Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction

Abstract

The solubility of orthophosphate (PO 4 3؊ ) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. Here we demonstrate that dissolved extracellular DNA can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus Shewanella. Shewanella oneidensis MR-1, Shewanella putrefaciens CN32, and Shewanella sp. strain W3-18-1 all grew with DNA but displayed different growth rates. W3-18-1 exhibited the highest growth rate with DNA. While strain W3-18-1 displayed Ca 2؉ -independent DNA utilization, both CN32 and MR-1 required millimolar concentrations of Ca 2؉ for growth with DNA. For S. oneidensis MR-1, the utilization of DNA as a sole source of phosphorus is linked to the activities of extracellular phosphatase(s) and a Ca 2؉ -dependent nuclease(s), which are regulated by phosphorus availability. Mass spectrometry analysis of the extracellular proteome of MR-1 identified one putative endonuclease (SO1844), a predicted UshA (bifunctional UDP-sugar hydrolase/5 nucleotidase), a predicted PhoX (calcium-activated alkaline phosphatase), and a predicted CpdB (bifunctional 2,3 cyclic nucleotide 2 phosphodiesterase/3 nucleotidase), all of which could play important roles in the extracellular degradation of DNA under phosphorus-limiting conditions. Overall, the results of this study suggest that the ability to use exogenous DNA as the sole source of phosphorus is widespread among the shewanellae, and perhaps among all prokaryotes, and may be especially important for nutrient cycling in metal-reducing environments.Phosphorus (P) is a key element that often limits bacterial growth in various freshwater and marine habitats (13,40,44,51,53). Inorganic phosphate (P i ), or orthophosphate (PO 4 3Ϫ ), can serve as a direct source of P for essentially all physiological groups of microorganisms in both natural environments and laboratory media. Measurements of soluble phosphate in different aquatic environments, however, suggest that concentrations of bioavailable P i are very low. Recent studies have revealed that P i represents only a small fraction of soluble reactive P in natural waters and that even in eutrophic systems, its concentration may be as low as 27 pM (2,20,25). This is not surprising, since in a variety of aquatic systems, soils, and sediments, P i bioavailability can be controlled by adsorption to metal oxides (3, 16, 59) and through chemical reactions with hydrous oxides, amorphous and crystalline complexes of Fe, Al, and Ca, and organic matter (2, 41, 49). In particular, the reaction of P i with Fe(III) oxides such as goethite can result in the precipitation of tinticite [Fe 6 (PO 4 ) 4 (OH) 6 · 7H 2 O] (22) or griphite [Fe 3 Mn 2 (PO 4 ) 2 · 5(OH) 2 ] (32) depending on the solution and surface conditions. The latter findings entail important physiological implications for dissimilatory metal-reducing bacteria residing in zones with high concentration...

Characterization of phosphorus forms in lake macrophytes and algae by solution 31P nuclear magnetic resonance spectroscopy

“…DNA was the main component of orthophosphate diester in aquatic macrophytes and algae in Tai Lake. DNA also could be an important source of P in aquatic environments especially when orthophosphate concentrations were small (Pinchuk et al 2008). They were degraded less than DNA, polyphosphate, and phospholipids, but they were rapidly mineralized under anaerobic conditions.…”

Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1

“…Discussion eDNA occurs in significant amounts in terrestrial and aquatic environments where it may serve as important nutrient reservoirs, particularly for nitrogen and phosphorus (Deflaun et al, 1986;Paul et al, 1991;Niemeyer and Gessler, 2002;Dell'Anno and Danovaro, 2005). Accordingly, a previous study showed that Shewanella species are capable of using DNA as source of phosphorus, nitrogen, carbon and energy (Pinchuk et al, 2008). Here we demonstrate that, in addition, eDNA has a major role in surface attachment and development of threedimensional structures during S. oneidensis MR-1 biofilm formation.…”

Organic phosphorus in the aquatic environment

“…[40,48] In a series of mesocosm experiments using radioactive labelled orthophosphate, adenosine triphosphate (ATP) and DNA, Løvdal et al [49] showed that, even though orthophosphate was the preferred P substrate for bacteria and algae, both ATP and DNA were utilised in mesocosms where orthophosphate was also present. In mesocosms without added orthophosphate the turnover time for dissolved DNA decreased by a factor of 10 (from 15.6 to 1.5 h) with no liberation of free orthophosphateindicating a tight coupling between hydrolysis and uptake.…”

“…However, most studies attribute DNA breakdown to a suite of extracellular enzymes including phosphatase and nucleases. [40,41] Abiotic hydrolysis facilitated by mineral phases [42] is potentially an alternate pathway for the degradation of DNA in aquatic ecosystems -but it has not been demonstrated. The only abiotic degradation pathway that has been demonstrated to date is the breaking of DNA double strands induced by radiation from dissolved uranium.…”

“…A laboratory study has shown that several Shewanella species were capable of using extracellular DNA not only as their sole P source but also as their sole source of both carbon and energy. [40] Exogenous DNA plays an important role in the ecology of biofilm-forming bacteria including Shewanella sp. and Vibrio cholera.…”