Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Parameters
• Instruments
• Deployments
• Project Information
• Program Information
• Funding

Bacteria in the water and bacteria from the same location but directly associated (in the cuticle) with copepods were collected from several locations world-wide with pumps and nets from saline and fresh water.  The acquired DNA was sequenced and sent to GenBank.  The links are here.

These data will be available after January, 2017.

The water samples were collected this way:    Approximately 10 liters of water were collected from a depth of 1 meter near the shore and filtered through a 3.0 micron filter to exclude sediment, algae, and other large particles.   Then the water was passed through a 0.1 micron filter to collect bacteria. DNA was extracted from the filter with a  MoBio PowerWater DNA isolation kit.

The copepods and their associated bacteria were collected this way:  100 pooled adult male and female Eurytemora affinis were collected via plankton tow from depth of ~1-2 meters from near the shore. These animals were isolated from the zooplankton community under a microscope, and homogenized in a glass pestle tissue grinder.  DNA was extracted with a MoBio UltraClean Microbial DNA isolation kit.

There was no way to isolate bacteria from their copepod hosts, so the entire sample was processed and the DNA from the whole thing was extracted.

Copepods form the largest biomass of metazoans on the planet, yet their microbiota remain largely unexplored. The microbial community associated with copepods might perform key metabolic processes that affect host fitness and ecosystem functioning. The copepod Eurytemora affinis is dominant in coastal habitats throughout the world, and recently has invaded inland freshwater habitats. Associated with E. affinis, preliminary sequencing revealed high diversity of microbial taxa, including many undescribed genera and families. There also were parallel shifts in microbial composition during independent invasions from saline to freshwater habitats. Yet, a core set of microbial taxa remained present in all copepod populations across all locations. The copepod microbiome is likely to play fundamental roles in biogeochemical processes in many aquatic ecosystems. Microbial-host interactions could influence invasive success, and exotic microbes in the invading consortia could have vital impacts on the invaded community. This study will address the following questions: (1) What is the taxonomic composition of the copepod microbiome, and how does it shift during habitat invasions? (Taxonomy, Genetics); (2) What metabolic functions are performed by the copepod microbiome? (Function, Genetics); and  (3) What is the nature of copepod host-microbial interactions, and how do these interactions shift during invasions? (Functional Integration)

Research to address these questions includes: (1) high-throughput 16S sequencing, to identify the taxonomic composition of microbial assemblages associated with the copepod host in saline and freshwater environments, (2) shotgun sequencing of metagenomes and fosmids, and also comprehensive genome sequencing of key microbial taxa, to characterize the functional repertoire of genes in the copepod microbiome, and (3) reciprocal inoculation experiments, to explore functional interactions between the copepod host and its microbiome and whether the interactions evolve during invasions into novel habitats.

Characterizing the copepod microbiome will expose a largely undiscovered realm of microbial diversity. Moreover, this gene-centric analysis will provide invaluable insights into metabolic functions of the copepod microbiome, and how these functions might shift during copepod invasions. Results are expected to yield transformative insights into the taxonomic, functional, and genetic diversity of a largely unexplored component of the ecosystem, and how this diversity might become altered following invasions into novel habitats.

This study will provide integrated insights into the taxonomic, genetic, and functional diversity of the copepod microbiome. The assembled sequences will link specific metabolic functions with particular microbial taxa, illuminating functional diversity across deeply divergent lineages. Sequence data also will reveal genetic diversity of metabolic functions within microbial taxa, and the potential sharing of functions across taxa (e.g. via horizontal gene transfer). Moreover, these findings will reveal functional integration of the microbial-host consortia, including between the microbial community and its host.

Preliminary sequencing of the E. affinis microbiome uncovered a wide variety of potentially pathogenic taxa, including Salmonella, Shigella, Campylobacter, Corynebacterium diphtheriae, Yersinia, and Vibrio cholerae. Thus, E. affinis might play an important role as a reservoir and vector of waterborne disease.

(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF]

The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.