| 1. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 2. |
- Csitári, Bianka, et al.
(författare)
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Anion-type modulates the effect of salt stress on saline lake bacteria
- 2022
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Ingår i: Extremophiles. - : Springer Nature. - 1431-0651 .- 1433-4909. ; 26
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Tidskriftsartikel (refereegranskat)abstract
- Beside sodium chloride, inland saline aquatic systems often contain other anions than chloride such as hydrogen carbonate and sulfate. Our understanding of the biological effects of salt composition diversity is limited; therefore, the aim of this study was to examine the effect of different anions on the growth of halophilic bacteria. Accordingly, the salt composition and concentration preference of 172 strains isolated from saline and soda lakes that differed in ionic composition was tested using media containing either carbonate, chloride or sulfate as anion in concentration values ranging from 0 to 0.40 mol/L. Differences in salt-type preference among bacterial strains were observed in relationship to the salt composition of the natural habitat they were isolated from indicating specific salt-type adaptation. Sodium carbonate represented the strongest selective force, while majority of strains was well-adapted to growth even at high concentrations of sodium sulfate. Salt preference was to some extent associated with taxonomy, although variations even within the same bacterial species were also identified. Our results suggest that the extent of the effect of dissolved salts in saline lakes is not limited to their concentration but the type of anion also substantially impacts the growth and survival of individual microorganisms.
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| 3. |
- Malki, Kema, et al.
(författare)
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Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
- 2020
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Ingår i: mBio. - 2161-2129 .- 2150-7511. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- Aquifers, which are essential underground freshwater reservoirs worldwide, are understudied ecosystems that harbor diverse forms of microbial life. This study investigated the abundance and composition of prokaryotic and viral communities in the outflow of five springs across northern Florida, USA, as a proxy of microbial communities found in one of the most productive aquifers in the world, the Floridan aquifer. The average abundances of virus-like particles and prokaryotic cells were slightly lower than those reported from other groundwater systems, ranging from 9.6 × 10 3 ml −1 to 1.1 × 10 5 ml −1 and 2.2 × 10 3 ml −1 to 3.4 × 10 4 ml −1 , respectively. Despite all of the springs being fed by the Floridan aquifer, sequencing of 16S rRNA genes and viral metagenomes (viromes) revealed unique communities in each spring, suggesting that groundwater microbial communities are influenced by land usage in recharge zones. The prokaryotic communities were dominated by Bacteria , and though the most abundant phyla ( Proteobacteria , Cyanobacteria , and Bacteroidetes ) were found in relatively high abundance across springs, variation was seen at finer taxonomic resolution. The viral sequences were most similar to those described from other aquatic environments. Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses. Sequences similar to those of ssDNA viruses were detected at all spring sites and dominated the identifiable sequences at one spring site, showing that these small viruses merit further investigation in groundwater systems.
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| 4. |
- Malki, Kema, et al.
(författare)
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Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)
- 2021
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 87:18
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Tidskriftsartikel (refereegranskat)abstract
- How from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.
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| 5. |
- Scharnweber, Kristin, 1983-, et al.
(författare)
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Comprehensive analysis of chemical and biological problems associated with browning agents used in aquatic studies
- 2021
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Ingår i: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 19:12, s. 818-835
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Tidskriftsartikel (refereegranskat)abstract
- Inland waters receive and process large amounts of colored organic matter from the terrestrial surroundings. These inputs dramatically affect the chemical, physical, and biological properties of water bodies, as well as their roles as global carbon sinks and sources. However, manipulative studies, especially at ecosystem scale, require large amounts of dissolved organic matter with optical and chemical properties resembling indigenous organic matter. Here, we compared the impacts of two leonardite products (HuminFeed and SuperHume) and a freshly derived reverse osmosis concentrate of organic matter in a set of comprehensive mesocosm- and laboratory-scale experiments and analyses. The chemical properties of the reverse osmosis concentrate and the leonardite products were very different, with leonardite products being low and the reverse osmosis concentrate being high in carboxylic functional groups. Light had a strong impact on the properties of leonardite products, including loss of color and increased particle formation. HuminFeed presented a substantial impact on microbial communities under light conditions, where bacterial production was stimulated and community composition modified, while in dark potential inhibition of bacterial processes was detected. While none of the browning agents inhibited the growth of the tested phytoplankton Gonyostomum semen, HuminFeed had detrimental effects on zooplankton abundance and Daphnia reproduction. We conclude that the effects of browning agents extracted from leonardite, particularly HuminFeed, are in sharp contrast to those originating from terrestrially derived dissolved organic matter. Hence, they should be used with great caution in experimental studies on the consequences of terrestrial carbon for aquatic systems.
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| 6. |
- Bier, Raven L., et al.
(författare)
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Effects of ecosystem size-induced environmental fluctuations on the temporal dynamics of community assembly mechanisms
- 2022
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Ingår i: The ISME Journal. - : Springer Nature. - 1751-7362 .- 1751-7370. ; 16:12, s. 2635-2643
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Tidskriftsartikel (refereegranskat)abstract
- Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.
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| 7. |
- Boros, Emil, et al.
(författare)
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Macrophytes and groundwater drive extremely high organic carbon concentration of soda pans
- 2020
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 65:9, s. 1555-1568
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Tidskriftsartikel (refereegranskat)abstract
- Endorheic soda pans are among the highest dissolved organic carbon (DOC) content aquatic systems on the planet with concentrations up to 1 g/L. Considering the importance of inland waters in the global carbon cycle, understanding the drivers of such outstanding organic carbon pools is eminent. The soda pans of the Carpathian Basin present a wide variability of biotic and abiotic characteristics that provide an adequate system to assess the determinants of extreme high DOC concentrations. Here, we demonstrate through a multi‐site comparison, a multi‐year seasonal monitoring, and a laboratory experiment that the dissolved organic matter content of the highest DOC concentration soda pans is primarily of groundwater and emergent macrophyte origin.More precisely, the multi‐site comparison of 14 soda pans revealed that variation of coloured dissolved organic matter (CDOM) content of the surface water of soda pans is partially explained by the CDOM content (22% of variation) of local groundwater, indicating the significant role of allochthonous terrestrial DOC sources. Further 23% of CDOM variation could be accounted for by Bolboschoenus maritimus species‐specific emergent macrophyte cover, while the contribution of Phragmites australis cover was only minor.In line with the results of the multi‐site comparison, our decomposition experiment demonstrated that both B. maritimus and P. australis have the potential to release substantial amount of organic matter into soda pans. However, the organic matter release of B. maritimus leads to twice as high DOC and 3.5‐times higher CDOM concentrations than P. australis. Considering previous organic matter release studies, we concluded that P. australis is a relatively low organic matter releaser emergent macrophyte, and therefore the species composition of emergent macrophytes has to be carefully considered in autochthonous plant‐derived DOM estimations.Finally, the multi‐year seasonal monitoring of two distinctive soda pans showed that the high organic matter concentrations depend not only on their intrinsic characteristics but also on interannual variability. More precisely, we demonstrated that the highest CDOM and DOC concentrations that occurred in a coloured (i.e. brown, low total suspended solids) soda pan with extensive (95%) macrophyte cover dominated by B. maritimus were measured in a period characterised by high pH and low water levels, which were presumably the consequence of increased evaporation due to decreased precipitation and above average temperature.Our results indicate that considering climate change trends common for most endorheic regions (i.e. increased temperature and modified precipitation regimes), extremely high organic matter concentrations might become more frequent in the near future in local water bodies, particularly in those highly influenced by groundwater inflow. Furthermore, soda pans with vast specific macrophyte cover and substantial groundwater inflow might become organic carbon processing hotspots.
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| 8. |
- Felfoldi, Tamas, et al.
(författare)
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Biological treatment of coke plant effluents : from a microbiological perspective
- 2020
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Ingår i: BIOLOGIA FUTURA. - : SPRINGER HEIDELBERG. - 2676-8615 .- 2676-8607. ; 71:4, s. 359-370
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Forskningsöversikt (refereegranskat)abstract
- During coke production, large volume of effluent is generated, which has a very complex chemical composition and contains several toxic and carcinogenic substances, mainly aromatic compounds, cyanide, thiocyanate and ammonium. The composition of these high-strength effluents is very diverse and depends on the quality of coals used and the operating and technological parameters of coke ovens. In general, after initial physicochemical treatment, biological purification steps are applied in activated sludge bioreactors. This review summarizes the current knowledge on the anaerobic and aerobic transformation processes and describes key microorganisms, such as phenol- and thiocyanate-degrading, floc-forming, nitrifying and denitrifying bacteria, which contribute to the removal of pollutants from coke plant effluents. Providing the theoretical basis for technical issues (in this case the microbiology of coke plant effluent treatment) aids the optimization of existing technologies and the design of new management techniques.
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| 9. |
- Isaksson, Frida, et al.
(författare)
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Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden
- 2022
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Ingår i: Environments. - : MDPI. - 2076-3298. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- The detection of SARS-CoV-2 RNA fragments in feces has paved the way for wastewater-based epidemiology to contribute to COVID-19 mitigation measures, with its use in a public health context still under development. As a way to facilitate data comparison, this paper explores the impact of using alternative normalization approaches (wastewater treatment plant (WWTP) flow, population size estimates (derived using total nitrogen (TN), total phosphorus (TP) and census data) and pepper mild mottle virus (PMMoV)) on the relationship between viral wastewater data and clinical case numbers. Influent wastewater samples were collected at two WWTPs in Luleå, northern Sweden, between January and March 2021. TN and TP were determined upon sample collection, with RNA analysis undertaken on samples after one freeze–thaw cycle. The strength of the correlation between normalization approaches and clinical cases differed between WWTPs (r ≤ 0.73 or r ≥ 0.78 at the larger WWTP and r ≤ 0.23 or r ≥ 0.43 at the smaller WWTP), indicating that the use of wastewater as an epidemiological tool is context-dependent. Depending on the normalization approach utilized, time-shifted analyses imply that wastewater data on SARS-CoV-2 RNA pre-dated a rise in clinical cases by 0–2 and 5–8 days, for the lager and smaller WWTPs, respectively. SARS-CoV-2 viral loads normalized to the population or PMMoV better reflect the number of clinical cases when comparing wastewater data between sewer catchments.
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| 10. |
- Lundy, Lian, et al.
(författare)
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Making Waves : Collaboration in the time of SARS-CoV-2 - rapid development of an international co-operation and wastewater surveillance database to support public health decision-making
- 2021
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 199
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Tidskriftsartikel (refereegranskat)abstract
- The presence of SARS-CoV-2 RNA in wastewater was first reported in March 2020. Over the subsequent months, the potential for wastewater surveillance to contribute to COVID-19 mitigation programmes has been the focus of intense national and international research activities, gaining the attention of policy makers and the public. As a new application of an established methodology, focused collaboration between public health practitioners and wastewater researchers is essential to developing a common understanding on how, when and where the outputs of this non-invasive community-level approach can deliver actionable outcomes for public health authorities. Within this context, the NORMAN SCORE “SARS-CoV-2 in sewage” database provides a platform for rapid, open access data sharing, validated by the uploading of 276 data sets from nine countries to-date. Through offering direct access to underpinning meta-data sets (and describing its use in data interpretation), the NORMAN SCORE database is a resource for the development of recommendations on minimum data requirements for wastewater pathogen surveillance. It is also a tool to engage public health practitioners in discussions on use of the approach, providing an opportunity to build mutual understanding of the demand and supply for data and facilitate the translation of this promising research application into public health practice.
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