f Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus and V. vulnificus populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) as indicators of V. parahaemolyticus and the hemolysin gene vvhA for V. vulnificus. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic V. parahaemolyticus and V. vulnificus. Other predictors included chlorophyll a, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.

Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4–V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

The progressive loss and fragmentation of longleaf pine forests throughout the southeastern United States has led to severe declines in habitat specialists such as the federally listed gopher tortoise Gopherus polyphemus. However, little is known of the range-wide historical genetic structure of this species or how habitat loss may have impacted the genetic diversity of this species over time. As genetic data are lacking in many parts of the gopher tortoise range, management of federally listed populations in Louisiana and Mississippi have been based on conservation units delineated by rivers. However, this current management strategy has been formulated without any knowledge of how riverine barriers might relate to genetic population structure. Here, we examine variability of mitochondrial and nuclear microsatellite markers in gopher tortoise populations across their natural range in the southeastern United States. Results from the mitochondrial data showed a historical phylogenetic break that is coincident with the Apalachicola River and a novel population assemblage located within western Georgia. Genetic structure based on microsatellite loci revealed high levels of genetic differentiation in some regions and a pattern of isolation by distance at two spatial scales. We also find that rivers across the federally listed portion of the range, do not significantly influence gene flow. Coalescent analyses of population demographic change in gopher tortoises indicate evidence of an ancient and severe population decline at sites across the range. Findings from this study provide important information that will aid in the identification of distinct population units for management and in the formulation of recommendations for the future maintenance of genetic diversity in this species.Population genetic structure of threatened tortoise R. W. Clostio et al.Population genetic structure of threatened tortoise R. W. Clostio et al.

Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus – a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP dataset (16 tortoises from 4 populations sequenced at 17,901 SNPs) to two microsatellite datasets, a full dataset of 101 tortoises and a partial dataset of 16 tortoises previously genotyped at 10 microsatellites. For the full microsatellite dataset, observed heterozygosity, expected heterozygosity, and FST were correlated between SNPs and microsatellites; however, allelic richness was not. The same was true for the partial microsatellite dataset, except that allelic richness, but not observed heterozygosity, was correlated. The number of clusters estimated by Structure differed for each dataset (SNPs = 2; partial microsatellite = 3; full microsatellite = 4). PCA showed four clusters for all datasets. More than 800 SNPs were needed to correlate with allelic richness, observed heterozygosity, and expected heterozygosity, but only 100 were needed for FST. The number of SNPs typically obtained from NGS far exceeds the number needed to correlate with microsatellite parameter estimates. Our study illustrates that diversity, FST, and PCA results from microsatellites can mirror those obtained with SNPs. These results may be generally applicable to small populations, a defining feature of endangered and threatened species, because theory predicts that genetic drift will tend to outweigh selection in small populations.

Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and nonthreatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises). Genetic diversity at the MHC class II locus and microsatellites was greater in populations in the nonthreatened portion of the gopher tortoise's range (MHC class II difference in mean A = 8.11, AR = 0.79, HO = 0.51, and HE = 0.16; microsatellite difference in mean A = 1.05 and AR = 0.47). Only MHC class II sequences showed evidence of positive selection (dN/dS > 1, Z = 1.81, P = 0.04). Historical gene flow as estimated with Migrate-N was greater than recent migration estimated with BayesAss, suggesting that populations were better connected in the past when habitat was less fragmented. MHC genetic differentiation was correlated with microsatellite differentiation (Mantel r = 0.431, P = 0.001) suggesting neutral genetic processes are influencing MHC evolution, and advantageous MHC alleles could be lost due to genetic drift.