Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

Abstract

Chemoheterotrophic marine bacteria of the SAR11 clade are Earth's most abundant organisms. Following the first cultivation of a SAR11 bacterium, 'Candidatus Pelagibacter ubique' strain HTCC1062 (Ca. P. ubique) in 2002, unusual nutritional requirements were identified for reduced sulfur compounds and glycine or serine. These requirements were linked to genome streamlining resulting from selection for efficient resource utilization in nutrient-limited ocean habitats. Here we report the first successful cultivation of Ca. P. ubique on a defined artificial seawater medium (AMS1), and an additional requirement for pyruvate or pyruvate precursors. Optimal growth was observed with the collective addition of inorganic macro-and micronutrients, vitamins, methionine, glycine and pyruvate. Methionine served as the sole sulfur source but methionine and glycine were not sufficient to support growth. Optimal cell yields were obtained when the stoichiometry between glycine and pyruvate was 1:4, and incomplete cell division was observed in cultures starved for pyruvate. Glucose and oxaloacetate could fully replace pyruvate, but not acetate, taurine or a variety of tricarboxylic acid cycle intermediates. Moreover, both glycine betaine and serine could substitute for glycine. Interestingly, glycolate partially restored growth in the absence of glycine. We propose that this is the result of the use of glycolate, a product of phytoplankton metabolism, as both a carbon source for respiration and as a precursor to glycine. These findings are important because they provide support for the hypothesis that some micro-organisms are challenging to cultivate because of unusual nutrient requirements caused by streamlining selection and gene loss. Our findings also illustrate unusual metabolic rearrangements that adapt these cells to extreme oligotrophy, and underscore the challenge of reconstructing metabolism from genome sequences in organisms that have non-canonical metabolic pathways.

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…On the other hand, specific and combinatorial nutrient requirements such as those described for Ca. U. copiosus present a complex problem for researchers attempting to cultivate microbes with reduced genomes 50 . Although Ca.…”

Implications of streamlining theory for microbial ecology

“…Pelagibacter metabolism is spare, lacking most common auxiliary functions of microbial cells, and as discussed below, even lacking some functions that are nearly universally distributed among related Alphaproteobacteria (Giovannoni et al, 2005;Tripp et al, 2008Tripp et al, , 2009Carini et al, 2012;Grote et al, 2012;Smith et al, 2013). But these organisms are efficient oxidizers of a range of common, low-molecularweight metabolites, including amino acids, organic acids and osmolytes.…”

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

“…As would be expected from a low percentage of unique genes in the SAGs, much of the metabolism of these organisms appeared to be similar to that of the surface strains, particularly the subclade Ia organisms. Collectively, the Ic subclades were predicted to be obligate aerobic organisms, with cytochrome c oxidase as the sole predicted terminal reductatse, a complete tricarboxylic acid cycle, conserved lesions in several glycolytic pathways (Schwalbach et al, 2010), a reliance on reduced sulfur compounds (Tripp et al, 2008) and pathways for the metabolism and oxidation of small organic molecules such as amino/carboxylic acids and one-carbon and methylated compounds (Yilmaz et al, 2011;Grote et al, 2012;Carini et al, 2012;Supplementary Table S1).…”

“…SAR11, or the 'Pelagibacterales,' is a diverse group, spanning at least 18% 16S rRNA gene divergence, and is comprised of subclades with unique spatiotemporal distributions (ecotypes) that follow seasonal patterns (Field et al, 1997;Carlson et al, 2009;Giovannoni and Vergin, 2012;Grote et al, 2012;Vergin et al, 2013). All genome-sequenced representatives are characterized by small (1.3-1.4 Mbp), streamlined genomes with low GC content, few gene duplications and an obligately aerobic, heterotrophic metabolism generally focused on oxidation of low-molecularweight carbon compounds, such as carboxylic and amino acids, osmolytes and methylated compounds (Schwalbach et al, 2010;Yilmaz et al, 2011;Carini et al, 2012;Grote et al, 2012). Representatives spanning the known subclade diversity have an unusually high level of core genome conservation and gene synteny, however, some subclade-specific genomic features have been identified (Grote et al, 2012).…”