New preprint from lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka

A new preprint has been posted from the lab: There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia | bioRxiv

Paper was led by Laetitia Wilkins and Cassie Ettinger (Guillaume Jospin and I are co authors).  

Abstract:

Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. Using a shotgun metagenomics approach, we assembled population-level genomes of bacteria and archaea from two pools using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and placed them in the context of the current microbial tree of life. We highlight MAGs representing previously underrepresented archaeal phyla (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study can be considered complementary to foregoing studies in the same ecosystem as it adds more comprehensive information about phylogenetic diversity and functional potential within this highly selective habitat.

I will try to write more about it later – I am so impressed by what Laetitia and Cassie did here.  This is what we call a “reboot” project in the lab – this was data that was generated and then not turned into a paper and was just sitting there.  A while ago we started a “reboot” program to start to try to turn such data sets into papers and they adopted this data set.  The data is Solexa shotgun metagenomic data from samples from hot springs in Kamchatka (yes, Solexa, read the paper for details).  The DNA used was leftover from an old project which included a collaboration with Juergen Wiegel’s lab (and some others) that had started, at least in terms of discussions, in 2001.  Anyway – I will try to write out more on the story behind this work soon.  But please, check out the paper, and feel free to provide feedback.

At @ucdavis: Marine aquaculture recruitment seminars

Forwarding this:

This week VetMed will be hosting two of the three candidates for the Marine Aquaculture Science faculty position. All are invited to the recruitment seminars which will be held in 1041 Valley Hall from 12-1 on Tuesday and Thursday.

CMSI will be hosting an afternoon meet & greet with coffee and dessert from 2:15-3:15.

The recruitment seminar flyers for the two candidates are attached.

Colleen Burge
June 12 12:00 – 1:00 (1041 Valley Hall): Seminar- “Host-Pathogen Interactions in a Changing Ocean: from Disease Emergence to Solutions"
2:15 – 3:15 (1347 Storer Hall): Meet & greet with CMSI faculty, staff, postdocs and students

Jan Lovy
June 14 12:00 – 1:00 (1041 Valley Hall): Seminar- “Research on microparasites affecting wild and farmed fish: From the farm to a laboratory disease model to gain insights on host-pathogen interactions"
2:15 – 3:15 (1347 Storer Hall): Meet & greet with CMSI faculty, staff, postdocs and students

Thu 5/31 at UC Davis: Rachel Sollman on Spatial capture-recapture: a flexible framework to study wildlife populations

Forwarding:

This week’s Ecology and Evolution Seminar series will be given by Rahel Sollmann, from the WFCB department here at UC Davis. For more about Rahel’s research, click here.

Her talk, titled: "Spatial capture-recapture: a flexible framework to study wildlife populations" will be tomorrow, Thursday, May 31 at 4:10 pm in Everson Hall.

UCB IB Dept Lecturer Pool for “General Biology”

Lecturer Positions in General Biology – BIO 1B

Department of Integrative Biology

University of California, Berkeley

The Department of Integrative Biology at UC Berkeley is generating an applicant pool of qualified temporary full or part-time lecturers to teach the General Biology laboratory class, BIO 1B (http://ib.berkeley.edu/courses/bio1b/), should the need arise. The pool will remain in place for one calendar year; those interested in remaining in the pool after the year must reapply. Appointments may be renewable based on need, funding, and performance. Positions range from 50% – 100%, depending on the number of sections taught. Vacancies may arise during Fall, Spring, or Summer.

The laboratory class currently covers three major sections: Evolution, Ecology, and Organismal Diversity. Exercises include investigations into population genetics, phylogenetic relationships, macroevolution, predator/prey interactions, competition, bioindicators, and structure and function of organisms. BIO 1B is a gateway course to the major field of Integrative Biology that consists of three one-hour lectures and one four-hour combined discussion and lab each week. The class has 48 sections with a maximum of 18 students in each section. Lecturers will be required to lead one discussion and lab per week, create quizzes, grade assignments, attend a Friday instructional meeting, be familiar with lecture, proctor exams, hold office hours and complete other instructional duties as assigned. Senior lecturers mentor new hires and Graduate Student Instructors (GSIs).

Minimum Basic Qualifications (by time of application): The completion of all Ph.D. degree requirements except the dissertation is required at the time of application.

Additional Qualifications (by start date): A Ph.D. or equivalent degree in biology or a closely related discipline is required by the time of appointment. Experience teaching a college-level course (previously employed as a graduate student instructor, teaching assistant, lecturer, etc.) of the biological sciences is also required.

Preferred Qualifications: Experience working with computer-based phylogenetic programs and familiarity with online course and grading systems is preferred. Preference will be given to those with experience teaching a class similar to UC Berkeley’s Bio 1B lab courses.

Minimum full-time annual salary is $53,402. Salary is commensurate with experience and education.

Appointments for fall semesters are usually reviewed in May and finalists are selected once funding is confirmed for the next academic year. Spring semester appointments are reviewed in September. Reviews for Summer are in January.

Application requirements to apply: Cover letter, curriculum vitae, statement of teaching philosophy, student evaluations of teaching, and names and email addresses of three references. One miscellaneous teaching document is optional. Please include career highlights in the cover letter that specifically address the subject matter of our course. The CV should include teaching experience with a listing of dates, courses, units, and title (Lecturer, Graduate Student Instructor/Teaching Assistant, Guest Lecturer, etc.). Statement of Teaching Philosophy should be no more than three pages. Student evaluations of teaching should include all respondents (quantitative and qualitative). For those with considerable teaching experience, complete student evaluations of teaching from the last three courses taught will suffice. The cover letter, CV, and complete student teaching evaluations are very important. To receive full consideration, please ensure your application is complete by the time of review. To apply:

ib_recruit.

Letters of recommendation may be requested of finalists. If reference letters are later solicited by the Department, they will be treated as confidential per University of California policy and California state law. Please refer potential referees, including when letters are provided via a third party (i.e., dossier service or career center), to the UC Berkeley statement of confidentiality

(http://apo.berkeley.edu/evalltr.html) prior to submitting their letters.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see:

http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct. The department is interested in candidates who will contribute to diversity and equal opportunity in higher education through their teaching.

Bio 1B Lecturer Pool Ad for 2018-2019v2.pdf

New lab paper: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

New paper out from the lab. This is from a collaboration with Stan Marks in the Vet School at UC Davis. The work was led by Katti Horng with assistance from Holly Ganz.

Citation: Horng KR, Ganz HH, Eisen JA, Marks SL. (2018) Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6:e4827https://doi.org/10.7717/peerj.4827

Abstract: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research.

Source: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota