Summer community structure of aerobic anoxygenic phototrophic bacteria in the western Arctic Ocean

RESEARCH ARTICLE Summer community structure of aerobic anoxygenic phototrophic bacteria in the western Arctic Ocean Dominique Boeuf1,2, Matthew T. Cottrell3, David L. Kirchman3, Philippe Lebaron4,5 & Christian Jeanthon1,2 UPMC, Univ Paris VI, UMR 7144, Adaptation et Diversit
e en Milieu Marin, Station Biologique, Roscoff, France; 2CNRS, UMR 7144, Adaptation et Diversit
e en Milieu Marin, Station Biologique, Roscoff, France; 3School of Marine Science and Policy, University of Delaware, Lewes, DE, USA; 4 UPMC, Univ Paris VI, UMR 7621, LOMIC, Observatoire Oc
eanologique, Banyuls-sur-mer, France; and 5CNRS, UMR 7621, LOMIC, Observatoire Oc
eanologique, Banyuls-sur-mer, France 1 Received 13 December 2012; revised 2 April 2013; accepted 2 April 2013. Final version published online 1 May 2013. DOI: 10.1111/1574-6941.12130 MICROBIOLOGY ECOLOGY Editor: Patricia Sobecky Keywords photoheterotroph; aerobic anoxygenic phototrophic bacteria; pufM gene; bacteriochlorophyll; Arctic Ocean; Mackenzie River. Abstract Aerobic anoxygenic phototrophic (AAP) bacteria are found in a range of aquatic and terrestrial environments, potentially playing unique roles in biogeochemical cycles. Although known to occur in the Arctic Ocean, their ecology and the factors that govern their community structure and distribution in this extreme environment are poorly understood. Here, we examined summer AAP abundance and diversity in the North East Pacific and the Arctic Ocean with emphasis on the southern Beaufort Sea. AAP bacteria comprised up to 10 and 14% of the prokaryotic community in the bottom nepheloid layer and surface waters of the Mackenzie plume, respectively. However, relative AAP abundances were low in offshore waters. Environmental pufM clone libraries revealed that AAP bacteria in the Alphaproteobacteria and Betaproteobacteria classes dominated in offshore and in river-influenced surface waters, respectively. The most frequent AAP group was a new uncultivated betaproteobacterial clade whose abundance decreased along the salinity gradient of the Mackenzie plume even though its photosynthetic genes were actively expressed in offshore waters. Our data indicate that AAP bacterial assemblages represented a mixture of freshwater and marine taxa mostly restricted to the Arctic Ocean and highlight the substantial influence of riverine inputs on their distribution in coastal environments. Introduction Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that require oxygen for their growth and for bacteriochlorophyll a (Bchl a) synthesis. They inhabit a wide variety of illuminated habitats in diverse terrestrial, freshwater, and marine environments (B
eja et al., 2002; Csotonyi et al., 2010; Atamna-Ismaeel et al., 2012). First discovered in coastal marine waters (Shiba et al., 1979), AAP bacteria have been intensively studied in the marine environment (Cottrell et al., 2006; Mas
ın et al., 2006; Lehours et al., 2010). Their abundance and distribution vary greatly among oceanic regimes, suggesting that there is a broad range of potential ecological niches for these microorganisms. AAP bacteria seem to be FEMS Microbiol Ecol 85 (2013) 417–432 more abundant in shelf and coastal areas than in the open ocean (Schwalbach & Fuhrman, 2005; Sieracki et al., 2006). Although their abundance can be high in some oligotrophic regions (Lami et al., 2007), AAP bacteria typically constitute a small percentage (2–4%) of total prokaryotes in oceanic environments (Cottrell et al., 2006; Jiao et al., 2007). However, their proportions can exceed 10% in eutrophic estuaries (Waidner & Kirchman, 2007). Despite the lower abundances in most oligotrophic pelagic marine environments, AAP bacteria constitute a very dynamic part of the bacterial community and potentially contribute significantly to the cycling of organic carbon in the upper ocean (Kobl
ızek et al., 2007). Culture-dependent and -independent studies have shown AAP bacteria to be genetically diverse with members of the Alpha-, ª 2013 Federation of European Microbiological Societies Published by John Wiley & Sons Ltd. All rights reserved Correspondence: Christian Jeanthon, Station Biologique, Place Georges Teissier, 29680 Roscoff, France. Tel.: +33 298292563; fax: +33 298292324; e-mail: D. Boeuf et al. 418 ª 2013 Federation of European Microbiological Societies Published by John Wiley & Sons Ltd. All rights reserved Materials and methods Study area, sampling, and oceanographic parameters The MALINA cruise took place onboard the Canadian research icebreaker CCGS Amundsen during summer 2009 from Victoria (BC, Canada) to the Beaufort Sea (Leg 1b) and then throughout the Beaufort Sea (Leg 2b) (Fig. 1). Most of the stations sampled on the west–east transect in the Beaufort Sea (Leg 2b) were ice free. However, surface waters of eastward offshore waters were still ice covered. Surface seawater samples were collected with an acid cleaned bucket during Leg 1b and in the Mackenzie plume (stations 395, 398, 694, and 697) during Leg 2b. In the Beaufort Sea, seawater was collected from six depths using Niskin bottles mounted on a conductivity temperature depth probe (CTD) rosette. Ancillary data of temperature, salinity, pH, dissolved oxygen, colored dissolved organic matter, inorganic and organic nutrients, and chlorophyll a are given in Table S1 (Supporting Information). Bacterioplankton biomass for DNA and total RNA extraction was collected onboard. Seawater samples were prefiltered through 47-mm-diameter and 3-lm pore-size polycarbonate filters (Cyclopore, Whatman) before the final collection of bacterioplankton cells onto 0.22-lm pore-size Sterivex cartridges (Millipore, Billerica, MA) for DNA extraction or onto 25-mm-diameter and 0.22-lm pore-size Durapore filters (Millipore) for RNA extraction. Sterivex cartridges were filled with 1.6 mL of lysis buffer (0.75 M sucrose, 50 mM Tris-HCl, pH 8), immediately frozen in liquid nitrogen, and stored at 80 °C until analysis. To limit the degradation of mRNA, small volumes of seawater (~ 1 L) were filtered as rapidly as possible, immediately upon retrieval of the CTD. RNA filters were transferred in collection tubes containing 0.8 mL of RLT buffer (Qiagen, Hamburg, Germany) with 1% of b-mercaptoethanol, frozen in liquid nitrogen, and stored at 80 °C until analysis. The time from the start of filtration to storage was 15–20 min. Microscopic enumeration of AAP bacteria and total prokaryotes Prokaryotes were enumerated by epifluorescence microscopy of paraformaldehyde-fixed samples that were filtered onto 0.2-lm pore-size black polycarbonate filters (Cottrell et al., 2006). Filters were stored at 80 °C for up to 4 months prior to analysis. Total prokaryotes were enumerated after staining with 4′,6-diamidino-2-phenylindole (DAPI), 1 lg mL 1 final concentration in 19 phosphatebuffered saline (PBS) for 10 min. The AAP bacteria were FEMS Microbiol Ecol 85 (2013) 417–432 Beta-, and Gammaproteobacte (...truncated)