Competition and niche separation of pelagic bacteria in freshwater habitats

Abstract

Summary Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free‐living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far‐reaching implications for their respective life styles and niche partitioning. The co‐occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non‐equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics

“…Furthermore, data available for lakes are still scarce compared to other systems, even though these environments are characterized by dynamic cycling of CH 4 , serving both as its major sources and major sinks. The principal studies have focused on a few models and their sedimentary compartments (Rahalkar et al 2009;Chistoserdova and Lidstrom 2013); but few studies have addressed pelagic freshwater environments (Pernthaler, 2017). However, the importance of this latter compartment is certainly largely underestimated for the overall understanding of CH 4 cycling as evidenced by the active CH 4 production in the oxygenated waters of many lakes (Schulz et al 2001;Grossart et al 2011;Tang et al 2016) as well as the intensive CH 4 oxidation in anoxic waters in stratified lakes (Karr et al 2006).…”

A Swiftian Voyage from Brobdingnag to Lilliput: Freshwater Planctomycetes drifting towards the poles of the genome size spectrum

“…Even though the composition of lake prokaryotic communities is usually depicted as being regulated by environmental filtering [59], the ways in which the niche shapes the bacterial genomic architecture and metabolic circuitry was previously unexplored. Here, we investigate the niche-genome interactions and show that: i) freshwater Planctomycetes bear in their genomes not only the marks of their ancestry but also the signatures of their lifestyle strategies, ii) substrate generalists (Nixeaceae and Vodnikaceae) maintain larger genomes than their more specialists counterparts (Nemodlikiaceae) and that iii) niche indirectly imposes constraints on the genome size through modulating the number of genes that could be lost (through genetic drift).…”

Environmental determinants of pyoverdine production, exploitation and competition in naturalPseudomonascommunities

“…In pond communities, this is a reasonable scenario because the prevailing conditions of high strain mixing, severe iron limitation and low carbon availability have been shown to promote cheating in laboratory experiments (Brockhurst et al, 2008;Kümmerli et al, 2009;. Furthermore, aquatic bacteria often assemble on particles (Pernthaler, 2017), enabling non-producers to be close to producers, which is important for cheating (Cordero et al, 2012;Weigert and Kümmerli, 2017). In soil communities, on the other hand, cheaters could be favoured because this habitat sustains high cell densities, a factor previously shown to promote cheating (Ross-Gillespie et al, 2009;Scholz and Greenberg, 2015).…”