An investigation of the physiology and potential role of components of the deep ocean bacterial community (of the NE Atlantic) by enrichments carried out under minimal environmental change Simon T. Egan, David M. McCarthy, John W. Patching, Gerard T.A. Fleming n Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland article info Article history: Received 9 August 2011 Received in revised form 10 November 2011 Accepted 12 November 2011 Available online 21 November 2011 Keywords: Diversity Deep-sea Pressure NE Atlantic Bacterial community 16S rDNA PCR DGGE abstract Samples of deep-ocean water (3170 m) taken from the Rockall Trough (North-East Atlantic) were incubated for one-month at atmospheric and in-situ pressure (31 MPa), at 4 1C and in the absence and presence of added nutrients. Prokaryotic abundance (direct cell counts) increased by at least 28-fold in enrichments without added nutrients. However, the magnitude of increase in abundance was less for incubations carried out at in-situ pressure (131–181-fold) than those incubations at surface pressure (163–1714-fold increase in abundance). Changes in the prokaryotic community profile as a result of one-month incubation were measured by means of Denaturing Gel Electrophoresis (DGGE) of extracted 16S rDNA. The profiles of post-incubation samples incubated at in-situ pressure were separated from all other profiles as were those of unpressurised samples with added nutrients. The behaviour (fitness) of individual community members (Operational Taxonomic Units: OTUs) was determined on the basis of change in relative DGGE band intensities between pre- and post-incubation samples. Of twenty-one OTUs examined, six were fitter when incubated in the presence of added nutrients and at in-situ pressure and one of these was advantaged when grown in the absence of added nutrients and at in-situ pressure. These represented autochthonous and active members of the deep-ocean prokaryotic community. In contrast, seven OTUs were disadvantaged when grown under in-situ pressure and were indicative surface-derived allochtonous microorganisms. A further two OTUs came to dominance in incubations with added nutrients (pressurised and unpressurised) and similar to the previous category were probably surface-derived microorganisms. A single OTU showed characteristics of piezophilic and oliogrophic behaviour and four OTUs were disadvantaged under all incubation conditions examined. The twenty-one DGGE bands were sequenced and the bacterial communities were dominated by Gamma proteobactria and to a lesser extent members of the Cytophaga–Flavobacterium–Bacteroides and d groups of prokaryotes. & 2011 Elsevier Ltd. All rights reserved. 1. Introduction The deep-sea is the largest ecosystem on the planet and supports some of the highest levels of diversity on Earth (Etter and Mullineaux, 2001; Snelgrove and Smith, 2002; Stuart et al., 2003; Danovaro et al., 2010; Ramirez-Llodra et al., 2010), yet remains one of the least studied and understood environments largely due to the difficulties surrounding its exploration. Deep- sea bacteria play a significant role in the recycling of organic matter and are thought to be responsible for approximately half of the global net mineralisation of organic matter in marine ecosystems (Ogawa et al., 2001; Yokokawa and Nagata, 2010). The aphotic zone of the water column ( 4  500 m depth) is in permanent darkness and thus contains an allochtonous ecosys- tem which is mainly driven by the deposition of organic matter from the euphotic zone (Steinberg et al., 2008). It is estimated that only 1–3% of surface primary production reaches the abyssal benthos (Deuser, 1986). Marine bacteria may be divided into two groups depending on their response to nutrient supply. The ‘generalists’, which are metabolically flexible, can respond quickly to changes in the quantity and type of nutrient input (Church, 2009). These may be indigenous to the deep-sea or surface- derived in that they settle to depths with sedimenting particu- lates (Fellows et al., 1981; Fuhrman and Azam, 1983; Tamburini et al., 2006; Grossart and Gust, 2009). The ‘specialists’ are more specific in their nutrient requirements and are slower to adapt to changes in nutrient input (Crump et al., 2003; Langenheder et al., 2005). These ‘specialists’ may include microorganisms that can grow preferentially at high pressures and in an oligotrophic environment. Contents lists available at SciVerse ScienceDirect journal homepage: www.elsevier.com/locate/dsri Deep-Sea Research I 0967-0637/$ - see front matter & 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.dsr.2011.11.005 n Corresponding author. Tel.: þ353 91493562. E-mail address: ger.fleming@nuigalway.ie (G.T.A. Fleming). Deep-Sea Research I 61 (2012) 11–20