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The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails with Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content

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The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails with Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content University of Rhode Island DigitalCommons@URI Graduate School of Oceanography Faculty Publications Graduate School of Oceanography 2019 The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content Roxanne A. Beinart University of Rhode Island, [email protected] Chengwei Luo Konstantinos T. Konstantinidis Frank J. Stewart Peter R. Girguis Follow this and additional works at: https://digitalcommons.uri.edu/gsofacpubs Citation/Publisher Attribution Beinart RA, Luo C, Konstantinidis KT, Stewart FJ and Girguis PR (2019) The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. Front. Microbiol. 10:1818. doi: 10.3389/fmicb.2019.01818 Available at: https://doi.org/10.3389/fmicb.2019.01818 This Article is brought to you for free and open access by the Graduate School of Oceanography at DigitalCommons@URI. It has been accepted for inclusion in Graduate School of Oceanography Faculty Publications by an authorized administrator of DigitalCommons@URI. For more information, please contact [email protected]. fmicb-10-01818 August 13, 2019 Time: 15:59 # 1 ORIGINAL RESEARCH published: 14 August 2019 doi: 10.3389/fmicb.2019.01818 The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content Roxanne A. Beinart1*, Chengwei Luo2†, Konstantinos T. Konstantinidis2,3, Frank J. Stewart3 and Peter R. Girguis4 Edited by: 1 Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, United States, 2 School of Civil Sébastien Duperron, and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States, 3 School of Biological Sciences, Muséum National d’Histoire Naturelle, Georgia Institute of Technology, Atlanta, GA, United States, 4 Department of Organismic and Evolutionary Biology, Harvard France University, Cambridge, MA, United States Reviewed by: Horst Felbeck, Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic University of California, San Diego, United States bacterial lineages. At the broadest level, these symbioses share primary function: the Sylvie Gaudron, bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals Sorbonne Universités, France to power the fixation of inorganic carbon and/or other nutrients, providing the bulk *Correspondence: Roxanne A. Beinart of host nutrition. However, it is unclear to what extent the ecological niche of the [email protected] host species is influenced by differences in symbiont traits, particularly those involved †Present address: in chemoautotrophic function and interaction with the geochemical environment. Chengwei Luo, Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and DeepBiome Therapeutics, Inc., Cambridge, MA, United States physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine Specialty section: This article was submitted to whether differences in chemoautotrophic capacity exist among these symbionts that Microbial Symbioses, could explain the observed distribution of these snail species into distinct geochemical a section of the journal habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four Frontiers in Microbiology distinct lineages in the classes g-proteobacteria or Campylobacteria. The genomes Received: 08 April 2019 Accepted: 23 July 2019 differed with respect to genes related to motility, adhesion, secretion, and amino Published: 14 August 2019 acid uptake or excretion, though were quite similar in chemoautotrophic function, Citation: with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, Beinart RA, Luo C, Konstantinidis KT, Stewart FJ and and oxygen and nitrate respiration. This indicates that differences in the presence or Girguis PR (2019) The Bacterial absence of symbiont chemoautotrophic functions does not likely explain the observed Symbionts of Closely Related geochemical habitat partitioning. Rather, differences in gene expression and regulation, Hydrothermal Vent Snails With Distinct Geochemical Habitats Show biochemical differences among these chemoautotrophic pathways, and/or differences Broad Similarity in Chemoautotrophic in host physiology could all influence the observed patterns of habitat partitioning. Gene Content. Front. Microbiol. 10:1818. Keywords: symbiosis, chemosynthesis, genomics, Campylobacteria, Gammaproteobacteria, gastropod, doi: 10.3389/fmicb.2019.01818 Alviniconcha, Ifremeria Frontiers in Microbiology| www.frontiersin.org 1 August 2019| Volume 10| Article 1818 fmicb-10-01818 August 13, 2019 Time: 15:59 # 2 Beinart et al. Genomics of Vent Snail Symbionts INTRODUCTION they represent different bacterial lineages and do not show a pattern of co-divergence with host species (Suzuki et al., Symbiosis with chemosynthetic bacteria has independently 2006a; Beinart et al., 2012), the symbionts are thought to be evolved in many hydrothermal vent, cold seep, and shallow- acquired horizontally from the environment. However, there is water invertebrate taxa. Broadly speaking, the animal hosts strong specificity between each snail species and its symbiont rely on the fixed carbon produced by their obligate symbionts phylotypes(s): surveys of hundreds of individuals across a range for the majority of their nutrition (Dubilier et al., 2008). of habitats have demonstrated that each snail species associates The bacterial partners of such associations are phylogenetically with only one or two of the symbiont phylotypes, with individual diverse, representing multiple bacterial lineages across two phyla. snails usually dominated by just one symbiont phylotype at a time Nevertheless, with respect to energy metabolism, they perform (Table 1; Beinart et al., 2012; Seston et al., 2016). similar metabolic functions: these symbionts use reduced As such, it is plausible that differences in gene content chemicals like hydrogen sulfide as electron donors, respire among these symbionts could influence the geochemical niche oxygen and/or nitrate, and fix inorganic carbon into organic of the host snails at the Eastern Lau Spreading Center. Indeed, carbon (Dubilier et al., 2008; Childress and Girguis, 2011). each snail species is restricted to associations with only one Chemoautotrophic symbionts can, at times, exhibit marked or two of the symbiont phylotypes, so differences in symbiont differences in gene content, which can subsequently confer physiological traits could partition host species into distinct differences in metabolism that may have ecological implications habitats based on these traits. The four snail species have for their host species. For example, a comparison of the genomic similar anatomy in terms of overall body size, as well as gill content among some of the g-proteobacterial symbionts of vent and circulatory structure (Waren and Bouchet, 1993; Johnson animals has shown that they can differ in a diversity of genes and et al., 2015). Despite these shared features, Alviniconcha and gene networks, from energy metabolism to nitrogen acquisition I. nautilei occupy distinct geochemical habitats (Waite et al., (Kleiner et al., 2012). While it is reasonable to assert that genomic 2008; Podowski et al., 2009, 2010; Beinart et al., 2012), and content that confers symbiont functional traits could affect this segregation is thought to primarily be driven by the the distribution of host species into distinct physicochemical distribution of reducing compounds that could be used by habitats, it is still unknown whether this occurs. Interpretation of their particular symbionts for chemoautotrophy (Henry et al., the similarities and differences in the genomes of chemosynthetic 2008; Beinart et al., 2012, 2015; Sanders et al., 2013). Within symbionts has been confounded by the fact that the comparisons a single vent field, Alviniconcha and I. nautilei show consistent to date have been made among symbionts from highly patterns of zonation, with Alviniconcha species found nearest divergent host taxa and/or from different geographical locations to vent orifices and I. nautilei on the edges of Alviniconcha with distinct environmental characteristics and biogeographic patches (Podowski et al., 2009, 2010). Thus, compared to histories. Thus, it is difficult to untangle whether observed I. nautilei, Alviniconcha species occur where concentrations differences in symbiont gene content are driven by co-evolution of vent-derived reductants and temperatures are higher, and with physiologically and ecologically distinct host taxa, or oxygen and thiosulfate concentrations are lower (Waite et al., adaptation to dissimilar habitats. Comparisons among the 2008; Podowski et al., 2009, 2010). However, at a regional symbionts of closely related host species can help resolve whether scale, the dominant Alvinconcha species at each vent field varies differences in symbiont genomic traits impact their distribution according to the particular geochemistry of that site (Beinart into distinct geochemical habitats. et al., 2012). Specifically, the Alviniconcha species (A. boucheti) The hydrothermal vent snail genera Alviniconcha and hosting the Campylobacterial symbiont dominates at vent fields Ifremeria provide a unique opportunity to examine gene
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