The Experts below are selected from a list of 273 Experts worldwide ranked by ideXlab platform
Shinichi Nakano - One of the best experts on this subject based on the ideXlab platform.
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Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi
2018Co-Authors: Maliheh Mehrshad, Shinichi Nakano, Michaela M. Salcher, Yusuke Okazaki, Karel Šimek, Adrian-stefan Andrei, Rohit GhaiAbstract:Abstract Background Representatives of the phylum Chloroflexi, though reportedly highly abundant (up to 30% of total prokaryotes) in the extensive deep water habitats of both marine (SAR202) and freshwater (CL500-11), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. Results Here we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the Hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake Hypolimnion provides a globally stable habitat reflected in lower species diversity among Hypolimnion specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion specific SL56 cluster. Cell volume analyses show that the CL500-11 are amongst the largest prokaryotic cells in the water column of deep lakes and with a biomass:abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. Conclusions Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and Hypolimnion.
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Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
BMC, 2018Co-Authors: Maliheh Mehrshad, Shinichi Nakano, Michaela M. Salcher, Yusuke Okazaki, Karel Šimek, Adrian-stefan Andrei, Rohit GhaiAbstract:Abstract Background Representatives of the phylum Chloroflexi, though reportedly highly abundant in the extensive deep water habitats of both marine (SAR202 up to 30% of total prokaryotes) and freshwater (CL500-11 up to 26% of total prokaryotes), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11. Results Here, we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism, and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the Hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake Hypolimnion provides a globally stable habitat reflected in lower species diversity among Hypolimnion-specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion-specific SL56 cluster. Cell volume analyses show that the CL500-11 are among the largest prokaryotic cells in the water column of deep lakes and with a biomass to abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway. Conclusions Extending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity; however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and Hypolimnion
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Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated Hypolimnion of deep freshwater lakes
The ISME Journal, 2017Co-Authors: Yusuke Okazaki, Shohei Fujinaga, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Shinichi NakanoAbstract:The oxygenated Hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of Hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that the communities in the oxygenated hypolimnia were distinct from those in the epilimnia and identified several predominant lineages inhabiting multiple lakes. Catalyzed reporter deposition fluorescence in situ hybridization revealed that abundant Hypolimnion-specific lineages, CL500-11 ( Chloroflexi ), CL500-3, CL500-37, CL500-15 ( Planctomycetes ) and Marine Group I ( Thaumarchaeota ), together accounted for 1.5–32.9% of all bacterioplankton in the Hypolimnion of the lakes. Furthermore, an analysis of single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of different sub-populations between lakes and water layers among the lineages occurring in the entire water layer (for example, acI-B1 and acI-A7). Collectively, these results provide the first comprehensive overview of the bacterioplankton community in the oxygenated Hypolimnion of deep freshwater lakes.
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Growth and mortality rates of prokaryotes in the Hypolimnion of a deep freshwater lake (Lake Biwa, Japan)
Inland Waters, 2017Co-Authors: Hiroyuki Takasu, Shinichi NakanoAbstract:AbstractThe presence of pico-sized cyanobacteria (genus Synechococcus) in hypolimnetic waters has been reported, and investigators have suggested that Synechococcus contribute more to ecological processes in the Hypolimnion than previously hypothesized; however, the ecological role of Synechococcus in food webs and/or matter cycling in the Hypolimnion remains unknown. To address this issue, we assessed protistan grazing and the virus-mediated mortality of Synechococcus in the oxygenated Hypolimnion of a large freshwater lake (Lake Biwa, Japan) during the stratification period. In addition, we compared the carbon flux through mortality of Synechococcus to that of heterotrophic bacteria to evaluate the role of Synechococcus in ecological processes within a hypolimnetic ecosystem. Our results suggest that the biomass of Synechococcus and heterotrophic bacteria in the Hypolimnion was removed primarily by protistan grazing. The abundance of Synechococcus was highest in August, when the average Synechococcus:ba...
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Ubiquity and quantitative significance of bacterioplankton lineages inhabiting the oxygenated Hypolimnion of deep freshwater lakes
2016Co-Authors: Yusuke Okazaki, Shohei Fujinaga, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Shinichi NakanoAbstract:Freshwater bacterioplankton in the oxygenated Hypolimnion are reportedly dominated by specific members that are distinct from those in the epilimnion. However, no consensus exists regarding the ubiquity and abundance of these bacterioplankton, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes. Despite the broad geochemical characteristics of the lakes, 16S rRNA gene sequencing demonstrated that many predominant lineages in the Hypolimnion were shared by several lakes and consisted of members occurring in the entire water layer and members specific to the Hypolimnion. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) revealed that representative Hypolimnion-specific lineages, CL500-11 ( Chloroflexi ), CL500-3, CL500-37, CL500-15 ( Planctomycetes ), and the MGI group ( Thaumarchaeota ), together accounted for 1.5-32.9% of all bacterioplankton in the Hypolimnion of the lakes. Furthermore, an analysis of micro-diversification based on single-nucleotide variation in the partial 16S rRNA gene sequence (oligotyping) suggested the presence of Hypolimnion-specific ecotypes among the lineages occurring in the entire water layer (e.g., acI and Limnohabitans ). Collectively, these results demonstrate the uniqueness, ubiquity, and quantitative significance of bacterioplankton in the oxygenated Hypolimnion, motivating future studies to focus on their eco-physiological characteristics.
Jorge Ramírez-zierold - One of the best experts on this subject based on the ideXlab platform.
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Physical and chemical limnology of a wind-swept tropical highland reservoir
Aquatic Ecology, 2008Co-Authors: Martin Merino-ibarra, Emiliano Monroy-ríos, Gloria Vilaclara, Fermin S. Castillo, Margarita E. Gallegos, Jorge Ramírez-zieroldAbstract:Valle de Bravo (VB) is a tropical reservoir located (19°21′30″ N, 100°11′00″ W) in the highlands of Mexico. The reservoir is daily swept by strong (7.4 m s^−1 mean speed) diurnal (12:00–19:00 h) winds that blow along its two main arms. As expected from its fetch (6.9 km) and its depth (21.1 m mean), the reservoir behaves as a warm monomictic water body. During 2001, VB was stratified from February to October, and well mixed from November to January. Its mean temperature was 19.9°C; the maximum found was 23.8°C in the epilimnion, while a minimum of 17.8°C was registered during mixing. VB exhibited a thermal regime similar to other water bodies of the Mexican tropical highlands, except for a steady increase of its hypolimnetic temperature during stratification, which is attributed to entrainment of epilimnetic water into the Hypolimnion. During stratification, the Hypolimnion was anoxic, while the whole water column remained under-saturated (60%) during mixing. The flushing time is 2.2 years. Mineralization and total alkalinity are low, which allows strong changes in pH. Ammonia remained low (2.4 μmol l^−1 mean) in the epilimnion, but reached up to 60 μmol l^−1 in the Hypolimnion. Soluble reactive phosphorous had a mean of 0.28 μmol l^−1 in the epilimnion and a mean of 1.25 μmol l^−1 in the Hypolimnion. Nitrate exhibited maxima (up to 21 μmol l^−1) during mixing, and also in the metalimnion (2 μmol l^−1) during stratification. Low dissolved inorganic nitrogen indicated nitrogen limitation during stratification. Eutrophication is an emerging problem in VB, where cyanobacteria dominate during stratification. At VB chlorophyll a is low during mixing (mean of 9 μg l^−1), and high during stratification (mean 21 μg l^−1), when blooms (up to 88 μg l^−1) are frequent. This pattern is similar to that found in other eutrophic tropical water bodies. We propose that in VB the wind regime causes vertical displacements of the thermocline (0.58–1.10 m hr^−1) and boundary mixing, enhancing the productivity during the stratification period in this tropical reservoir.
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Physical and chemical limnology of a wind-swept tropical highland reservoir
Aquatic Ecology, 2008Co-Authors: Martin Merino-ibarra, Emiliano Monroy-ríos, Gloria Vilaclara, Fermin S. Castillo, Margarita E. Gallegos, Jorge Ramírez-zieroldAbstract:Valle de Bravo (VB) is a tropical reservoir located (19°21′30″ N, 100°11′00″ W) in the highlands of Mexico. The reservoir is daily swept by strong (7.4 m s^−1 mean speed) diurnal (12:00–19:00 h) winds that blow along its two main arms. As expected from its fetch (6.9 km) and its depth (21.1 m mean), the reservoir behaves as a warm monomictic water body. During 2001, VB was stratified from February to October, and well mixed from November to January. Its mean temperature was 19.9°C; the maximum found was 23.8°C in the epilimnion, while a minimum of 17.8°C was registered during mixing. VB exhibited a thermal regime similar to other water bodies of the Mexican tropical highlands, except for a steady increase of its hypolimnetic temperature during stratification, which is attributed to entrainment of epilimnetic water into the Hypolimnion. During stratification, the Hypolimnion was anoxic, while the whole water column remained under-saturated (60%) during mixing. The flushing time is 2.2 years. Mineralization and total alkalinity are low, which allows strong changes in pH. Ammonia remained low (2.4 μmol l^−1 mean) in the epilimnion, but reached up to 60 μmol l^−1 in the Hypolimnion. Soluble reactive phosphorous had a mean of 0.28 μmol l^−1 in the epilimnion and a mean of 1.25 μmol l^−1 in the Hypolimnion. Nitrate exhibited maxima (up to 21 μmol l^−1) during mixing, and also in the metalimnion (2 μmol l^−1) during stratification. Low dissolved inorganic nitrogen indicated nitrogen limitation during stratification. Eutrophication is an emerging problem in VB, where cyanobacteria dominate during stratification. At VB chlorophyll a is low during mixing (mean of 9 μg l^−1), and high during stratification (mean 21 μg l^−1), when blooms (up to 88 μg l^−1) are frequent. This pattern is similar to that found in other eutrophic tropical water bodies. We propose that in VB the wind regime causes vertical displacements of the thermocline (0.58–1.10 m hr^−1) and boundary mixing, enhancing the productivity during the stratification period in this tropical reservoir.
Winfried Lampert - One of the best experts on this subject based on the ideXlab platform.
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Finding the optimal vertical distribution: behavioural responses of Daphnia pulicaria to gradients of environmental factors and the presence of fish
Freshwater Biology, 2012Co-Authors: Petter Larsson, Winfried LampertAbstract:Summary 1. The vertical distribution of zooplankton results from active habitat choice aiming to optimise fitness gain in a system of trade-offs. 2. Using large, controlled indoor mesocosms (Plon Plankton Towers), we monitored the behavioural response of Daphnia pulicaria to vertical gradients of temperature, food, oxygen and light, in the presence and absence of fish predation. 3. In the absence of fish, Daphnia distributed as predicted by an ideal ‘free distribution with costs’. If the food was distributed homogeneously, they stayed in the warm epilimnion, while they balanced their time dwelling in epi- and Hypolimnion if the food was concentrated in a deep-water maximum. 4. However, oxygen depletion in the Hypolimnion, representing an additional cost, prevented Daphnia from completely exploiting the hypolimnetic food maximum. Consequently, the proportion dwelling in the Hypolimnion was larger if oxygen was not limiting. 5. Fish predation had an overwhelming effect, driving Daphnia into the Hypolimnion under all experimental conditions. If permitted by oxygen availability, Daphnia used the whole Hypolimnion, but oxygen depletion reduced their possible habitat to the upper Hypolimnion with oxygen concentrations above c. 0.7 mg L−1. As fish were less tolerant of low oxygen, the layer below the thermocline formed a predation refuge for Daphnia.
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upward phosphorus transport by daphnia diel vertical migration
Limnology and Oceanography, 2010Co-Authors: Florian Haupt, Maria Stockenreiter, Elke S Reichwaldt, Michaela Baumgartner, Winfried Lampert, Maarten Boersma, Herwig StiborAbstract:In many lakes, zooplankton show a distinct diel vertical migration (DVM) behavior, especially during periods of stratification. Excretion products of these zooplankton could potentially cause an upward nutrient transport and consequent nutrient enrichment for phytoplankton in the epilimnion. We quantified the upward transport of phosphorus by the cladoceran Daphnia DVM experimentally by adding a radioactive tracer (33P) to the Hypolimnion of large indoor mesocosms and measuring tracer accumulation in the epilimnion over time. During the daytime, when all Daphnia were found in the Hypolimnion, no phosphorus transport from the Hypolimnion into the epilimnion took place. As soon as the Daphnia started their upward migration, around dusk, we observed a continuous increase in phosphorus concentration in the epilimnion. The amount of phosphorus transported was in a biologically meaningful range. Our results strongly suggest that Daphnia vertical migration presents a continuous nutrient supply for the epilimnion. Diel vertical migration (DVM) of zooplankton is one of the world’s largest synchronized movements of animals (Hays 2003). It is a daily habitat shift of zooplankton from deeper water regions during the day to surface waters at
Martin Merino-ibarra - One of the best experts on this subject based on the ideXlab platform.
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Physical and chemical limnology of a wind-swept tropical highland reservoir
Aquatic Ecology, 2008Co-Authors: Martin Merino-ibarra, Emiliano Monroy-ríos, Gloria Vilaclara, Fermin S. Castillo, Margarita E. Gallegos, Jorge Ramírez-zieroldAbstract:Valle de Bravo (VB) is a tropical reservoir located (19°21′30″ N, 100°11′00″ W) in the highlands of Mexico. The reservoir is daily swept by strong (7.4 m s^−1 mean speed) diurnal (12:00–19:00 h) winds that blow along its two main arms. As expected from its fetch (6.9 km) and its depth (21.1 m mean), the reservoir behaves as a warm monomictic water body. During 2001, VB was stratified from February to October, and well mixed from November to January. Its mean temperature was 19.9°C; the maximum found was 23.8°C in the epilimnion, while a minimum of 17.8°C was registered during mixing. VB exhibited a thermal regime similar to other water bodies of the Mexican tropical highlands, except for a steady increase of its hypolimnetic temperature during stratification, which is attributed to entrainment of epilimnetic water into the Hypolimnion. During stratification, the Hypolimnion was anoxic, while the whole water column remained under-saturated (60%) during mixing. The flushing time is 2.2 years. Mineralization and total alkalinity are low, which allows strong changes in pH. Ammonia remained low (2.4 μmol l^−1 mean) in the epilimnion, but reached up to 60 μmol l^−1 in the Hypolimnion. Soluble reactive phosphorous had a mean of 0.28 μmol l^−1 in the epilimnion and a mean of 1.25 μmol l^−1 in the Hypolimnion. Nitrate exhibited maxima (up to 21 μmol l^−1) during mixing, and also in the metalimnion (2 μmol l^−1) during stratification. Low dissolved inorganic nitrogen indicated nitrogen limitation during stratification. Eutrophication is an emerging problem in VB, where cyanobacteria dominate during stratification. At VB chlorophyll a is low during mixing (mean of 9 μg l^−1), and high during stratification (mean 21 μg l^−1), when blooms (up to 88 μg l^−1) are frequent. This pattern is similar to that found in other eutrophic tropical water bodies. We propose that in VB the wind regime causes vertical displacements of the thermocline (0.58–1.10 m hr^−1) and boundary mixing, enhancing the productivity during the stratification period in this tropical reservoir.
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Physical and chemical limnology of a wind-swept tropical highland reservoir
Aquatic Ecology, 2008Co-Authors: Martin Merino-ibarra, Emiliano Monroy-ríos, Gloria Vilaclara, Fermin S. Castillo, Margarita E. Gallegos, Jorge Ramírez-zieroldAbstract:Valle de Bravo (VB) is a tropical reservoir located (19°21′30″ N, 100°11′00″ W) in the highlands of Mexico. The reservoir is daily swept by strong (7.4 m s^−1 mean speed) diurnal (12:00–19:00 h) winds that blow along its two main arms. As expected from its fetch (6.9 km) and its depth (21.1 m mean), the reservoir behaves as a warm monomictic water body. During 2001, VB was stratified from February to October, and well mixed from November to January. Its mean temperature was 19.9°C; the maximum found was 23.8°C in the epilimnion, while a minimum of 17.8°C was registered during mixing. VB exhibited a thermal regime similar to other water bodies of the Mexican tropical highlands, except for a steady increase of its hypolimnetic temperature during stratification, which is attributed to entrainment of epilimnetic water into the Hypolimnion. During stratification, the Hypolimnion was anoxic, while the whole water column remained under-saturated (60%) during mixing. The flushing time is 2.2 years. Mineralization and total alkalinity are low, which allows strong changes in pH. Ammonia remained low (2.4 μmol l^−1 mean) in the epilimnion, but reached up to 60 μmol l^−1 in the Hypolimnion. Soluble reactive phosphorous had a mean of 0.28 μmol l^−1 in the epilimnion and a mean of 1.25 μmol l^−1 in the Hypolimnion. Nitrate exhibited maxima (up to 21 μmol l^−1) during mixing, and also in the metalimnion (2 μmol l^−1) during stratification. Low dissolved inorganic nitrogen indicated nitrogen limitation during stratification. Eutrophication is an emerging problem in VB, where cyanobacteria dominate during stratification. At VB chlorophyll a is low during mixing (mean of 9 μg l^−1), and high during stratification (mean 21 μg l^−1), when blooms (up to 88 μg l^−1) are frequent. This pattern is similar to that found in other eutrophic tropical water bodies. We propose that in VB the wind regime causes vertical displacements of the thermocline (0.58–1.10 m hr^−1) and boundary mixing, enhancing the productivity during the stratification period in this tropical reservoir.
Herwig Stibor - One of the best experts on this subject based on the ideXlab platform.
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upward phosphorus transport by daphnia diel vertical migration
Limnology and Oceanography, 2010Co-Authors: Florian Haupt, Maria Stockenreiter, Elke S Reichwaldt, Michaela Baumgartner, Winfried Lampert, Maarten Boersma, Herwig StiborAbstract:In many lakes, zooplankton show a distinct diel vertical migration (DVM) behavior, especially during periods of stratification. Excretion products of these zooplankton could potentially cause an upward nutrient transport and consequent nutrient enrichment for phytoplankton in the epilimnion. We quantified the upward transport of phosphorus by the cladoceran Daphnia DVM experimentally by adding a radioactive tracer (33P) to the Hypolimnion of large indoor mesocosms and measuring tracer accumulation in the epilimnion over time. During the daytime, when all Daphnia were found in the Hypolimnion, no phosphorus transport from the Hypolimnion into the epilimnion took place. As soon as the Daphnia started their upward migration, around dusk, we observed a continuous increase in phosphorus concentration in the epilimnion. The amount of phosphorus transported was in a biologically meaningful range. Our results strongly suggest that Daphnia vertical migration presents a continuous nutrient supply for the epilimnion. Diel vertical migration (DVM) of zooplankton is one of the world’s largest synchronized movements of animals (Hays 2003). It is a daily habitat shift of zooplankton from deeper water regions during the day to surface waters at
