Overview of Barcode the Lake Goals

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Introduction

Lake Merritt in Oakland, California  represents one of the most interesting anthropocene environments on the planet as its waters are filled with organisms from around the world that have made their way in the ballast water of ships  harboring at the nearby port. The study of marine invertebrates got its start at Lake Merritt and the park surrounding the lake is also filled with organisms from around the world, some by design, but most by accident.  The identification of organisms has classically been based on the physical features of the organism, the morphology, but as DNA sequencing has become cheaper it has become a great tool for identifying  organisms that have difficult morphology and elucidating lineages between organisms. The recent explosion of Citizen Science projects where non-professionals are engaged in solving problems or generating data used by the scientific community is changing the way large scientific problems are tackled and help build skills in communities engaged in the projects. This projects looks to use a Citizen Science approach to generate data down to a genetic level  on the organisms of Lake Merritt, build transferable lab skills and field identification skills in participants from the community.  

 A brief visual sampling of Lake Merritt's organisms: 

Evolving list of Lake Merritt organisms on iNaturalist. 

 

Goals

To engage the public and contribute scientific knowledge about the organisms that live around  and in Lake Merritt. Special emphasis through advertising and support will be used to get communities usually not engaged in citizen science projects involved.

The project has three goals in relation to the organisms

1. Visual observations of organisms collected into the citizen science platform iNaturalist, 500 per year.

2. Collections of organisms when appropriate and with permit for local herbarium or archive. 20 organisms per year with visual data in iNaturalist = BarcodeTheLake

3. DNA Sequencing of organisms with sequences going into GenBank. 20 organisms per year.

 

The project has three goals in relation to the community

1.Engage at least 50 to use iNaturalist to document organisms around Lake Merritt per year.

2.Increase the knowledge of participants about the diversity of life around the lake and their effects on us and our effects on them

3.Allow at least 25 people to have hands on experience extracting, amplifying and sequencing DNA from Lake Merritt organisms.

 

Methods

In order to hit the goals related to the organisms  taxa related Bioblitzes of the lake will take place throughout the year based upon when that taxa is most available.  The goal for the first year is three Bioblitzes. Permits will be obtained through the appropriate agencies for collection of organisms during these Bioblitzes to build a collection of specimens .  DNA extraction, amplification and send out for sequencing will take place at the Rotary Nature Center under the guidance of Damon Tighe a former researcher on the Human Genome project who has ample experience with DNA sequencing.  All data will be kept in a project on iNaturalist so anyone in the world can easily access the data generated by this project. DNA sequences will also be submitted to Genbank, the world’s repository for DNA sequences.  The first taxa to be worked with will be Fungi due to the large diversity that is coming up due to this wet year. The second taxa  to be worked on will be plants and then insects , marine crustaceans  and other marine invertebrates.

 

In order to hit the goals in relation to the community advertising will be done through local schools and community groups  to target individuals that might not usually have exposure to these sorts of activities.  Participants will be asked to fill out a survey with questions about their relationship to the natural world broadly and Lake Merritt specifically before their first event. A similar survey will be sent out after they have completed one or more events. For those interested in using this as a way to gain skills in the prospect of a job, help will be offered in terms of letters of recommendation or resume writing .

 

Budget

         Start up cost (durable goods)

                                Item                                      Cost

                      Thermalcycler                               2500

                      Centrifuge                                        500

                      Waterbath                                        200

                      Micropipettes                                  500

                      Powersupply                                    300

                      Horizontal Gel Box                          300

                  ------------------------------------------------------------

                        Total                                              $4,300

 

         Yearly cost (consumables + Labor)

                          Item                                             Cost

                      Primers                                            100

                      Master Mix                                       200

                      Micropipette tips                               50

                      plastics (PCR tubes)                           50

                      Agarose Gels                                       70

                      Running Buffer                                    25

                      DNA Stain                                             25

                      Sequencing Service (25 samples)   250

                      Labor ( 35 hours)                            700                                                                        

                  ------------------------------------------------------------

                        Total                                              $1, 470

          

      Total start up and 1 year operation cost $5,770