
-
Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 84:23
-
Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: Methylmercury is a potent human neurotoxin which biomagnifies in aquatic food webs. Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. Previous studies have implicated sulfate-reducing bacteria as the main mercury methylators in aquatic ecosystems. In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. Our results show that in the lake sediments, Methanomicrobiales and Geobacteraceae also represent abundant members of the mercury-methylating communities. In fact, incubation experiments with a mercury isotopic tracer and molybdate revealed that only between 38% and 45% of mercury methylation was attributed to sulfate reduction. These results suggest that methanogens and iron-reducing bacteria may contribute to more than half of the mercury methylation in boreal lakes.IMPORTANCE: Despite the global awareness that mercury, and methylmercury in particular, is a neurotoxin to which millions of people continue to be exposed, there are sizable gaps in the understanding of the processes and organisms involved in methylmercury formation in aquatic ecosystems. In the present study, we shed light on the diversity of the microorganisms responsible for methylmercury formation in boreal lake sediments. All the microorganisms identified are associated with the processing of organic matter in aquatic systems. Moreover, our results show that the well-known mercury-methylating sulfate-reducing bacteria constituted only a minor portion of the potential mercury methylators. In contrast, methanogens and iron-reducing bacteria were important contributors to methylmercury formation, highlighting their role in mercury cycling in the environment.
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| 38. |
- Bravo, Andrea G., et al.
(författare)
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Molecular composition of organic matter controls methylmercury formation in boreal lakes
- 2017
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- A detailed understanding of the formation of the potent neurotoxic methylmercury is needed to explain the large observed variability in methylmercury levels in aquatic systems. While it is known that organic matter interacts strongly with mercury, the role of organic matter composition in the formation of methylmercury in aquatic systems remains poorly understood. Here we show that phytoplankton-derived organic compounds enhance mercury methylation rates in boreal lake sediments through an overall increase of bacterial activity. Accordingly, in situ mercury methylation defines methylmercury levels in lake sediments strongly influenced by planktonic blooms. In contrast, sediments dominated by terrigenous organic matter inputs have far lower methylation rates but higher concentrations of methylmercury, suggesting that methylmercury was formed in the catchment and imported into lakes. Our findings demonstrate that the origin and molecular composition of organic matter are critical parameters to understand and predict methylmercury formation and accumulation in boreal lake sediments.
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| 39. |
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| 40. |
- Cabrol, Léa, et al.
(författare)
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Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea
- 2023
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Ingår i: mSystems. - : American Society for Microbiology. - 2379-5077. ; 8:4
-
Tidskriftsartikel (refereegranskat)abstract
- In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse—previously underappreciated—anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.
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| 41. |
- Capo, Eric, et al.
(författare)
-
Deltaproteobacteria andSpirochaetes-Like Bacteria AreAbundant Putative MercuryMethylators in Oxygen-DeficientWater and Marine Particles in theBaltic Sea
- 2020
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; , s. 1-11
-
Tidskriftsartikel (refereegranskat)abstract
- Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the compositionand distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial,seasonal and redox variability in the Baltic Sea water column. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were alsodetected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities of hgcAB genes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversityof the microorganisms with the potential to mediate MeHg production in the BalticSea and pinpoint the important ecological niches for these microorganisms within themarine water column.
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| 42. |
- Capo, Eric, et al.
(författare)
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Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters
- 2022
-
Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 56:18, s. 13119-13130
-
Tidskriftsartikel (refereegranskat)abstract
- Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (Hg-II) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not know nif the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved Hg-II-sulfide species were strong predictors of both the Hg-II methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc(+) microorganisms by reconstructing their genomes from metagenomes (i.e., hgc(+) MAGs), which highlighted the versatility of putative Hg-II methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the Hg-II methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficientzones.
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| 43. |
- Capo, Eric, et al.
(författare)
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Oxygen-deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments
- 2022
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Ingår i: Limnology and Oceanography. - : Wiley. - 1939-5590 .- 0024-3590. ; 67:1, s. 135-146
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Tidskriftsartikel (refereegranskat)abstract
- Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand.
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- Catalán, Núria, 1985-, et al.
(författare)
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Effects of beaver impoundments on dissolved organic matter quality and biodegradability in boreal riverine systems
- 2017
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Ingår i: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 793:1, s. 135-148
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Tidskriftsartikel (refereegranskat)abstract
- Beaver impoundments modify the structure of river reaches and lead to changes in ecosystem function and biogeochemical processes. Here, we assessed the changes in dissolved organic matter (DOM) quality and the biodegradation patterns in a set of beaver systems across Sweden. As the effect of beaver impoundments might be transient and local, we compared DOM quality and biodegradability of both pond and upstream sections of differentially aged beaver systems. Newly established dams shifted the sources and DOM biodegradability patterns. In particular, humic-like DOM, most likely leached from surrounding soils, characterized upstream sections of new beaver impoundments. In contrast, autochthonous and processed compounds, with both higher biodegradation rates and a broader spectrum of reactivities, differentiated DOM in ponds. DOM in recently established ponds seemed to be more humic and less processed compared to older ponds, but system idiosyncrasies determined by catchment particularities influenced this ageing effect.
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