Freshwater bacterial lifestyles inferred from comparative genomics

Abstract

While micro-organisms actively mediate and participate in freshwater ecosystem services, we know little about freshwater microbial genetic diversity. Genome sequences are available for many bacteria from the human microbiome and the ocean (over 800 and 200, respectively), but only two freshwater genomes are currently available: the streamlined genomes of Polynucleobacter necessarius ssp. asymbioticus and the Actinobacterium AcI-B1. Here, we sequenced and analysed draft genomes of eight phylogentically diverse freshwater bacteria exhibiting a range of lifestyle characteristics. Comparative genomics of these bacteria reveals putative freshwater bacterial lifestyles based on differences in predicted growth rate, capability to respond to environmental stimuli and diversity of useable carbon substrates. Our conceptual model based on these genomic characteristics provides a foundation on which further ecophysiological and genomic studies can be built. In addition, these genomes greatly expand the diversity of existing genomic context for future studies on the ecology and genetics of freshwater bacteria.

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

“…The oligotype assignments to lifestyle strategies generally supported existing knowledge about the ecology of these lineages. Freshwater Actinobacteria lineage acI, Alphaproteobacteria lineage LD12, and some members of the genus Polynucleobacter are considered ubiquitous, abundant members of freshwater lakes (Newton et al 2011) with passive oligotrophic lifestyles (Hahn et al 2012, Ghylin et al 2014, Livermore et al 2014. This assertion supports generally the spatial/temporal patterns we observed in Lake Michigan surface waters, where 15 oligotypes from these groups were classified as having oligotroph-like distribution patterns, including both abundant (≥0.1% maximum) and rare members.…”

“…Marine copiotrophs also had relatively more exoenzymes, which were hypothesized to be related to a predominately particle-associated lifestyle. Similarly, it has been suggested that copiotrophs are more likely to be motile (Livermore et al 2014, Lever et al 2015, have larger investments in signal transduction mechanisms, and have the genetic capacity to use a wider array of carbon substrates (Livermore et al 2014). Finally, there was some evidence that oligotrophs have more secondary metabolite biosynthetic pathways (Lauro et al 2009).…”

“…This is possibly because the number of available freshwater microbial genomes is considerably less than the number of marine genomes, which precludes comparative genomic assessment of trophic strategies. In one analysis by Livermore et al (2014), the authors inferred from their genomic data 4 lifestyle strategies: (1) passive and streamlined, (2) slow augmented responders, (3) fast reduced responders, and (4) vagabonds. The passive streamlined genomes were considered oligotrophs, while the other 3 groups were considered copiotrophs because of high predicted growth rate and/or diverse carbon substrate utilization pathways.…”

“…One important distinguishing microbial trait is trophic strategy. Determining the strategies of heterotrophic bacteria has a long legacy in microbial ecology and has experienced a recent reinvigoration of interest (Giovannoni & Stingl 2007, Livermore et al 2014, Neuenschwander et al 2015. The conceptual delineation falls between oligotrophic and copiotrophic heterotrophs, which are generally defined by growth rate and responsiveness to local increases in resources.…”

Ecological Insights from the Evolutionary History of Microbial Innovations

“…For example, genome size and the number of metabolic pathways may distinguish generalists and specialist organisms 30 . Furthermore, gene transition rates may provide evidence into evolutionary strategies and high rates may be a signature of evolutionary diversification.…”