The California environmental DNA “CALeDNA” program

Rs, Meyer; Ee, Curd; Schweizer, Teia M.; Gold, Zachary; Dr, Ramos; Shirazi, Sabrina; Kandlikar, Gaurav S.; Kwan, Wai-Yin; Ma, Lin; Freise, Amanda C.; Moberg-Parker, J; Mm, Ramos; Shapiro, Beth; Jp, Sexton; Pipes, Lenore; Ag, Vedrenne; Mp, Mejia; Aronson, Emma L.; Moore, Tiara; Nielsen, Rasmus; Lewin, Harris A.; Barber, Paul H.; Wall, Jeff; Kraft, Nathan J. B.; Rk, Wayne

doi:10.1101/503383

Cited by 15 publications

(17 citation statements)

References 22 publications

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“…Our research project assignment capitalized on data generated by the California Environmental DNA (CALeDNA) community science program (Meyer et al., 2019) to increase student engagement through active and inquiry‐based learning. In this structured activity, students combined community science data with open‐access bioinformatics tools (Kandlikar et al., 2018; https://gauravsk.shinyapps.io/ranacapa/).…”

Section: Adapting An Active‐learning Flipped Classroom To Remote Learmentioning

confidence: 99%

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

Garcia‐Vedrenne

Orland

Ballare

et al. 2020

Ecology and Evolution

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Section: Adapting An Active‐learning Flipped Classroom To Remote Learmentioning

confidence: 99%

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

Garcia‐Vedrenne

Orland

Ballare

et al. 2020

Ecology and Evolution

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“…The sample data used here and in the tutorials was generated by UCLA students in the winter and spring quarters of 2018, where they investigated the effect on rhizosphere microbial communities following the Skirball wildfire of December 2017 ( Skirball Fire, 2020 ). Sample collection kits and sample sequencing were provided by the California Environmental DNA (CALeDNA) program, a community science initiative monitoring California’s biodiversity through eDNA ( Meyer et al, 2019 ), and the 16S sequences were processed using the Anacapa toolkit ( Curd et al, 2019 ). The sample data for QIIME 2 is the same as the “moving pictures” human microbiome example dataset available on the QIIME 2 website 2 .…”

Section: Pumaa – Program For Unifying Microbiome Analysis Applicationmentioning

confidence: 99%

“…Recent course projects have involved collaborations with researchers at UCLA and beyond studying plant–microbe interactions in California grasslands ( Kandlikar et al, 2020 ), analysis of the soil microbial communities of a Los Angeles urban farm ( St. Clair et al, 2020 ), and a longitudinal study on the recovery of soil microbial communities following the 2017 Skirball fire in Los Angeles, CA, United States. The Skirball fire project was conducted in conjunction with the California Environmental DNA (CALeDNA) program’s efforts to catalog California’s biodiversity ( Meyer et al, 2019 ).…”

Section: Pumaa – Curriculum Overviewmentioning

confidence: 99%

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

et al. 2020

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Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.

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“…e metagenomic soil DNA samples were collected according to the CalEDNA citizen science instructional videos and sent to UCLA for sequencing using Illumina technology. e total DNA was extracted using the Pow-erSoil DNA Extraction kit, followed by amplification using 16S metabarcoding primers and purification [23]. Quality control was carried out in QIIME.…”

Section: Metagenomic Analysismentioning

confidence: 99%

Analysis of the Soil Microbiome of a Los Angeles Urban Farm

Clair

Saraylou

Melendez

et al. 2020

Applied and Environmental Soil Science

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This research aimed to address health and food security challenges affecting Los Angeles and beyond in our own backyard. One possible way to combat these challenges is through biotechnology. The purpose of this research was to characterize the arable soils at Los Angeles Pierce College and their potential uses. The methods employed were collection of soil physical and chemical properties, cultivation of soil microorganisms, and 16S rDNA sequencing with a citizen science platform. Statistical analysis in R revealed associations between field conditions and life in the soil. The testing of plant-based antimicrobial agents on antibiotic-resistant bacteria revealed that plant oils could be more efficacious for control than common antibiotics. We found evidence of plant growth-promoting, antibiotic-producing, and bioremediating bacteria in different fields with distinct microclimates based on the 16S rDNA taxonomy results and inferred functional profiles. The major findings included an abundance of Streptomyces, Bacillus, Methylobacteria, and others with desirable functions. Numerous Streptomyces isolates cultivated on selective media demonstrated the ability to reduce nitrate. These results will empower future trials and product development by identifying target soil microorganisms and the most viable fields.

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The California environmental DNA “CALeDNA” program

Abstract: 22Global change is leading to habitat shifts that threaten species persistence throughout 23 California's unique ecosystems. Baseline biodiversity data provide opportunities for 24 ecosystems to be managed for community complexity and connectivity. In 2017, the 25

Cited by 15 publications

References 22 publications

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

Analysis of the Soil Microbiome of a Los Angeles Urban Farm

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