Population structure between environmentally transmitted vibrios and bobtail squids using nested clade analysis

Abstract

Squids from the genus Euprymna (Cephalopoda: Sepiolidae) and their symbiotic bacteria Vibrio fischeri form a mutualism in which vibrios inhabit a complex light organ within the squid host. A host-mediated daily expulsion event seeds surrounding seawater with symbiotically capable V. fischeri that environmentally colonize newly hatched axenic Euprymna juveniles. Competition experiments using native and non-native Vibrio have shown that this expulsion/re-colonization phenomenon has led to cospeciation in this system in the Pacific Ocean; however, the genetic architecture of these symbiotic populations has not been determined. Using genetic diversity and nested clade analyses we have examined the variation and history of three allopatric Euprymna squid species (E. scolopes of Hawaii, E. hyllebergi of Thailand, and E. tasmanica from Australia) and their respective Vibrio symbionts. Euprymna populations appear to be very genetically distinct from each other, exhibiting little or no migration over large geographical distances. In contrast, Vibrio symbiont populations contain more diverse haplotypes, suggesting both host presence and unidentified factors facilitating long-distance migration structure in Pacific Vibrio populations. Findings from this study highlight the importance of how interactions between symbiotic organisms can unexpectedly shape population structure in phylogeographical studies.

Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid–Vibrio mutualism

“…Conversely, symbiotically viable Vibrio bacteria are cycled out of the host daily exposing them to environmental factors (i.e., currents) that allow for movement into novel areas where they are able to recruit into a new host. While bacteria alone cannot cross great expanses of ocean, the use of rafting has been shown to be an effective dispersal mechanism for marine bacteria like V. fischeri (Jones et al., 2006; Theil & Gutow, 2005). The ability for vibrios to cross great expanses of oceans has been previously reported in other marine bacteria and undoubtedly will allow symbiotically viable vibrios to be shuttled to new areas and novel hosts (González‐Escalona, Gavilan, Brown & Martinez‐Urtaza, 2015).…”

“…All genomic DNA extractions were visualized on a 1% agarose gel and quantified using a Nanodrop 9600 (ThermoFisher Scientific, Waltham, MA). Total DNA extracted from each individual squid sample was used to amplify a 658‐bp fragment of the cytochrome c oxidase subunit I (COI, Table 2; (Folmer, Black, Hoeh, Lutz & Vrijenhoek, 1994; Jones et al., 2006; Zamborsky & Nishiguchi, 2011). The cytochrome c oxidase subunit I gene has been shown to be highly conserved, at least at the amino acid level, across invertebrate taxa (Folmer et al., 1994; Jacobs & Grimes, 1986) and has been used extensively to elucidate population structure (Calderon, Garrabou & Aurelle, 2006; Lessios, Kane & Evolution, 2003; Palumbi, Grabowsky, Duda, Geyer & Tachino, 1997).…”

“…Purified V. fischeri DNA was visualized on a 1% agarose gel and quantified using a Nanodrop 9600 (ThermoFisher Scientific, Waltham, MA). Isolated DNA extracted from each V. fischeri isolate was used to amplify a portion of the glyceraldehyde phosphate dehydrogenase ( gapA ) locus (~900 bp) by PCR, using previously described Vibrio ‐specific primers (Table 2; (Jones et al., 2006; Nishiguchi & Nair, 2003). The gapA locus has been used reliably to estimate deep phylogenetic connections between bacterial families (Nelson, Whittam & Selander, 1991) within the Vibrionaceae (Thompson, Gomez‐Gil, Vasconcelos & Sawabe, 2007) as well local population structure of mutualist V. fischeri (Jones et al., 2006; Nishiguchi & Nair, 2003).…”

“…Earlier work on sepiolid squids has focused on the influence of geographic distance on symbiont prevalence and genotype in both sympatric and allopatric populations (Jones, Lopez, Huttenburg & Nishiguchi, 2006; Kimbell, McFall‐Ngai & Roderick, 2002; Zamborsky & Nishiguchi, 2011). Allopatric and sympatric populations for both squids and Vibrio bacteria show distinct population breaks that are not necessarily driven by host specificity.…”

“…Additionally, host‐mediated factors along with abiotic variables such as water temperature and salinity have been known to shape these mutualist assemblages (McFall‐Ngai, 2014; McFall‐Ngai et al., 2012; Nishiguchi, 2000; Soto, Gutierrez, Remmenga & Nishiguchi, 2009). Collectively, either genomic comparison of closely related populations (Bongrand et al., 2016) or haplotype comparisons of allopatric populations of Indo‐west Pacific squid and their vibrio symbionts (Jones et al., 2006) do not address the connectivity of populations across physical and biogeographic barriers like those in the Philippines or across the IPB. Therefore, we examined the genetic architecture of Euprymna albatrossae (Cephalopoda: Sepiolidae) and their V. fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach to determine whether host specificity or geographic location influence the distribution of symbiotic Vibrios in this region.…”