We kicked off collecting samples for our California Conservation Genomics Project where we are sequencing the native California lichen Acarospora socialis. This work is the core of Julia Adam‘s Dissertation which is focusing on study of population genetic and phylogeographic patterns and how the fungal and bacteria microbiome is related to ecological context of this crustose lichen across an elevation gradient in multiple landscapes. The CCGP project will generate a reference genome for this species as well as population genomic dataset from ~150 samples. We are excited to examine the population structure of this lichen.
Julia’s been studying lichens for several years and currently helps curate the UCR Herbarium lichen collection. Jason is definitely not a lichenologist, but we are excited to apply genomic approaches to the study of this fascinating symbiosis.
Jesús Peña introduces his research on sexual reproduction in the zygomycete fungi in the lab through a new video as part of the UCR Microbiology Graduate Ambassador. Have a watch and learn more about the research Jesús is working on.
The end of summer meant goodbye to our excellent REU student Saisuki Putumbaka. Suki was here for two months and worked on fungal-bacteria interactions project as part of the UCR Research Experiences for Undergraduates organized through the Center for Plant Cell Biology. Under the guidance of Derreck she tested ideas about the bacteria harbored by a broad range of zygomycete fungi from our draft genome sequencing projects. She also learned how to take pictures of some of these fungi and observing how they sped up the rotting process in fruit. Alas the best laid plans to compare microbiomes of these samples did not come to fruition but I think there were some lessons in there about how science works some of the time.
It was really a joy having her in the group and we are excited about her finishing her senior year at The College of New Jersey and applying to graduate school next. Many of the lab members helped to make sure Suki was properly introduced her to Southern California delights from Joshua Tree National Park, the Pacific Ocean, and In-n-Out Burger.
I am delighted to announce that Yan Wang a current postdoc in our group, will be a starting his next position as an Assistant Professor in the Department of Biology at the University of Toronto-Scarborough. Yan has spent the last two years in the lab working on Zygolife and Neocallomastigomycota fungi projects. We are super proud of all he has accomplished in his training and research. This includes multiple publications from his thesis work and several papers submitted from his current projects. The lab has greatly benefited from his phylogenetic and insect-fungi expertise. Luckily we still have ~6 more month together to continue projects and help him prepare for his next step in his career.
Congrats Derreck! He was selected by the California Council on Science and Technology (CCST) to give a presentation and represent Dept of Microbiology and Plant Pathology and UCR at the California Science Translators Showcase. He will be giving a talk about his research at the California State Capitol to legislators/state senators, agency managers, and senior policy leaders. He was chosen out of a pool of California PhD students, post-docs, and career scientists from all different STEM fields and universities to talk about plant pathology/fungi.
Nat visited New Mexico State University several times this summer to complete work at the Jornada LTER site working with Nicole Pietrasiak (@drylandalgae) on the micro- and myco-biomes of biological crusts. Visits to Anza Borrego and Boyd Deep Canyon for Tania to scope out UCNRS research sites to explore desert rock varnish and rock or crust associated black fungi. Julia continued to develop her Joshua Tree research sites for lichen studies and has collected and sequenced new accessions for a reference library of lichens from Joshua Tree NP.
There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.
Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, a ascomycete black yeast, complemented some reference genome work we published last year . Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc . Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolifeproject here . Graduate students Nat Pombubpa collaborated with Plant Sciences and Jeff Diez lab graduate student Courtney Collins on her thesis work looking at the mycobiome differences of soils in an alpine gradient with and without invasive shrub introduction . Andrii Gryganskyi’s work on Rhizopus phylogeny with some of the first multi-genome work on this genus that was one of the earliest collaborations on some ZyGoLife questions questions . Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska . A collaboration lead by Tom Richard’s lab and Guy Leonard sequence and assembled and annotated a genome of a ‘pseudofungus’ hyphochytriomycete called Hyphochytrium catenoides . I think I forgot to also call out that last year postdoc Jinfeng Chen published work collaboratively with postdocs Lu Lu and Sofia Robb on the active Rice transposable element system mPing and Ping .
Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol.2018 Apr 19. doi: 10.1111/mec.14694.
Last week we hosted several visitors from our ZyGoLife collaborative team in sunny California. I wrote a few notes on Nicole Reynolds and Javier Tabima’s visit for the zygolife site on their extended research stay. We also got to host the Zygofornia Zygolife team meeting. Here are some pictures I took from the desert and mountain visits.