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Department of Ecology, Evolution & Marine Biology | UC Santa Barbara | Santa Barbara, CA 93106-9620

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What are the signatures of "cryptic" biogeochemical cycling?

How do trophic interactions shape the physiology, ecology & evolution of bacteria?

Over what scales do barriers to migration & gene flow structure bacterial populations?

The "berries" are millimeter-sized microbial aggregates found in the muddy pools of the Sippewissett Salt marsh on Cape Cod, Massachusetts.  These compact, charismatic consortia are primarily made up of different photosynthetic bacteria, which give them their characteristic pink or green colors.

We study the berries as model system of natural microbial consortia. 

The berries have been studied for many years by students as a part of the Microbial Diversity course at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts.  This is where Lizzy first started working with them!

The pink berries are dominated by the anoxygenic, sulfide-oxidizing phototrophic bacterial species (Thiohalocapsa sp. PB-PSB1).  The green berries, by contrast, are a mixture of a nitrogen-fixing unicellular cyanobacterial species GB-CYN1 and diatoms.   

 

Our published research has focused on the bacterial metabolism and biogeochemistry of these unusual aggregates, integrating by metagenomics, microscopy, and high-resolution geochemistry (stable isotopes, nanoSIMS, microsensors).   In the pink berries, we found direct evidence for a cryptic sulfur cycle between the two dominant species: sulfide oxidizing phototroph PB-PSB1 and the sulfate reducing bacterial species, Desulfofustis sp. PB-SRB1.  

 

We have also used the pink berries as a model system to test different approaches in metagenomic sequencing, binning and assembly.  Our datasets – in preparation for publication – include Moleculo, PacBio, and Oxford Nanopore long read sequencing, in addition to parallel deep sequencing with Illumina.

BACKGROUND & PREVIOUS WORK

In collaboration with Gabriel Leventhal and Otto Cordero at MIT, we are examining the biogeography and co-evolution of species within the pink berries, with population (meta)genomics from individual aggregates. 

 

Metagenomic studies of viruses and bacterial CRISPRs in the pink berries was the focus of several summer projects this year by Audra Devoto, a 2017 summer student in the Wilbanks lab, and students from the quantitative biology summer course at UCSB’s Kavli Insitute for Theoretical Physics

We have also been working to culture the different bacterial species from the berries, using a variety of aerobic and anaerobic enrichments.  Isolates will not only allow us to better describe, but open up the possibility of creating experimental communities in the lab

Other future plans include continuing investigations of ecophysiology & trophic interactions (carbon & nitrogen dynamics), and mathematical modeling of metabolism and community dynamics. 

CURRENT WORK & FUTURE IDEAS
SELECTED PUBLICATIONS

Wilbanks EG, Salman-Carvalho V, Jaekel U, Humphrey PT, Eisen JA, Buckley DH, Zinder SH. (2017). The green berry consortia of the Sippewissett salt marsh: millimeter-sized aggregates of diazotrophic unicellular cyanobacteria. Frontiers in Microbiology. 8: 1623.   https://doi.org/10.3389/fmicb.2017.01623

Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Zinder SH, Buckley DH, Druschel GK, Fike DA, Orphan VJ. (2014). Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environmental Microbiology. 16: 3398–3415. http://doi.org/10.1111/1462-2920.12388