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.
Highlights
The extent to which environmental factors constrain the distribution of bacterial freshwater taxa and promote their diversity is a critical subject in microbial ecology
While Polynucleobacter and Limnohabitans belong to the best-studied genera in freshwater ecosystems, the relative importance of each of the three factors for their prevalence and diversity has not been investigated in a single study so far
As we focus in particular on Polynucleobacter (1,076,191 reads; 852 operational taxonomic units (OTUs)) and Limnohabitans lineages (729,321 reads; 1 230 OTUs), we assigned the respective OTUs to subclusters of these genera (PnecA, PnecB1, PnecB2, PnecC, and PnecD within Polynucleobacter and LimA, LimB, LimC, LimD, and LimE within Limnohabitans)
Summary
The extent to which environmental factors constrain the distribution of bacterial freshwater taxa and promote their diversity is a critical subject in microbial ecology. Ubiquitously distributed genera such as Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) comprise a broad diversity of species differentially adapted to physico-chemical parameters including pH and climate conditions (Kasalický et al, 2013; Hahn et al, 2015, 2016; Jezberová et al, 2017). The species diversity harbored by each of these two genera can phylogenetically be clustered into groups characterized by differences in their 16S rRNA genes PnecC is the best-studied subcluster so far It comprises multiple described and presumably a large number of undescribed species with diverse ecophysiological and genomic traits, which contrasts their relatively low 16S rRNA gene sequence diversity (Hahn et al, 2016). Ample knowledge on the ecology of Limnohabitans is based on studies employing the R-BT065 FISH probe, which targets bacteria affiliated to four of the subclusters (LimB, LimC, LimD, and LimE) (Simek et al, 2001; Jezbera et al, 2013)
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