Projects:
1. Pelagic GOM Microbial Community Analyses (by C. EassonJ. White, J. Lopez)

The DEEPEND consortium has the opportunity to expand these initial surveys beyond the Macondo well vicinity.  The microbial genetics group of DEEPEND will characterize microbial communities of the northern Gulf of Mexico (GOM) to establish a post oil spill baseline for prokaryotic communities (Bacteria and Archaea), and to understand the dynamics of these communities over time and space, across depths (Surface-1500m), and in relation to oceanographic features. 

GOM microbial communities (microbiomes) will be sequenced using Illumina MiSeq technology following methods developed and used by the both Earth Microbiome Project and Human Microbiome project.  From the sequence data, we can obtain measures of microbial community richness, diversity, and composition for all samples.  Additionally, we can characterize the interaction among samples as a measure of microbial community connectivity in an open ocean environment, and relate this connectivity to oceanographic features and other biological data collected during the cruise. 

Initial results from year 1 indicate temporal variation in microbial community diversity as well as clear depth stratification in microbial community composition.  Current research is focused on assessing microbial community interactions and relating diversity and composition patterns to data types collected in other DEEPEND research groups.

To provide an initial evaluation of differences in functional capacity among sampling sites and water column depths, we are employing a unique strategy developed by the Huttenhower Lab at Harvard School of Public Health called PICRUSt. PICRUSt allows us to estimate the relative richness of functional categories for each marine sample using only 16S taxonomic profiling information as input. From this analysis, we have already observed significant differences in several functions between sampling sites and water depths, including those involving hydrocarbon degradation, and we plan to further analyze these functional shifts in the context of biochemical and geographic metadata.

Cruise 1 NMDS plot of Bray-Curtis dissimilarity by depth. Microbial community composition (Bray-Curtis dissimilarity) varied significantly across depths (adonis, P = 0.001) and accounted for approximately 38% of the variance among samples.


 

Cruise 2 NMDS plot of Bray-Curtis dissimilarity by depth. Microbial community composition (Bray-Curtis dissimilarity) was most influenced by depth (adonis, P = 0.001), which accounted for 50% of the variance among samples.

 

Relative abundance of microbial phyla by depth.  Microbial community composition varied among depths (Figures 4 & 8).  Temporal variation is likely due to differential abundances of several abundant microbial phyla
 

 


2. Microbial Symbionts Associated with Angler Fish Lures (Esca) (by L. Freed, D. Fenolio, T. Hendry, J. Lopez)

While many deep sea fish are capable of producing light within specialized light organs (photophores), deep sea anglerfish have instead developed a unique symbiotic relationship with bioluminescent bacteria. These bacteria are contained within the anglers’ lure (esca), but it is still unclear exactly how the bacteria are obtained.  It is hypothesized that the bacteria may be transferred vertically from parent to larvae or acquired from the water. In order to tease out more details on this symbiotic relationship, we are examining the microbiome of several species of deep sea angler fish to determine whether bacterial symbionts are contained solely in the esca or are found in other body parts.  Applying qPCR and bioinformatics techniques, angler fish-specific symbionts will be verified for detectable levels in the water column, and also using phylogenetic tools to examine the evolutionary relationship between symbionts of differing host species.