Diversity Initiative
for the
Southern California Ocean

Discovering and documenting
the diversity of marine life

Events in 2017

31 JanSpecimens ready for shipment to the Smithsonian Institution

Two more 96-well plates of specimens were prepared for sequencing at the LAB facility.

20 JanCompleted Naturalist article on DISCO

Collaborating with Jessica Portner, we have prepared an article for the next Naturalist.

18 JanField collection of vernal pool eDNA near San Diego

USC Intern Katya Balakovsky, Adam Wall, and Jenessa Wall spent a day in San Diego County collecting eDNA from vernal pools, which we are using as an eDNA testbed.

17 JanZack Gold visits NHM from UCLA on eDNA stategies

From the laboratory of collaborators at UCLA (PI Paul Barber), Zack Gold visited us at NHM to develop strategies for environmental DNA (eDNA) collection in vernal pools.

17 JanWetzer & Mowery publication in ZooKeys

R. Wetzer, G. Mowery (2017) Redescription of Dynoides elegans (Boone, 1923) (Crustacea, Isopoda, Sphaeromatidae) from the north-eastern Pacific. ZooKeys 646: 1-16. dx.doi.org/10.3897/zookeys.646.10626. This publication represents a joint effort by DISCO PI Wetzer and USC undergraduate Gracie Mowery.

10 JanMARINe survey site visit to Cabrillo National Monument

Leslie Harris accompanied members of the Multi-Agency Rocky Intertidal Network on a survey site near San Diego. Because this site is off-limits to the public, it has high value as a sampling locality. Based on this visit, we are pursuing state and federal permitting.

9 JanKatya Balakovsky and Savannah Benes begin internships

We have taken on two interns from USC’s Environmental Studies Program for Spring 2017.

 

Events in 2016

DecSequencing progress

The major achivement for the month was the highly successful trip by Adam Wall and Jenessa Wall to sequence our first large group of barcode specimens. For most taxa, the COI gene was sequenced; 16S was sequenced for a couple of hundred. Success rates were very high, particularly considering that this was the first attempt at a large-scale sequencing effort. Most taxa had success for over 75% of the specimens; polychaete worms had 92% success. We are extremely encouraged by this first run. We are now processing the hundreds of barcode sequences, uniting them with specimen collection metadata and photographs, and preparing to upload them to the international genetic barcode database.

13 DecField collection: Ports O’ Call

Thanks to collaboration from executive staff at the Port of Los Angeles, DISCO was able to take advantage of the demolition of an aging marina at “Ports O’ Call” in San Pedro. Port cranes picked up and turned over the floating docks so that DISCO biologists could sample their fouling community. We were also able to open the event to staff from the Aquarium of the Pacific and the Cabrillo Marine Aquarium, who came to pick up local live specimens.

2 DecScreening of A Closer Look at USC

Katya Balakovsky and Shaina Wooley chose NHM’s staff involved in the DISCO project as subjects for their documentary film, A Closer Look, part of their class project at USC Cinematic Arts. The film, which explores some of the work and some of the motivations of museum collections researchers, was screened at USC’s Eileen Norris Cinema Theatre, and can also be viewed online.

NovBegin sequencing at Smithsonian/George Washington University

In mid-November, six 96-well specimen plates (576 separate specimens) were prepared for sequencing and shipped on dry ice to Keith Crandall’s lab at GWU. Adam Wall and Jenessa Wall successfully completed DNA extractions between 27–30 November. They will continue with sequencing during the first week of December.

29 NovField collection: MARINe “Old Stairs” site in Ventura County

Partnering with BOEM and MARINe, NHM staff collected intertidal specimens at the MARINe sampling site “Old Stairs”. The site has been surveyed continually since 1994.

19 NovField collection: Ship-borne sampling off southern L.A.

On R/V Yellowfin of the Southern California Marine Institute (SCMI), NHM staff joined Kimo Morris of Santa Ana College to collect offshore dredge and trawl specimens.

17 NovMARINe survey assistance at Point Fermin

As part of our collaboration with MARINe, NHM staff assisted with their intertidal survey.

15 NovField collection: Salinas de San Pedro, L.A. Harbor

Working with Cabrillo Marine Aquarium, NHM staff sampled muddy-bottom fauna in the remediated salt marsh in L.A. Harbor.

4 NovMeeting with Lisa Gilbane of Bureau of Energy Management

Lisa Gilbane is the primary contact at the federal Bureau of Energy Management (BOEM) for the Multi-Agency Rocky Intertidal Network (MARINe). Working with Jennifer Burnaford (CSU Fullerton), BOEM and MARINe are beginning to voucher specimens from long-term intertidal monitoring. They are now including us on monitoring trips (to sample), and they will use NHM as the research repository for their own voucher specimens.

OctPlanning for Smithsonian/George Washington University program

In November, two MBC staff (Adam Wall and Jenessa Wall) will take several hundred specimens to work with Keith Crandall’s institute at GWU to learn high-efficiency sequencing techniques and use the Smithsonian’s robotic sequencing facility. Specimen processing for this scale of sequencing requires detailed planning.

OctCollection/specimen database launched

We now have a full-featured database that links and tracks field collection information, specimens from those collecting events, DNA extracts and photographs from those specimens, and multiple molecular analyses of each specimen.

OctSpecimen photography rig built and tested

Barcode reference sequences posted to the BOLD repository are accompanied by photographs. We have designed and built equipment to take publication-quality images of marine invertebrates, immersed in seawater, using a camera or dissecting microscope.

31 OctMeeting with Eric Stein at SCCWRP

The research group at SCCWRP (the state joint powers agency linking all the coastal wastewater treatment facilities) is a strong potential partner in developing the library of genetic barcodes for Southern California marine species as well as eDNA and whole- community barcode analysis.

21 OctMeeting with UCLA’s Paul Barber and Zack Gold

The Barber laboratory is working on environmental DNA (eDNA) analysis of seawater samples and is interested in collaborating with us on several sub-projects.

20 OctUCLA IoES Earth Now/Earth 2050 event

By invitation, DISCO provided a hands-on marine biodiversity event with live marine invertebrates for 150 high school students attending the inaugural Luskin Endowment Symposium at UCLA.

19 OctScience communication: Story Circles

DISCO staff members particpated in science communication training led by Randy Olson.

13 OctFilming with USC and sampling at Cabrillo Marine Aquarium

Two USC Cinematic Arts students (Katya Balakhovsky and Shaina Wooley) filmed DISCO staff sampling at a CMA beach survey.

A new program at the Natural History Museum of Los Angeles County aims to develop research and monitoring tools to enormously accelerate our ability to discover and investigate marine invertebrate biodiversity of California’s nearshore waters. The Diversity Initiative for the Southern California Ocean (DISCO) is based in the NHM’s Marine Biodiversity Center, and incorporates partnerships with organizations both inside and outside of the Museum.

There are good things to see in the tidepools and there are exciting and interesting thoughts to be generated from the seeing. Every new eye applied to the peep hole which looks out at the world may fish in some new beauty and some new pattern, and the world of the human mind must be enriched by such fishing.

John Steinbeck. 1948. Foreword to:
E.F. Ricketts & J. Calvin, Between Pacific Tides.

Why a new diversity intiative?

We know that our oceans are changing quickly, and our coastal biota are responding. Successful management requires that we know what species are where, and how their distributions change with time.

Current monitoring technology, based on specialist identifications of individual organisms, just cannot keep pace. Standard approaches to ecological research and monitoring efforts that look at marine species distributions depend on highly trained taxonomists to sort and identify the animals in environmental samples. Identification of marine macroinvertebrates is challenging because of their small size, complex morphology, and extreme diversity. Therefore, because of the expertise and time required, relatively few sites can be sampled, and often studies are restricted to a handful of “indicator” species, rather than comprehensively looking at the community. This cripples our ability to see the widespread but subtle changes to our coastal biota that accompany variations in ocean temperature and acidity. We need quicker and more effective ways to identify the species in marine samples.

New genetic approaches

Over the last decade, molecular identification tools, called “genetic barcoding,” have been developed to identify the species of any specimen based on its DNA. Species share a handful of particular genes that exhibit just the right amount of variation for dependable identification. Individual specimens can be identified to species by sequencing a single (or very few) short gene sequences and then comparing those sequences against a reference library of sequences from independently (non-genetically) identified specimens.

Of course, for that system to work, the reference library of “barcode” sequences (the Barcode of Life Database [BOLD] run by the University of Guelph) must contain at least one reference sequence for each species of interest. Expert taxonomists must reputably identify specimens, get the appropriate DNA sequences from them, deposit the sequences in BOLD, and deposit the voucher specimens in a museum for permanent storage.

Building the library

Sadly, the estimated 3,000 to 5,000 marine invertebrate species of Southern California are poorly represented in the BOLD reference library. NHM’s DISCO project aims to fill in the missing entries. We will use a combination of existing NHM specimens, new collections, and external contributions. NHM taxonomists have the expertise and professional collaborators necessary to undertake and complete this task. All specimens collected and processed in this project will be archived as permanent voucher specimens at the NHM and all sequences will be publicly available at BOLD.

Dramatic inventory improvements

Being able to attribute an individual specimen to a species based on its genetic sequence can be useful. But much more exciting are the prospects offered by combining a well-populated barcode reference library with modern high-throughput genetic sequencing.

It is now possible to extract DNA from an entire community at once (e.g. combined scrapings from a floating dock) and then retrieve all of the unique sequences in the entire community with a single run of a high-throughput sequencer. Even more extraordinary, just sampling DNA from the seawater around a community can yield genetic diversity information. Sequencing of DNA from the environment, or eDNA, is possible because all organisms naturally shed DNA into the environment around them. There can be enough DNA in seawater samples that it is unnecessary to sample the organisms directly.

These approaches yield a list of unique genetic sequences. By searching those sequences against a well-populated reference library, the list of sequences can be interpreted as a list of species.

Whole-community and eDNA technology is at the prototype stage for coastal marine systems. Another goal of NHM’s DISCO project is to work with partner organizations to develop this technology to the point that it is routinely applicable in marine research and monitoring.

Being able to inventory full species diversity quickly and efficiently will permit far more frequent sampling in monitoring applications, and much more taxonomically broad coverage in research programs.

Who we are

The DISCO program comes from the marine invertebrate group at the Natural History Museum of Los Angeles County.

DISCO is led by Regina Wetzer (Associate Curator) and based out of the Marine Biodiversity Center (MBC). Other key personnel include Dean Pentcheff (Project Coordinator), Leslie Harris (Collections Manager, Polychaetes), Kathy Omura (Collections Manager, MBC), Adam Wall (Collections Manager, Crustacea), and Jenessa Wall (Assistant Collections Manager, MBC).

Further information

Additional information about genetic barcoding and its applications to ecological research and monitoring (both marine and terrestrial) can be found in the following references.

Blaxter, M. 2016. Imagining Sisyphus happy: DNA barcoding and the unnamed majority. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150329.

Bohmann, K., A. Evans, M. T. P. Gilbert, G. R. Carvalho, S. Creer, M. Knapp, D. W. Yu, and M. de Bruyn. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution 29:358–367.

Cristescu, M. E. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends in Ecology & Evolution 29:566–571.

Gibson, J., S. Shokralla, T. M. Porter, I. King, S. van Konynenburg, D. H. Janzen, W. Hallwachs, and M. Hajibabaei. 2014. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences 111:8007–8012.

Goldberg, C. S., K. M. Strickler, and D. S. Pilliod. 2015. Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms. Biological Conservation 183:1–3.

Hajibabaei, M. 2012. The golden age of DNA metasystematics. Trends in Genetics 28:535–537.

Hajibabaei, M., D. J. Baird, N. A. Fahner, R. Beiko, and G. B. Golding. 2016. A new way to contemplate Darwin’s tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150330.

Hebert, P. D. N., P. M. Hollingsworth, and M. Hajibabaei. 2016a. From writing to reading the encyclopedia of life. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150321.

Hebert, P. D. N., S. Ratnasingham, E. V. Zakharov, A. C. Telfer, V. Levesque-Beaudin, M. A. Milton, S. Pedersen, P. Jannetta, and J. R. deWaard. 2016b. Counting animal species with DNA barcodes: Canadian insects. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150333.

Ji, Y., L. Ashton, S. M. Pedley, D. P. Edwards, Y. Tang, A. Nakamura, R. Kitching, P. M. Dolman, P. Woodcock, F. A. Edwards, T. H. Larsen, W. W. Hsu, S. Benedick, K. C. Hamer, D. S. Wilcove, C. Bruce, X. Wang, T. Levi, M. Lott, B. C. Emerson, and D. W. Yu. 2013. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters 16:1245–1257.

Kelly, R. P., J. L. O’Donnell, N. C. Lowell, A. O. Shelton, J. F. Samhouri, S. M. Hennessey, B. E. Feist, and G. D. Williams. 2016. Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4:e2444.

Kelly, R. P., J. A. Port, K. M. Yamahara, and L. B. Crowder. 2014. Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE 9:e86175.

La Salle, J., K. J. Williams, and C. Moritz. 2016. Biodiversity analysis in the digital era. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150337.

Leray, M., and N. Knowlton. 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences 112:2076–2081.

Leray, M., and N. Knowlton. 2016. Censusing marine eukaryotic diversity in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150331.

Miller, S. E., A. Hausmann, W. Hallwachs, and D. H. Janzen. 2016. Advancing taxonomy and bioinventories with DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150339.

Pansu, J., S. De Danieli, J. Puissant, J.-M. Gonzalez, L. Gielly, T. Cordonnier, L. Zinger, J.-J. Brun, P. Choler, P. Taberlet, and L. Cécillon. 2015. Landscape-scale distribution patterns of earthworms inferred from soil DNA. Soil Biology and Biochemistry 83:100–105.

Ratnasingham, S., and P. D. N. Hebert. 2007. BOLD: The Barcode of Life Data System (http://www. barcodinglife.org). Molecular Ecology Notes 7:355–364.

Ratnasingham, S., and P. D. N. Hebert. 2013. A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. PLoS ONE 8:e66213.

Shokralla, S., T. M. Porter, J. F. Gibson, R. Dobosz, D. H. Janzen, W. Hallwachs, G. B. Golding, and M. Hajibabaei. 2015. Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports 5:9687.

Shokralla, S., G. Singer, and M. Hajibabaei. 2010. Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol. BioTechniques 48:233–234.

Shokralla, S., J. L. Spall, J. F. Gibson, and M. Hajibabaei. 2012. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology 21:1794–1805.

Stein, E., B. P. White, R. D. Mazor, P. E. Miller, and E. M. Pilgrim. 2013. Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates. PLoS ONE 8:e51273.

Thomsen, P. F., and E. Willerslev. 2015. Environmental DNA — An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183:4–18.

Yahr, R., C. L. Schoch, and B. T. M. Dentinger. 2016. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philosophical Transactions of the Royal Society B: Biological Sciences 371:20150336.

Yu, D. W., Y. Ji, B. C. Emerson, X. Wang, C. Ye, C. Yang, and Z. Ding. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution 3:613–623.

Zhou, X., Y. Li, S. Liu, Q. Yang, X. Su, L. Zhou, M. Tang, R. Fu, J. Li, and Q. Huang. 2013. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. GigaScience 2:4.