Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

Abstract

Metaproteomics is one of a suite of new approaches providing insights into the activities of microorganisms in natural environments. Proteins, the final products of gene expression, indicate cellular priorities, taking into account both transcriptional and posttranscriptional control mechanisms that control adaptive responses. Here, we report the proteomic composition of the o 1.2 lm fraction of a microbial community from Oregon coast summer surface waters, detected with two-dimensional liquid chromatography coupled with electrospray tandem mass spectrometry. Spectra corresponding to proteins involved in protein folding and biosynthesis, transport, and viral capsid structure were the most frequently detected. A total of 36% of all the detected proteins were best matches to the SAR11 clade, and other abundant coastal microbial clades were also well represented, including the Roseobacter clade (17%), oligotrophic marine gammaproteobacteria group (6%), OM43 clade (1%). Viral origins were attributed to 2.5% of proteins. In contrast to oligotrophic waters, phosphate transporters were not highly detected in this nutrient-rich system. However, transporters for amino acids, taurine, polyamines and glutamine synthetase were among the most highly detected proteins, supporting predictions that carbon and nitrogen are more limiting than phosphate in this environment. Intriguingly, one of the highly detected proteins was methanol dehydrogenase originating from the OM43 clade, providing further support for recent reports that the metabolism of one-carbon compounds by these streamlined methylotrophs might be an important feature of coastal ocean biogeochemistry.

Metaproteomic analysis of a winter to spring succession in coastal northwest Atlantic Ocean microbial plankton

“…Numerous proteins related to C1 metabolism were identified here (Table 3). Consistent with other coastal studies (Sowell et al, 2011;Williams et al, 2012), we detected the expression of methanol dehydrogenase large subunit proteins derived from the Beta-proteobacteria OM43 clade (Table 3). Methanol dehydrogenase was detected in all samples and exhibited highest similarity to homologs from two methylotrophic strains (HTCC2181 and KB13; Supplementary Table S8; Giovannoni et al, 2008).…”

“…The majority of both types of transporters were represented by periplasmic-binding proteins (PBPs). The high representation of soluble PBPs is commonly observed in metaproteomic studies (Sowell et al, 2009(Sowell et al, , 2011Williams et al, 2012) and is likely due to a combined effect of high expression level, which enhances the frequency of substrate capture, as well as the inherent difficulty in extracting membrane proteins from microbial cells compared with soluble proteins such as PBPs (Morris et al, 2010).…”

“…Nevertheless, a number of community metaproteomics studies have been recently performed on a variety of marine habitats, including the Sargasso Sea (Sowell et al, 2009), along a productivity gradient in the South Atlantic (Morris et al, 2010), a site along the Oregon coast (Sowell et al, 2011), coastal waters of the Antarctic Peninsula and a phytoplankton bloom in the North Sea (Teeling et al, 2012).…”

Expression patterns reveal niche diversification in a marine microbial assemblage

“…The most highly expressed gene was methanol dehydrogenase, accounting for 39% of all KB13 transcripts (Tables 3 and 5 agreement with a proteomic study of coastal bacterioplankton (Sowell et al 2011). Methylotrophy was likely supplemented by light-driven proton pumping, as suggested by the high expression of a xanthorhodopsin (which has not been experimentally differentiated from proteorhodopsin in KB13).…”

Implications of streamlining theory for microbial ecology

“…OM43 is a coastal species that is found associated with phytoplankton (Morris et al, 2006). Recent reports of high turnover rates for methanol in the ocean surface (Dixon et al, 2011), a report describing many alternative OM43 substrates (trimethylamine, trimethylamine oxide, dimethylamine and methyl chloride; Halsey et al, 2012), and a report that OM43 xoxF was 2.3% of the identified spectra in a productive coastal ocean metaproteome (Sowell et al, 2011), all suggest future studies will aim to understand this unusual organism.…”