The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline Nikole E. Kimes, 1 Wesley R. Johnson, 2 Manolito Torralba, 3 Karen E. Nelson, 3 Ernesto Weil 4 and Pamela J. Morris 1 * 1 Belle W. Baruch Institute for Marine and Coastal Sciences, University of South Carolina, Georgetown, SC 29442, USA. 2 Ecosystem Solutions Inc., Edgewater, MD 21037, USA. 3 J. Craig Venter Institute, Rockville, MD 20850, USA. 4 Department of Marine Sciences, University of Puerto Rico, Mayaguez, PR 00681, USA. Summary Coral-associated microbial communities, including protists, bacteria, archaea and viruses, are important components of the coral holobiont that influence the health of corals and coral reef ecosystems. Evidence suggests that the composition of these microbial communities is affected by numerous parameters; however, little is known about the confluence of these ecological and temporal effects. To examine the influ- ence of physical niche, health state and season on the Montastraea faveolata microbiome, we used ribos- omal RNA gene sequencing to identify the zooxan- thellae, bacteria and archaea associated with tagged healthy and yellow band diseased colonies sampled in March and September of 2007 in La Parguera, Puerto Rico. To the best of our knowledge, this is the first coral microbiome study to examine sequences from the zooxanthellar, bacterial and archaeal communities simultaneously from individual coral samples. Our results confirm differences in the zooxanthellar, bacterial and archaeal communities based on all of the ecological parameters examined. Moreover, we provide evidence of a dynamic holobi- ont that is most significantly influenced by seasonal changes. These data suggest that global climate change may affect the coral microbiome in a manner previously unrecognized. Introduction Coral reef ecosystems are experiencing severe declines, with one-third of coral species threatened by extinction (Carpenter et al., 2008) due to the effects of climate change, anthropogenic impacts and increased disease incidence (Weil et al., 2006; 2009; Bruno et al., 2007; Harvell et al., 2007; Wilkinson, 2008; Bourne et al., 2009). The diverse microbiota associated with corals, which include zooxanthellae (reviewed in Baker, 2003), bacteria (reviewed in Rosenberg et al., 2007; Mouchka et al., 2010), archaea (Rosenberg et al., 2007; reviewed in Olson and Kellogg, 2010) and viruses (reviewed in van Oppen et al., 2009; Thurber and Correa, 2011), play important roles in sustaining the coral holobiont. Zooxanthellae, for example, provide essential energy (Muller-Parker and D’Elia, 1997), while bacterial com- munities provide multiple resources through biogeo- chemical cycling (Kimes et al., 2010; Raina et al., 2010) and intrinsic defence mechanisms (Geffen et al., 2009; Shnit-Orland and Kushmaro, 2009; Vizcaino et al., 2010). The role of coral-associated archaea is less fully charac- terized but may involve chemical transformations of nitro- gen (Beman et al., 2007; Siboni et al., 2008). Similarly, viruses are thought to play a role in the stability of the coral holobiont even though the mechanisms involved remain unknown (van Oppen et al., 2009). Due to these critical roles, disruption of the coral microbiome is thought to be a key factor in coral decline (Ainsworth and Hoegh-Guldberg, 2009; Bourne et al., 2009; Garren and Azam, 2011). Coral diseases can alter zooxanthellar (Ben-Haim et al., 2003; Cervino et al., 2004a; Sussman et al., 2008; 2009) and bacterial communities (Bourne et al., 2009; Mouchka et al., 2010), resulting in changes to the func- tional potential of the coral microbiome during disease (Kimes et al., 2009). Elucidating the importance of microbial community shifts during disease, however, is complicated by the variability attributed to temporal (e.g. season) and ecological (e.g. temperature) para- meters, independent of disease. Some coral-associated bacterial studies reveal increased diversity associated with the summer months (Koren and Rosenberg, 2006; Hong et al., 2009), while others reveal temporal Received 24 March, 2012; accepted 18 February, 2013. *For corre- spondence. E-mail pjmorris@belle.baruch.sc.edu; Tel. (+1) 843 991 8355; Fax (+1) 843 546 1632. Toppan Best-set Premedia Limited Journal Code: EMI Proofreader: Mony Article No: EMI12130 Delivery date: 16 Apr 2013 Page Extent: 14 EMI12130 Environmental Microbiology (2013) doi:10.1111/1462-2920.12130 © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology 1 2 3 1