Disturbance induced decoupling between host genetics and composition of the associated microbiome

Abstract

BackgroundStudies of oyster microbiomes have revealed that a limited number of microbes, including pathogens, can dominate microbial communities in host tissues such as gills and gut. Much of the bacterial diversity however remains underexplored and unexplained, although environmental conditions and host genetics have been implicated. We used 454 next generation 16S rRNA amplicon sequencing of individually tagged PCR reactions to explore the diversity of bacterial communities in gill tissue of the invasive Pacific oyster Crassostrea gigas stemming from genetically differentiated beds under ambient outdoor conditions and after a multifaceted disturbance treatment imposing stress on the host.ResultsWhile the gill associated microbial communities in oysters were dominated by few abundant taxa (i.e. Sphingomonas, Mycoplasma) the distribution of rare bacterial groups correlated to relatedness between the hosts under ambient conditions. Exposing the host to disturbance broke apart this relationship by removing rare phylotypes thereby reducing overall microbial diversity. Shifts in the microbiome composition in response to stress did not result in a net increase in genera known to contain potentially pathogenic strains.ConclusionThe decrease in microbial diversity and the disassociation between population genetic structure of the hosts and their associated microbiome suggest that disturbance (i.e. stress) may play a significant role for the assembly of the natural microbiome. Such community shifts may in turn also feed back on the course of disease and the occurrence of mass mortality events in oyster populations.

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection

“…Thus, the lower community stability at 22 1C (Figure 4b) and temperature-or stressrelated increase in potentially pathogenic bacteria (Supplementary File 2) could have contributed to the observed mortality pattern. However, microbiomes often remain stable and pathogen-free even in stressful conditions (Erwin et al, 2012;Simister et al, 2012;Pita et al, 2013;Wegner et al, 2013), indicating their potential role in host acclimation (Rosenberg et al, 2007). Phylogenetic similarity of the microbiomes suggests a common origin from the local seawater microbiota (Lozupone et al, 2007).…”

“…Tissues of healthy marine invertebrates usually harbor species-rich microbial communities (Prieur et al, 1990;Gomez-Gil et al, 1998;Romero et al, 2002;Gomez-Gil et al, 2010;King et al, 2012;Trabal et al, 2012;Wegner et al, 2013). This also applies to the hemolymph (Olafsen et al, 1993;Garnier et al, 2007, Wendling et al, 2014-the functional analog of blood in vertebrates (Bachere et al, 2004).…”

Adaptation to enemy shifts: rapid resistance evolution to local Vibrio spp. in invasive Pacific oysters

“…Vibrio spp. are virtually absent from oyster tissue during winter months [41], and their abundance and diversity increases from spring to summer, reaches a peak during spawning season before decreasing towards autumn [24]. Thus, Pacific oysters do not have a constant Vibrio community but rather take up strains from the local environment making it highly unlikely that the strains used here share a longer coevolutionary history exceeding the time since invasion into the Wadden Sea.…”

“…This indicates that the taxonomic composition of strains used here was independent of the invasion source of the host. While oyster associated microbiota can assemble according to host genotype [41], Vibrio spp. in oyster haemolymph are most probably taken up from the environment and vary seasonally with environmental temperature [24,42].…”

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach

“…Several recent works (Aravindraja et al 2013;Bartram et al 2014;Bowen et al 2012;Dohrmann et al 2013;Gibbons et al 2013;Kim et al 2013;Logares et al 2013;Oh et al 2013;Portillo et al 2013;Sánchez et al 2013;Székely and Langenheder 2014;Wegner et al 2013), mainly performed with nextgeneration sequencing technologies, have demonstrated that most bacterial communities are composed of a few abundant taxa and a plethora of rare ones (Pedrós-Alió 2012). Such different fractions may have in theory different taxonomic signatures (at the various taxonomic levels), in relation to the physiological features of the groups of taxa present.…”