Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
- S. Neuenschwander, R. Ghai, J. Pernthaler, M. Salcher
- Biology, Environmental ScienceThe ISME Journal
- 13 October 2017
A new order within Actinobacteria is proposed (‘Candidatus Nanopelagicales’) with two new genera and nine new species and a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands.
The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
- M. Salcher, S. Neuenschwander, T. Posch, J. Pernthaler
- Environmental Science, BiologyThe ISME Journal
- 5 May 2015
Two planktonic freshwater lineages affiliated with Methylophilaceae in Lake Zurich, Switzerland, are studied by a combination of molecular and cultivation-based approaches to propose a new genus with two species, ‘Candidatus Methylopumilus planktonicus’ (LD28) and ‘PRD01a001B“, which confirmed a methylotrophic lifestyle with a reduced set of genes involved in C1 metabolism.
Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae
- M. Salcher, Daniel Schaefle, Melissa Kaspar, S. Neuenschwander, R. Ghai
- Biology, Environmental ScienceThe ISME Journal
- 10 July 2019
This study provides first genomic evidence of genome reduction taking place during habitat transitions, and identifies genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes.
Abrupt stop of deep water turnover with lake warming: Drastic consequences for algal primary producers
- Yana Yankova, S. Neuenschwander, O. Köster, T. Posch
- Environmental ScienceScientific Reports
- 23 October 2017
It is shown that repeated lack (since 1977) and complete stop (since 2013) of holomixis caused drastic epilimnetic phosphorus depletions and an absence of phytoplankton spring blooms in Lake Zurich (Switzerland), confirming that intended fertilizations are highly questionable.
Fluorescence in situ hybridization and sequential catalyzed reporter deposition (2C-FISH) for the flow cytometric sorting of freshwater ultramicrobacteria
- S. Neuenschwander, M. Salcher, J. Pernthaler
- BiologyFrontiers in Microbiology
- 31 March 2015
A CARD based flow sorting protocol modified with the aim of increasing its sensitivity to a level sufficient for ultramicrobacteria affiliated with LD12 Alphaproteobacteria could be successfully sorted to high purity by flow cytometry.
Seasonal growth potential of rare lake water bacteria suggest their disproportional contribution to carbon fluxes.
- S. Neuenschwander, J. Pernthaler, T. Posch, M. Salcher
- Environmental ScienceEnvironmental Microbiology
- 1 March 2015
The seasonal growth potential of opportunistic bacterial populations in Lake Zurich is studied by a series of grazer-free dilution culture assays to hint at a tight control by bacterivorous grazers and at a consequently accelerated carbon flux to higher trophic levels.
Application of a nifH microarray to assess the impact of environmental factors on free-living diazotrophs in a glacier forefield.
- L. Duc, S. Neuenschwander, H. Rehrauer, J. Zeyer
- Environmental ScienceCanadian Journal of Microbiology (print)
- 25 January 2011
Monitoring of diazotrophic populations in the field over a season indicated strong carbon limitation in young glacier forefield soils related to the genus Methylocystis, which are particularly adapted to the extreme nutritional conditions found in glacier forefields.
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
- T. Junier, M. Huber, A. Lebrand
- MedicineGenes
- 28 August 2019
The results suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5–10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage.
Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield.
- L. Duc, S. Neuenschwander, J. Zeyer
- BiologyEnvironmental Microbiology
- 1 August 2009
It is demonstrated that extensive experimental tests of probe-hybridization behaviour against sequences present in the studied environment remain a prerequisite for meaningful probe selection.
Evolution in action: Habitat-transition leads to genome-streamlining in Methylophilaceae (Betaproteobacteriales)
- M. Salcher, Daniel Schaefle, Melissa Kaspar, S. Neuenschwander, R. Ghai
- Biology, Environmental SciencebioRxiv
- 27 May 2019
This study provides first genomic evidence of genome-reduction taking place during habitat transitions, and identifies genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes.
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