Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients

Abstract

Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.

Quantifying the information content of lake microbiomes using a machine learning-based framework

“…Applying our framework to a microbial ecology dataset collected in a large-scale survey of European lakes, the results suggest that lower levels of microbial taxonomy share a higher level of information with lake parameters (figures 1 and 2B). This supports the hypothesis that OTUs from the same species can react to environmental change differently and might, therefore, inhabit different ecological niches [44,47,[84][85][86]. Furthermore, our results show that, for most physico-chemical parameters, higher levels of taxonomy do not contain information not already present on the OTU level (see figure 3B), which is in contrast to the findings of others [87].…”

“…Sampling was part of a pan-European study conducted in August 2012 (eukaryotic sequences are published in [40]; NCBI Bioproject PRJNA414052, prokaryotic sequences are published and described in [47] and [42]; NCBI Bioproject PR-JNA559862). To analyze the effects of bio-geo-chemical factors on bacterial and protist freshwater communities on a large scale, 280 lakes were sampled, covering a broad latitudinal gradient ranging from Spain to the South of Scandinavia and altitudes from sea level to 3110 m.a.s.l.…”

“…Samples were commercially sequenced (Fasteris, Geneva, Switzerland) using paired-end Illumina HiSeq 2500 sequencing in the 'rapid run' mode to generate 2 x 300 bp reads. For details, please see [40,47] and [42].…”

Factors shaping community patterns of protists and bacteria on a European scale

“…For the prokaryotic data, sequences were generated (V2-V3 region of the 16S rRNA gene) based on the same extracted DNA. Prokaryotic sequences were deposited at NCBI under Bioproject accession number PRJNA559862 (part of the prokaryotic data focusing of two specific taxa was used in Nuy et al, 2020). Briefly, genomic DNA was extracted using the my-Budget DNA Mini Kit (Bio-Budget Technologies GmbH, Krefeld, Germany) following the protocol of the manufacturer and modifications after Boenigk et al (2018).…”

Sediment Metagenomes as Time Capsules of Lake Microbiomes

“…Our explorations of captured and free metagenomes detected key bacterioplankton groups for which ecotypic diversity is well described, e.g., Polynucleobacter and Limnohabitans. The microdiversity of ubiquitous Polynucleobacter and Limnohabitans has been investigated in a wide variety of freshwater lakes and has been physiologically characterized through culture, transplant experiments, and genome sequencing (55)(56)(57)(58). The niche specificities of Polynucleobacter or Limnohabitans ecotypes in DNA time series could potentially describe historical water column conditions (e.g., pH, carbon and other nutrient substrates, light penetration, temperature, and oxygen levels).…”