Microbial Inventory Research Across Diverse Aquatic Long Term Ecological Research Sites
MIRADA LTERs is carrying out a Microbial Biodiversity Survey and Inventory across all the major aquatic (marine and freshwater) Long Term Ecological Research (LTER) sites established by the NSF’s US LTER Program
. Our inventory takes advantage of the aquatic sampling locations that are part of the established LTER network of sites and builds on existing infrastructure for coordination at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts set in place by the Alfred P. Sloan Foundation supported Census of Marine Life (CoML)
ocean realm project called the International Census of Marine Microbes (ICoMM)
Our Microbial Inventory Research Across Diverse Aquatic (MIRADA) LTERs has adopted ICoMM’s massively-parallel, 454-based rDNA tag sequencing strategy that allows extensive sampling of both common and rare members of microbial populations and provides a common metric for integrating studies of microbial diversity across aquatic LTER sites. This methodology not only enables cross-site comparisons, but also provides valuable baseline data for integrating population structures with ecosystem change, and understanding microbially-mediated trophic dynamics and biogeochemical processes - areas of study already underway at many of the LTERs.
To view a status report of the MIRADA LTERs progress click here.
Our specific objectives are to:
1. Document and describe both microbial (Bacteria, Archaea and Eukarya) baseline diversity and relative abundance data for microbial operational taxonomic units (OTUs) as defined by SSU rDNA hypervariable tags at aquatic LTER sites.
2. Determine which microbial OTUs are common to both freshwater and marine LTERs.
3. Determine whether diverse aquatic LTER sites possess “signature” assemblages characterized by space, time and environmental parameters.
4. Discover novel tag sequences that likely represent novel microorganisms that LTER researchers and students can further characterize and study.
MIRADA Collaborators and Contacts (LTER PIs in bold):
Arctic: John Hobbie
(MBL), Byron Crump, Joanna Green (Horn Point Laboratory), George Kling (U Michigan)
California Current Ecosystems: Mark Ohman
, Brian Palenik, Farooq Azam (U California, San Diego -UCSD)
Coweeta: Ted Gragson
, Catherine Pringle, John Frisch∗ (U Georgia, Atlanta -UGA)
Florida Coastal Everglades: Daniel Childers
, Joseph Boyer, Christina Pisani∗ (Florida International University)
Georgia Coastal Ecosystems: Tim Hollibaugh
, Mary Ann Moran, Melissa Booth, Scott Gifford∗, Merryl Alber (UGA)
Hubbard Brook: Charles Driscoll
(Syracuse University), Don Buso (Institute for Ecosystem Studies), Gene Likens (Cary Institute for Ecosystem Studies)
McMurdo: John Priscu
, Amy Chiuchiolo (Montana State U), Brian Lanoil, Chao Tang∗, Hans Sukkyun∗∗ (U California at Riverside-UCR), Michael Madigan (Southern Illinois University)
Moorea Coral Reef: Russell Schmitt
, Alice Alldredge, Craig Carlson, Andrew Brooks (U California, Santa Barbara-UCSB), Jan Witting (SEA)
North Temperate Lakes: Stephen Carpenter
, Trina McMahon, Todd Miller ∗∗(U of Wisconsin)
Palmer Station: Hugh Ducklow
, Kristen Myers∗ (MBL) Alison Murray (Desert Research Institute)
Plum Island: Chuck Hopkinson
(UGA), Anne Giblin
, Aaron Strong (MBL), Martin Polz, Sarah Preheim∗ Jennifer Benoit∗(MIT)
Santa Barbara: Dan Reed
, Craig Carlson (UCSB)
Virginia Coastal Ecosystems:Karen McGlathery
, Linda Blum, Aaron Mills (U Virginia)
∗= graduate student collaborators; ∗∗postdoctoral collaborators.
MIRADA Methods and Protocols:
Our sampling protocol involves selecting 8 sites per LTER and sampling these in duplicate for each of the three domains of life- for a total of 48 samples per run of the GS-FLX 454 machine. Sampling for MIRADA involves sterile collection of 1 or more liters of water followed by processing of the samples onto 0.22 µm sterivex filters for DNA extraction, filtration of a portion of the sample onto membrane filters to provide an archive sample for future Fluorescence In Situ Hybridization (FISH), and archival cryopreservation of a portion of the samples in both DMSO and glycerol for future culturing. Click on the links below to view protocols we have established for our collaborators to help collect samples for the MIRADA project:
Sterivex filtration movie
Sterivex manifold components
Sterivex DNA extraction
All MIRADA voucher DNA samples and cryopreserved samples are available upon request to the lead PI. MIRADA cryopreserved samples are being deposited with Dan Distel at the Ocean Genome Legacy