Metatranscriptional Response of Chemoautotrophic Ifremeria Nautilei Endosymbionts to Differing Sulfur Regimes
Total Page：16
File Type：pdf, Size：1020Kb
ORIGINAL RESEARCH published: 19 July 2016 doi: 10.3389/fmicb.2016.01074 Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes Sherry L. Seston 1‡, Roxanne A. Beinart 2 †‡, Neha Sarode 3, Abigail C. Shockey 4, Piyush Ranjan 3, Sangita Ganesh 3, Peter R. Girguis 2 and Frank J. Stewart 3* 1 Department of Biology, Alverno College, Milwaukee, WI, USA, 2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA, 3 School of Biology, Georgia Institute of Technology, Atlanta, GA, USA, 4 Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA Edited by: Shana Goffredi, Occidental College, USA Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at Reviewed by: hydrothermal vents. These environments are distinguished by high physico-chemical Satoshi Nakagawa, variability, yet we know little about how these symbioses respond to environmental Kyoto University, Japan fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent Sébastien Duperron, Université Pierre et Marie Curie, snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard France high-pressure incubations, we subjected snails to 105 µM hydrogen sulfide (LS), *Correspondence: 350 µM hydrogen sulfide (HS), 300 µM thiosulfate (TS) and seawater without any Frank J. Stewart [email protected] added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes †Present Address: were largely consistent across treatments, HS and TS treatments stimulated genes Roxanne A. Beinart, for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously Department of Geology and reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these Geophysics, Woods Hole Oceanographic Institution, Woods treatments. Transcripts for genes mediating oxidative damage were enriched in the ND Hole, MA, USA and LS treatments, potentially due to a reduction in O2 scavenging when electron donors ‡ These authors have contributed were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and equally to this work. LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic Specialty section: electron donors are limiting. These data reveal the extent to which I. nautilei symbionts This article was submitted to respond to changes in sulfur concentration and species, and, interpreted alongside Microbial Symbioses, a section of the journal coupled biochemical metabolic rates, identify gene targets whose expression patterns Frontiers in Microbiology may be predictive of holobiont physiology in environmental samples. Received: 25 April 2016 Keywords: Ifremeria nautilei, chemoautotroph, endosymbiont, methanotrophic bacteria, Sulfur oxidizers, Accepted: 27 June 2016 metatranscriptomics, deep sea vents Published: 19 July 2016 Citation: Seston SL, Beinart RA, Sarode N, INTRODUCTION Shockey AC, Ranjan P, Ganesh S, Girguis PR and Stewart FJ (2016) Hydrothermal vents are dynamic ecosystems where the vigorous emission of hot, chemically Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei reduced fluid from the seafloor into the surrounding seawater results in a temporally and Endosymbionts to Differing Sulfur spatially variable physico-chemical environment. The dominant animals in these habitats live in Regimes. Front. Microbiol. 7:1074. partnership with bacterial symbionts that oxidize chemical reductants from the venting fluid, doi: 10.3389/fmicb.2016.01074 including hydrogen sulfide, methane, and hydrogen (Tivey, 2007), as well as thiosulfate, an Frontiers in Microbiology | www.frontiersin.org 1 July 2016 | Volume 7 | Article 1074 Seston et al. Metatranscriptional Response of Chemoautotrophic Snail Endosymbionts intermediate oxidation product of sulfide that accumulates at symbiont gene expression (metatranscriptomes) under varying some vents (Gru et al., 1998; Waite et al., 2008; Gartman et al., regimes of reduced sulfur species and availability. 2011). The symbionts oxidize these reduced compounds to fuel I. nautilei lives in mixing zones around hydrothermal vents in carbon fixation (chemoautotrophy), which provides primary the southwestern Pacific, deriving its nutrition from intracellular nutrition for themselves and their animal hosts (Cavanaugh et al., gill symbionts that can oxidize both sulfide and thiosulfate to 2006; Dubilier et al., 2008). fuel autotrophy (thioautotrophy; Beinart et al., 2015). Previous To acquire the chemical substrates needed for symbiont characterization of the I. nautilei gill symbiont community metabolism, symbiotic vent animals live where they can access revealed associations with a lineage of γ-proteobacterial sulfur both emitted fluid and oxygenated seawater (Stewart et al., 2005). oxidizers from the Order Chromatiales (Urakawa et al., 2005; Vent symbioses thrive in mixing zones where fluid turbulence Suzuki et al., 2006). Methanotrophic bacteria may also be causes conditions to change rapidly over small spatial scales present (Gal’chenko et al., 1992; Borowski et al., 2002), although such that adjacent animals may experience vastly different their representation across host populations is inconsistent chemical and physical environments (Johnson et al., 1986). Sulfur (Windoffer and Giere, 1997; Suzuki et al., 2006) and molecular chemistry in these zones can be particularly dynamic, with characterization of I. nautilei methanotrophs is lacking (Petersen concentrations of hydrogen sulfide and derivatives of sulfide and Dubilier, 2009). We herein present 16S rRNA gene oxidation (e.g., thiosulfate) varying temporally and in proximity and metatranscriptome data elucidating symbiont community to vent sites (Gru et al., 1998; Mullaugh et al., 2008; Waite composition and metabolism over a range of environmentally et al., 2008; Gartman et al., 2011). Furthermore, venting can halt, relevant conditions: (i) no electron donor (ND), (ii) 105 µM either transiently or permanently, due to changes in volcanic hydrogen sulfide (LS), (iii) 350 µM hydrogen sulfide (HS), and activity or the path of fluid flow (Butterfield et al., 1997). The (iv) 300 µM thiosulfate (TS). These experiments clarify pathways dynamic nature of hydrothermal vents thus exposes organisms of sulfur, nitrogen, and carbon metabolism in the Ifremeria- to fluctuating concentrations of diverse reductants and oxidants associated bacterial community and provide the first molecular (Shank et al., 1998), and may drive variation in the metabolism evidence for the activity of methanotrophic bacteria in the gill- and growth dynamics of symbiotic partners (Duperron et al., associated community. The results are derived from experiments 2007; Dubilier et al., 2008; Robidart et al., 2011). designed to study the effects of geochemical dynamics on sulfur Descriptive and experimental studies over the past 30 years oxidation and carbon fixation rates (Beinart et al., 2015). An have enabled a broad understanding of the chemoautotrophic analysis of symbiont transcripts in light of the observed metabolic metabolism of vent symbionts. Physiological experiments with rates reveals how I. nautilei symbionts sustain chemoautotrophic intact animal hosts (e.g., Childress et al., 1986, 1991; Girguis activity at low sulfide concentrations, but exhibit a marked et al., 2000; Girguis and Childress, 2006; Nyholm et al., 2008; change in their physiology as sulfur availability increases. Petersen et al., 2011; Goffredi et al., 2014; Beinart et al., 2015) and excised symbionts (Belkin et al., 1986; Fisher et al., 1987; Wilmot and Vetter, 1990; Childress et al., 1991; Nelson et al., 1995) MATERIALS AND METHODS have established that vent symbionts can fix inorganic carbon via the oxidation of hydrogen sulfide, thiosulfate, hydrogen Animal Collection and Experimental and/or methane. Separately, analyses of symbiont gene content Incubations (Kuwahara et al., 2007; Newton et al., 2007; Robidart et al., As described in Beinart et al. (2015) I. nautilei were collected 2008; Nakagawa et al., 2014), gene and protein expression and incubated in four separate experiments that were performed (Markert et al., 2007, 2011; Nyholm et al., 2008; Robidart to compare symbiont metabolism and gene expression when et al., 2011; Gardebrecht et al., 2012; Wendeberg et al., 2012; exposed to 105 µM hydrogen sulfide (low sulfide, LS), 300 Sanders et al., 2013), and enzyme activity (Felbeck, 1981; hydrogen sulfide µM (high sulfide, HS), 300 thiosulfate µM Stein et al., 1988; Robinson et al., 1998) from vent symbioses (TS), or no exogenous electron donor (no donor, ND). Snails have clarified the pathways that symbionts employ for these were collected from the vent fields ABE (HS and TS) or Tu’i metabolisms. Malila (LS and ND) at the Eastern Lau Spreading Center by the While it has been speculated that shifts in chemical availability remotely operated vehicle JASON II during expedition TM-235 are coupled to rapid physiological responses by the host, the in 2009 (Table 1). Snails were brought to the ship in insulated symbiont, or both (Girguis and Childress, 2006), inferences made containers and kept in 4◦C seawater. Individuals responsive to from freshly collected animals reveal at best a general picture the touch were either immediately preserved as described below of the conditions experienced in situ, making it challenging or were transferred to flow-through, 2.68 L titanium aquaria in