Stefan M Neuenschwander's research while affiliated with University of Zurich and other places

Publications (12)

Article
Full-text available
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we rec...
Preprint
Full-text available
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we rec...
Article
Full-text available
After strong fertilization in the 20th century, many deep lakes in Central Europe are again nutrient poor due to long-lasting restoration (re-oligotrophication). In line with reduced phosphorus and nitrogen loadings, total organismic productivity decreased and lakes have now historically low nutrient and biomass concentrations. This caused speculat...
Article
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes f...
Article
Full-text available
Methylotrophic planktonic bacteria fulfill a particular role in the carbon cycle of lakes via the turnover of single-carbon compounds. We studied two planktonic freshwater lineages (LD28 and PRD01a001B) affiliated with Methylophilaceae (Betaproteobacteria) in Lake Zurich, Switzerland, by a combination of molecular and cultivation-based approaches....
Data
Full-text available
Flow cytometric sorting is a powerful tool to physically separate cells within mixed microbial communities. If combined with phylogenetic staining (fluorescence in situ hybridization, FISH) it allows to specifically sort defined genotypic microbial populations from complex natural samples. However, the targeted enrichment of freshwater ultramicroba...
Article
Full-text available
Flow cytometric sorting is a powerful tool to physically separate cells within mixed microbial communities. If combined with phylogenetic staining (fluorescence in situ hybridization, FISH) it allows to specifically sort defined genotypic microbial populations from complex natural samples. However, the targeted enrichment of freshwater ultramicroba...
Article
We studied the seasonal growth potential of opportunistic bacterial populations in Lake Zurich (Switzerland) by a series of grazer free dilution culture assays. Pronounced shifts in the composition of the bacterial assemblages were observed within one doubling of total cell numbers, from initially abundant Actinobacteria to other fast growing micro...

Citations

... For instance, CARD-FISH analyses require the design of probes that target specific lineages, which may not be possible for many taxonomic groups of protists [31]. Similarly, ampliconbased studies provide no information on viruses, and culture-based approaches are biased towards relatively easily cultivable copiotrophs (e.g., Flavobacteria), overlooking many dominant, genome-streamlined oligotrophic microbes that remain hard to culture [32,33]. Finally, microscopic analyses alone are insufficient to reliably distinguish many heterotrophic nanoflagellates [34]. ...
... Burkholderiaceae is an ammonia-oxidizing bacteria (AOB) that has the ability to reduce ammonium and nitrite by nitrification and ammonia oxidation, and it can be found in a variety of aquatic and terrestrial environments (Salcher et al., 2019). Burkholderiaceae plays an important role in the growth of wetland plants and is beneficial for carbon turnover and nitrogen fixation (Di et al., 2020). ...
... The blooms of P. agardhii are globally distributed and have been recognised as a direct consequence of the eutrophication often caused by discharge of agricultural or urban wastewater [45][46][47]. In contrast, the development of P. rubescens in metalimnion of deep clearwater lakes is partially attributed to climate warming, stability of water column and reduced of water mixing [48][49][50]. With reference to all these characteristics, both species are similar, yet different in many ways. ...
... For instance, CARD-FISH analyses require the design of probes that target specific lineages, which may not be possible for many taxonomic groups of protists [31]. Similarly, ampliconbased studies provide no information on viruses, and culture-based approaches are biased towards relatively easily cultivable copiotrophs (e.g., Flavobacteria), overlooking many dominant, genome-streamlined oligotrophic microbes that remain hard to culture [32,33]. Finally, microscopic analyses alone are insufficient to reliably distinguish many heterotrophic nanoflagellates [34]. ...
... It has been argued that capturing such events with a fast turnover of the community in a matter of a few weeks necessitates a high-temporal sampling approach, i.e., sampling every 2/3 days to identify short-lived peaks of rapidly growing microbes (generation times in hours to days) as seasonal (e.g., spring, summer, winter) or monthly samplings are insufficient [6,11]. While long-term time series exploration of freshwater habitats is becoming increasingly common, and approaches ranging from amplicon analyses [12][13][14], fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) [15][16][17], and cultivation [18] to metagenomic sequencing [19,20] have been applied, studies with high-temporal sampling, particularly in freshwaters are limited [4-6, 21, 22]. Even so, many approaches have been applied to disentangle this complex phenomenon. ...
... Nanopelagicus' (acI-B1), MET1217 [122] targeting the family Methylophilaceae, LD28-1017 [123] targeting the genus 'Ca. Methylopumilus' , and LD12-115 [124] targeting the genus 'Ca. Fonsibacter' (LD12). ...
... It has been argued that capturing such events with a fast turnover of the community in a matter of a few weeks necessitates a high-temporal sampling approach, i.e., sampling every 2/3 days to identify short-lived peaks of rapidly growing microbes (generation times in hours to days) as seasonal (e.g., spring, summer, winter) or monthly samplings are insufficient [6,11]. While long-term time series exploration of freshwater habitats is becoming increasingly common, and approaches ranging from amplicon analyses [12][13][14], fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) [15][16][17], and cultivation [18] to metagenomic sequencing [19,20] have been applied, studies with high-temporal sampling, particularly in freshwaters are limited [4-6, 21, 22]. Even so, many approaches have been applied to disentangle this complex phenomenon. ...