Steffen Jost - Academia.edu (original) (raw)

Papers by Steffen Jost

Research paper thumbnail of AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

Research paper thumbnail of Protistan community analysis: key findings of a large-scale molecular sampling

The ISME journal, Sep 9, 2016

Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. Hi... more Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not so...

Research paper thumbnail of Seasonal variation of planktonic chrysophytes with special focus on Dinobryon

Research paper thumbnail of CULTIVATION-INDEPENDENT SPECIES IDENTIFICATION OF DINOBRYON SPECIES (CHRYSOPHYCEAE) BY MEANS OF MULTIPLEX SINGLE-CELL PCR1

Journal of Phycology, 2010

Research paper thumbnail of Medinger R, Nolte V, Pandey RV, Jost S, Ottenwälder B, Schlötterer C et al.. Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19: 32-40

Research paper thumbnail of Remias et al 2013 Hydrurus snow

Research paper thumbnail of Supplemantary Figures ISME J

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (H... more Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase and growth efficiency) and community composition of a natural HNF community from a freshwater reservoir. Pyrosequencing of eukaryotic small subunit rRNA amplicons was used to assess time-course changes in HNF community composition. All four Limnohabitans strains and the Polynucleobacter strain yielded significant HNF community growth while the actinobacterial strain did not although it was detected in HNF food vacuoles. Notably, even within the Limnohabitans strains we found significant prey-related differences in HNF growth parameters, which could not be related only to size of the bacterial prey. Sequence data characterizing the HNF com...

Research paper thumbnail of Magnesiothermic conversion of the silica-mineralizing golden algae Mallomonas caudata and Synura petersenii to elemental silicon with high geometric precision

Beilstein Journal of Nanotechnology, 2014

Chrysophyceae, also known as golden algae, contain characteristic, three-dimensional biomineraliz... more Chrysophyceae, also known as golden algae, contain characteristic, three-dimensional biomineralized silica structures. Their chemical composition and microscopic structure was studied. By high-temperature conversion of the skeleton of Mallomonas caudata and Synura petersenii into elementary silicon by magnesium vapour, nanostructured defined replicates were produced which were clearly seen after removal of the formed magnesium oxide with acid.

Research paper thumbnail of Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria

Research paper thumbnail of Hydrurus- related golden algae (Chrysophyceae) cause yellow snow in polar summer snowfields

Phycological Research, 2013

Research paper thumbnail of Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

Research paper thumbnail of Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

Research paper thumbnail of Ecology and community structure of ciliated protists in two alkaline-saline Rift Valley lakes in Kenya with special emphasis on Frontonia

Journal of Plankton Research, 2013

ABSTRACT Ciliated protist assemblages of the shallow soda lakes Bogoria and Nakuru in Kenya were ... more ABSTRACT Ciliated protist assemblages of the shallow soda lakes Bogoria and Nakuru in Kenya were studied weekly during the short rainy season in October and November 2008 to identify their taxonomic composition and possible interactions with abiotic and biotic factors. Overall, 22 ciliate morphotypes were detected. Cyclidium glaucoma was the most abundant, whereas Frontonia sp., Condylostoma sp. and Holophrya sp. dominated in terms of biovolume. Further, the assignment of ciliates to nutritional modes indicated that the abundance of bacterivorous ciliates was not related to bacterial abundance, most likely because of the very high bacterial food concentrations (83.0 10(6) cells mL(1) on average). The abundance of Frontonia sp. was positively correlated with chlorophyll a in Lake Bogoria, but not in Lake Nakuru. Morphometric measurements of Frontonia sp. indicated significant intraspecific differences in mean cell length, i.e. 116.1 2.3 vs. 139.0 2.7 m in Lake Bogoria and Lake Nakuru, respectively. Sequences of the 18S SSU rRNA, however, turned out to be identical for individuals of the two lakes. Phylogenetic relationships of the subclass Peniculia based on the 18S rRNA genes revealed that Frontonia from these lakes rather clustered with Apofrontonia and Paramecium than with other Frontonia species, indicating that the genus Frontonia is paraphyletic. With the exception of C. glaucoma and Euplotes moebiusi, the ciliate taxa from the two lakes could be identified only down to the genus level. We assume that these taxa are still not yet described and thus highlight the unique character of these ecosystems and the need for more studies.

Research paper thumbnail of Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008

Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicatin... more Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicating cryptic species. One of the best-investigated morphospecies with respect to molecular and ecophysiological variation are flagellates of the Spumella morphotype. Here, we have phylogenetically analysed three protein-coding genes (actin, alpha-tubulin, beta-tubulin), internal transcribed spacers (ITS1, ITS2) and the 5.8S rDNA of 17 Spumella-like strains isolated from soil, freshwater and marine samples in order to (i) test the validity of the current Spumella-like phylogenetic classification system based exclusively on small subunit (SSU) rDNA, (ii) elucidate the phylogenetic associations of SSU rDNA-unresolved strains and (iii) evaluate the validity of the assignment of ecophysiological adaptations to previously identified SSU rDNA sequence clades. All single-gene analyses show different patterns of support, are incongruent and identify a number of conflicting nodes. Likewise, a concatenation of all protein genes fails to recover specific SSU rDNA clades. However, a combined analysis of all genes confidently resolved the conflicts of the single genes and the protein-gene concatenations and resulted in a tree topology that is identical to the SSU rDNA analysis, but with enhanced phylogenetic resolution and decisively greater support. We conclude that, depending on the genes concatenated, a 'supergene' analysis minimizes artefactual effects of single genes and may be superior in its performance in phylogenetically analysing cryptic species. We confirm the validity of the SSU rDNA Spumella-like phyloclades and support the suggestion that these clades indeed seem to reflect certain ecophysiological adaptations.

Research paper thumbnail of Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones

Environmental Microbiology, 2007

Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we in... more Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we investigated the thermal adaptation of 19 strains of the same Spumella morphospecies (Chrysophyceae, Heterokonta). In order to test for local adaptation and the existence of specific ecotypes we analysed growth rates of these strains, which originated from different climate regions. We applied temperature-adaptation as an eco-physiological marker and analysed growth rates of the different Spumella strains at temperatures between 0 degrees C and 35 degrees C. The temperatures allowing for maximal growth of strains from temperate and warm climatic zones ranged between 19.9 degrees C and 33.4 degrees C. Phylogenetically, most of these 'warm'-adapted strains fall into two different previously defined 18S rDNA Spumella clusters, one of them consisting of mostly soil organisms and the other one being a freshwater cluster. As a rule, the 'warm'-adapted strains of the soil cluster grew slower than the 'warm'-adapted isolates within the freshwater cluster. This difference most probably reflect different strategies, i.e. the formation of cysts at the expense of lower growth rates in soil organisms. In contrast, as expected, all isolates from Antarctica were cold-adapted and grew already around melting point of freshwater. Surprisingly, optimum temperature for these strains was between 11.8 degrees C and 17.7 degrees C and maximum temperature tolerated was between 14.6 degrees C and 23.5 degrees C. Our data indicate that despite the relatively high optimal temperature of most Antarctic strains, they may have a relative advantage below 5-10 degrees C only. Based on the thermal adaptation of the flagellate strains the Antarctic strains were clearly separated from the other investigated strains. This may indicate a limited dispersal of flagellates to and from Antarctica. Even if the latter assumption needs support from more data, we argue that the high levels of eco-physiological and molecular microdiversity indicate that the current species concepts do not sufficiently reflect protist eco-physiological differentiation.

Research paper thumbnail of AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

Research paper thumbnail of Protistan community analysis: key findings of a large-scale molecular sampling

The ISME journal, Sep 9, 2016

Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. Hi... more Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not so...

Research paper thumbnail of Seasonal variation of planktonic chrysophytes with special focus on Dinobryon

Research paper thumbnail of CULTIVATION-INDEPENDENT SPECIES IDENTIFICATION OF DINOBRYON SPECIES (CHRYSOPHYCEAE) BY MEANS OF MULTIPLEX SINGLE-CELL PCR1

Journal of Phycology, 2010

Research paper thumbnail of Medinger R, Nolte V, Pandey RV, Jost S, Ottenwälder B, Schlötterer C et al.. Diversity in a hidden world: potential and limitation of next generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol 19: 32-40

Research paper thumbnail of Remias et al 2013 Hydrurus snow

Research paper thumbnail of Supplemantary Figures ISME J

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (H... more Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase and growth efficiency) and community composition of a natural HNF community from a freshwater reservoir. Pyrosequencing of eukaryotic small subunit rRNA amplicons was used to assess time-course changes in HNF community composition. All four Limnohabitans strains and the Polynucleobacter strain yielded significant HNF community growth while the actinobacterial strain did not although it was detected in HNF food vacuoles. Notably, even within the Limnohabitans strains we found significant prey-related differences in HNF growth parameters, which could not be related only to size of the bacterial prey. Sequence data characterizing the HNF com...

Research paper thumbnail of Magnesiothermic conversion of the silica-mineralizing golden algae Mallomonas caudata and Synura petersenii to elemental silicon with high geometric precision

Beilstein Journal of Nanotechnology, 2014

Chrysophyceae, also known as golden algae, contain characteristic, three-dimensional biomineraliz... more Chrysophyceae, also known as golden algae, contain characteristic, three-dimensional biomineralized silica structures. Their chemical composition and microscopic structure was studied. By high-temperature conversion of the skeleton of Mallomonas caudata and Synura petersenii into elementary silicon by magnesium vapour, nanostructured defined replicates were produced which were clearly seen after removal of the formed magnesium oxide with acid.

Research paper thumbnail of Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria

Research paper thumbnail of Hydrurus- related golden algae (Chrysophyceae) cause yellow snow in polar summer snowfields

Phycological Research, 2013

Research paper thumbnail of Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

Research paper thumbnail of Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

Research paper thumbnail of Ecology and community structure of ciliated protists in two alkaline-saline Rift Valley lakes in Kenya with special emphasis on Frontonia

Journal of Plankton Research, 2013

ABSTRACT Ciliated protist assemblages of the shallow soda lakes Bogoria and Nakuru in Kenya were ... more ABSTRACT Ciliated protist assemblages of the shallow soda lakes Bogoria and Nakuru in Kenya were studied weekly during the short rainy season in October and November 2008 to identify their taxonomic composition and possible interactions with abiotic and biotic factors. Overall, 22 ciliate morphotypes were detected. Cyclidium glaucoma was the most abundant, whereas Frontonia sp., Condylostoma sp. and Holophrya sp. dominated in terms of biovolume. Further, the assignment of ciliates to nutritional modes indicated that the abundance of bacterivorous ciliates was not related to bacterial abundance, most likely because of the very high bacterial food concentrations (83.0 10(6) cells mL(1) on average). The abundance of Frontonia sp. was positively correlated with chlorophyll a in Lake Bogoria, but not in Lake Nakuru. Morphometric measurements of Frontonia sp. indicated significant intraspecific differences in mean cell length, i.e. 116.1 2.3 vs. 139.0 2.7 m in Lake Bogoria and Lake Nakuru, respectively. Sequences of the 18S SSU rRNA, however, turned out to be identical for individuals of the two lakes. Phylogenetic relationships of the subclass Peniculia based on the 18S rRNA genes revealed that Frontonia from these lakes rather clustered with Apofrontonia and Paramecium than with other Frontonia species, indicating that the genus Frontonia is paraphyletic. With the exception of C. glaucoma and Euplotes moebiusi, the ciliate taxa from the two lakes could be identified only down to the genus level. We assume that these taxa are still not yet described and thus highlight the unique character of these ecosystems and the need for more studies.

Research paper thumbnail of Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008

Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicatin... more Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicating cryptic species. One of the best-investigated morphospecies with respect to molecular and ecophysiological variation are flagellates of the Spumella morphotype. Here, we have phylogenetically analysed three protein-coding genes (actin, alpha-tubulin, beta-tubulin), internal transcribed spacers (ITS1, ITS2) and the 5.8S rDNA of 17 Spumella-like strains isolated from soil, freshwater and marine samples in order to (i) test the validity of the current Spumella-like phylogenetic classification system based exclusively on small subunit (SSU) rDNA, (ii) elucidate the phylogenetic associations of SSU rDNA-unresolved strains and (iii) evaluate the validity of the assignment of ecophysiological adaptations to previously identified SSU rDNA sequence clades. All single-gene analyses show different patterns of support, are incongruent and identify a number of conflicting nodes. Likewise, a concatenation of all protein genes fails to recover specific SSU rDNA clades. However, a combined analysis of all genes confidently resolved the conflicts of the single genes and the protein-gene concatenations and resulted in a tree topology that is identical to the SSU rDNA analysis, but with enhanced phylogenetic resolution and decisively greater support. We conclude that, depending on the genes concatenated, a 'supergene' analysis minimizes artefactual effects of single genes and may be superior in its performance in phylogenetically analysing cryptic species. We confirm the validity of the SSU rDNA Spumella-like phyloclades and support the suggestion that these clades indeed seem to reflect certain ecophysiological adaptations.

Research paper thumbnail of Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones

Environmental Microbiology, 2007

Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we in... more Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we investigated the thermal adaptation of 19 strains of the same Spumella morphospecies (Chrysophyceae, Heterokonta). In order to test for local adaptation and the existence of specific ecotypes we analysed growth rates of these strains, which originated from different climate regions. We applied temperature-adaptation as an eco-physiological marker and analysed growth rates of the different Spumella strains at temperatures between 0 degrees C and 35 degrees C. The temperatures allowing for maximal growth of strains from temperate and warm climatic zones ranged between 19.9 degrees C and 33.4 degrees C. Phylogenetically, most of these 'warm'-adapted strains fall into two different previously defined 18S rDNA Spumella clusters, one of them consisting of mostly soil organisms and the other one being a freshwater cluster. As a rule, the 'warm'-adapted strains of the soil cluster grew slower than the 'warm'-adapted isolates within the freshwater cluster. This difference most probably reflect different strategies, i.e. the formation of cysts at the expense of lower growth rates in soil organisms. In contrast, as expected, all isolates from Antarctica were cold-adapted and grew already around melting point of freshwater. Surprisingly, optimum temperature for these strains was between 11.8 degrees C and 17.7 degrees C and maximum temperature tolerated was between 14.6 degrees C and 23.5 degrees C. Our data indicate that despite the relatively high optimal temperature of most Antarctic strains, they may have a relative advantage below 5-10 degrees C only. Based on the thermal adaptation of the flagellate strains the Antarctic strains were clearly separated from the other investigated strains. This may indicate a limited dispersal of flagellates to and from Antarctica. Even if the latter assumption needs support from more data, we argue that the high levels of eco-physiological and molecular microdiversity indicate that the current species concepts do not sufficiently reflect protist eco-physiological differentiation.