This is a self-archived version of an original article. This version may differ from the original... more This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details.
Sphingomonas fennica sp nov and Sphingomonas haloaromaticamans sp nov., outliers of the genus Sph... more Sphingomonas fennica sp nov and Sphingomonas haloaromaticamans sp nov., outliers of the genus Sphingomonas
The relatively unknown genus Iodobacter sp. has been repeatedly isolated from skin ulcers and sap... more The relatively unknown genus Iodobacter sp. has been repeatedly isolated from skin ulcers and saprolegniosis on freshwater fish in Finland, especially farmed salmonids. Genetic characterization verified that all 23 bacterial isolates studied here belonged to the species Iodobacter limnosediminis, previously undescribed from the fish microbiota. Whole-genome pulsed-field gel electrophoresis revealed variability between the I. limnosediminis strains, suggesting that they were most likely of environmental origin. Two I. limnosediminis strains caused lesions in 27%-53% of brown trout (Salmo trutta) injected intramuscularly (p ≤ .05). The lesions represented moderate to severe tissue damage, but for most fish, the tissues had been repaired by the end of the experiment through the accumulation of fibrocytes and macrophages at the site of the lesion. I. limnosediminis was reisolated from some lesions and/or internal organs. Phenotypically and biochemically, I. limnosediminis resembles seve...
CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, ba... more CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome.
Understanding the importance of the gut microbiota (GM) in non-alcoholic fatty liver disease (NAF... more Understanding the importance of the gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) has raised the hope for therapeutic microbes. We have shown that high hepatic fat content associated with low abundance of Faecalibacterium prausnitzii in humans and, further, the administration of F. prausnitzii prevented NAFLD in mice. Here, we aimed at targeting F. prausnitzii by prebiotic xylo-oligosaccharides (XOS) to treat NAFLD. First, the effect of XOS on F. prausnitzii growth was assessed in vitro. Then, XOS was supplemented or not with high (HFD, 60% of energy from fat) or low (LFD) fat diet for 12 weeks in Wistar rats (n = 10/group). XOS increased F. prausnitzii growth, having only a minor impact on the GM composition. When supplemented with HFD, XOS ameliorated hepatic steatosis. The underlying mechanisms involved enhanced hepatic β-oxidation and mitochondrial respiration. Nuclear magnetic resonance (1H-NMR) analysis of cecal metabolites showed that, compared to the HFD, ...
Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment o... more Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition. The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of ...
Understanding the importance of gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) ... more Understanding the importance of gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) has raised the hope for therapeutic microbes. We have shown that high hepatic fat associated with low abundance of Faecalibacterium prausnitzii in humans and further, administration of F. prausnitzii prevented NAFLD in mice. Here, we aimed to target F. prausnitzii by prebiotic xylo-oligosaccharides (XOS) to treat NAFLD. First, the effect of XOS on F. prausnitzii growth was assessed in vitro. Then, XOS was supplemented or not with high (HFD) or low (LFD) fat-diet for 12-weeks in Wistar rats (n=10/group). XOS increased F. prausnitzii growth having only minor impact on the GM composition. When supplemented with HFD, XOS prevented hepatic steatosis. The underlying mechanisms involved enhanced hepatic β-oxidation and mitochondrial respiration. 1H-NMR analysis of caecal metabolites showed that compared to HFD, LFD group had healthier caecal short-chain fatty acid profile and the combination of...
This is a self-archived version of an original article. This version may differ from the original... more This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details.
Freshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced throu... more Freshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced through anaerobic decomposition of organic matter (OM) in lake sediment and water column can be either oxidized to carbon dioxide (CO2) by methanotrophic microbes or emitted to the atmosphere. While the role of CH4 oxidation as a CH4 sink is widely accepted, neither the magnitude nor the drivers behind CH4 oxidation are well constrained. In this study, we aimed to gain more specific insight into CH4 oxidation in the water column of a seasonally stratified, typical boreal lake, particularly under hypoxic conditions. We used 13CH4 incubations to determine the active CH4 oxidation sites and the potential CH4 oxidation rates in the water column, and we measured environmental variables that could explain CH4 oxidation in the water column. During hypolimnetic hypoxia, 91% of available CH4 was oxidized in the active CH4 oxidation zone, where the potential CH4 oxidation rates gradually increased from...
Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the grea... more Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the greatest environmental concerns. Since plastics are fairly resistant to chemical decomposition, breakdown and reutilization of MP carbon complexes requires microbial activity. Currently, only a few microbial isolates have been shown to degrade MPs, and direct measurements of the fate of the MP carbon are still lacking. We used compound-specific isotope analysis to track the fate of fully labelled 13C-polyethylene (PE) MP carbon across the aquatic microbial-animal interface. Isotopic values of respired CO2 and membrane lipids showed that MP carbon was partly mineralized and partly used for cell growth. Microbial mineralization and assimilation of PE-MP carbon was most active when inoculated microbes were obtained from highly humic waters, which contain recalcitrant substrate sources. Mixotrophic algae (Cryptomonas sp.) and herbivorous zooplankton (Daphnia magna) used microbial mediated PE-MP ...
SummaryPrimary succession models focus on aboveground vascular plants. However, the prevalence of... more SummaryPrimary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, i.e. cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession.We linked aboveground vegetation, belowground bacterial and fungal community, and soil chemistry in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest.Compared to the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. The microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial community correlated better with soil chemistry than with vegetation, whereas the correlation of fungi with vegetation increased with vascular veg...
DNA sequencing and biomass analysis show strong vertical stratification of microbial communities ... more DNA sequencing and biomass analysis show strong vertical stratification of microbial communities in sediments of a small humic boreal lake.
Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significa... more Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZ I , nosZ II , amoA archaea , and amoA bacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2-1:15 in Keuruu, 1:3-1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems.
The role of anaerobic CH 4 oxidation in controlling lake sediment CH 4 emissions remains unclear.... more The role of anaerobic CH 4 oxidation in controlling lake sediment CH 4 emissions remains unclear. Therefore, we tested how relevant EAs (SO 4 2− , NO 3 − , Fe 3+ , Mn 4+ , O 2) affect CH 4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe 3+ and Mn 4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH 4-oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3.4% and 0.5% of archaeal and bacterial 16S rRNA genes, respectively), likely due to the low environmental stability associated with shallow depths. Consequently, the potential anaerobic CH 4 oxidation (0-2.1 nmol g −1 dry weight (DW) d −1) was not enhanced by the addition of EAs, nor important in consuming the produced CH 4 (0.6-82.5 nmol g −1 DW d −1). Instead, the increased EA availability suppressed CH 4 production via the outcompetition of methanogens by anaerobically respiring bacteria and via the increased protection of organic matter from microbial degradation induced by Fe 3+ and Mn 4+. Future studies could particularly assess whether anaerobic CH 4 oxidation has any ecological relevance in reducing CH 4 emissions from the numerous CH 4-emitting shallow lakes in boreal and tundra landscapes.
Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-ge... more Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5' end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.
Journal of Industrial Microbiology and Biotechnology, 2016
Molecular monitoring of bacterial communities can explain and predict the stability of bioprocess... more Molecular monitoring of bacterial communities can explain and predict the stability of bioprocesses in varying physicochemical conditions. To study methanol-fed denitrification biofilters of municipal wastewater treatment plants, bacterial communities of two full-scale biofilters were compared through fingerprinting and sequencing of the 16S rRNA genes. Additionally, 16S rRNA gene fingerprinting was used for 10-week temporal monitoring of the bacterial community in one of the biofilters. Combining the data with previous study results, the family Methylophilaceae and genus Hyphomicrobium were determined as suitable target groups for monitoring. An increase in the relative abundance of Hyphomicrobium-related biomarkers occurred simultaneously with increases in water flow, NOx − load, and methanol addition, as well as a higher denitrification rate, although the dominating biomarkers linked to Methylophilaceae showed an opposite pattern. The results indicate that during increased loadi...
This is a self-archived version of an original article. This version may differ from the original... more This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details.
Sphingomonas fennica sp nov and Sphingomonas haloaromaticamans sp nov., outliers of the genus Sph... more Sphingomonas fennica sp nov and Sphingomonas haloaromaticamans sp nov., outliers of the genus Sphingomonas
The relatively unknown genus Iodobacter sp. has been repeatedly isolated from skin ulcers and sap... more The relatively unknown genus Iodobacter sp. has been repeatedly isolated from skin ulcers and saprolegniosis on freshwater fish in Finland, especially farmed salmonids. Genetic characterization verified that all 23 bacterial isolates studied here belonged to the species Iodobacter limnosediminis, previously undescribed from the fish microbiota. Whole-genome pulsed-field gel electrophoresis revealed variability between the I. limnosediminis strains, suggesting that they were most likely of environmental origin. Two I. limnosediminis strains caused lesions in 27%-53% of brown trout (Salmo trutta) injected intramuscularly (p ≤ .05). The lesions represented moderate to severe tissue damage, but for most fish, the tissues had been repaired by the end of the experiment through the accumulation of fibrocytes and macrophages at the site of the lesion. I. limnosediminis was reisolated from some lesions and/or internal organs. Phenotypically and biochemically, I. limnosediminis resembles seve...
CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, ba... more CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome.
Understanding the importance of the gut microbiota (GM) in non-alcoholic fatty liver disease (NAF... more Understanding the importance of the gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) has raised the hope for therapeutic microbes. We have shown that high hepatic fat content associated with low abundance of Faecalibacterium prausnitzii in humans and, further, the administration of F. prausnitzii prevented NAFLD in mice. Here, we aimed at targeting F. prausnitzii by prebiotic xylo-oligosaccharides (XOS) to treat NAFLD. First, the effect of XOS on F. prausnitzii growth was assessed in vitro. Then, XOS was supplemented or not with high (HFD, 60% of energy from fat) or low (LFD) fat diet for 12 weeks in Wistar rats (n = 10/group). XOS increased F. prausnitzii growth, having only a minor impact on the GM composition. When supplemented with HFD, XOS ameliorated hepatic steatosis. The underlying mechanisms involved enhanced hepatic β-oxidation and mitochondrial respiration. Nuclear magnetic resonance (1H-NMR) analysis of cecal metabolites showed that, compared to the HFD, ...
Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment o... more Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition. The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of ...
Understanding the importance of gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) ... more Understanding the importance of gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) has raised the hope for therapeutic microbes. We have shown that high hepatic fat associated with low abundance of Faecalibacterium prausnitzii in humans and further, administration of F. prausnitzii prevented NAFLD in mice. Here, we aimed to target F. prausnitzii by prebiotic xylo-oligosaccharides (XOS) to treat NAFLD. First, the effect of XOS on F. prausnitzii growth was assessed in vitro. Then, XOS was supplemented or not with high (HFD) or low (LFD) fat-diet for 12-weeks in Wistar rats (n=10/group). XOS increased F. prausnitzii growth having only minor impact on the GM composition. When supplemented with HFD, XOS prevented hepatic steatosis. The underlying mechanisms involved enhanced hepatic β-oxidation and mitochondrial respiration. 1H-NMR analysis of caecal metabolites showed that compared to HFD, LFD group had healthier caecal short-chain fatty acid profile and the combination of...
This is a self-archived version of an original article. This version may differ from the original... more This is a self-archived version of an original article. This version may differ from the original in pagination and typographic details.
Freshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced throu... more Freshwater ecosystems represent a significant natural source of methane (CH4). CH4 produced through anaerobic decomposition of organic matter (OM) in lake sediment and water column can be either oxidized to carbon dioxide (CO2) by methanotrophic microbes or emitted to the atmosphere. While the role of CH4 oxidation as a CH4 sink is widely accepted, neither the magnitude nor the drivers behind CH4 oxidation are well constrained. In this study, we aimed to gain more specific insight into CH4 oxidation in the water column of a seasonally stratified, typical boreal lake, particularly under hypoxic conditions. We used 13CH4 incubations to determine the active CH4 oxidation sites and the potential CH4 oxidation rates in the water column, and we measured environmental variables that could explain CH4 oxidation in the water column. During hypolimnetic hypoxia, 91% of available CH4 was oxidized in the active CH4 oxidation zone, where the potential CH4 oxidation rates gradually increased from...
Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the grea... more Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the greatest environmental concerns. Since plastics are fairly resistant to chemical decomposition, breakdown and reutilization of MP carbon complexes requires microbial activity. Currently, only a few microbial isolates have been shown to degrade MPs, and direct measurements of the fate of the MP carbon are still lacking. We used compound-specific isotope analysis to track the fate of fully labelled 13C-polyethylene (PE) MP carbon across the aquatic microbial-animal interface. Isotopic values of respired CO2 and membrane lipids showed that MP carbon was partly mineralized and partly used for cell growth. Microbial mineralization and assimilation of PE-MP carbon was most active when inoculated microbes were obtained from highly humic waters, which contain recalcitrant substrate sources. Mixotrophic algae (Cryptomonas sp.) and herbivorous zooplankton (Daphnia magna) used microbial mediated PE-MP ...
SummaryPrimary succession models focus on aboveground vascular plants. However, the prevalence of... more SummaryPrimary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, i.e. cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession.We linked aboveground vegetation, belowground bacterial and fungal community, and soil chemistry in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest.Compared to the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. The microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial community correlated better with soil chemistry than with vegetation, whereas the correlation of fungi with vegetation increased with vascular veg...
DNA sequencing and biomass analysis show strong vertical stratification of microbial communities ... more DNA sequencing and biomass analysis show strong vertical stratification of microbial communities in sediments of a small humic boreal lake.
Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significa... more Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZ I , nosZ II , amoA archaea , and amoA bacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2-1:15 in Keuruu, 1:3-1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems.
The role of anaerobic CH 4 oxidation in controlling lake sediment CH 4 emissions remains unclear.... more The role of anaerobic CH 4 oxidation in controlling lake sediment CH 4 emissions remains unclear. Therefore, we tested how relevant EAs (SO 4 2− , NO 3 − , Fe 3+ , Mn 4+ , O 2) affect CH 4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe 3+ and Mn 4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH 4-oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3.4% and 0.5% of archaeal and bacterial 16S rRNA genes, respectively), likely due to the low environmental stability associated with shallow depths. Consequently, the potential anaerobic CH 4 oxidation (0-2.1 nmol g −1 dry weight (DW) d −1) was not enhanced by the addition of EAs, nor important in consuming the produced CH 4 (0.6-82.5 nmol g −1 DW d −1). Instead, the increased EA availability suppressed CH 4 production via the outcompetition of methanogens by anaerobically respiring bacteria and via the increased protection of organic matter from microbial degradation induced by Fe 3+ and Mn 4+. Future studies could particularly assess whether anaerobic CH 4 oxidation has any ecological relevance in reducing CH 4 emissions from the numerous CH 4-emitting shallow lakes in boreal and tundra landscapes.
Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-ge... more Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5' end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.
Journal of Industrial Microbiology and Biotechnology, 2016
Molecular monitoring of bacterial communities can explain and predict the stability of bioprocess... more Molecular monitoring of bacterial communities can explain and predict the stability of bioprocesses in varying physicochemical conditions. To study methanol-fed denitrification biofilters of municipal wastewater treatment plants, bacterial communities of two full-scale biofilters were compared through fingerprinting and sequencing of the 16S rRNA genes. Additionally, 16S rRNA gene fingerprinting was used for 10-week temporal monitoring of the bacterial community in one of the biofilters. Combining the data with previous study results, the family Methylophilaceae and genus Hyphomicrobium were determined as suitable target groups for monitoring. An increase in the relative abundance of Hyphomicrobium-related biomarkers occurred simultaneously with increases in water flow, NOx − load, and methanol addition, as well as a higher denitrification rate, although the dominating biomarkers linked to Methylophilaceae showed an opposite pattern. The results indicate that during increased loadi...
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