Seeking a Biological Tinkerer

Posted on December 8, 2023 by Daniel Kelley in Announcements

Join the Forest Entomology team at the University of Florida (www.ambrosiasymbiosis.org or www.ambrosiasymbiosis.org/development) for a project on perfecting bark beetle sampling and sample digitization.

Details

We are looking for a team member who will help us optimize bark beetle pheromone trapping, photography pipeline, quantification, and submission to an AI classifier. The ultimate goal is biodiversity research and invasive species detection.

We are open to applicants from various levels of education and experience, from a recent graduate to a post-doc or a technician. Both academic and non-academic applicants are welcome. Previous experience with insect sampling is appreciated but not required. What we value the most is interest in messing around with sampling technology, commitment to quantitative science, good organization and project management skills, and good writing skills.

Training in bark beetle systematics will be provided.

Publication of at least one research paper, based on the data collected, will be required as part of this position.

Duration

This is a temporary position spanning one (1) year following hire in Spring 2024. An extension to two years is possible, depending on performance and funding availability.

Dates

Application deadline: January 6, 2024.
Start: AS SOON AS POSSIBLE in Spring 2024

Salary

The salary for this position ranges from $35,000 – $50,000 depending on the level of experience.

This position is intended to be a full-time, 40-hour-week position, but this is negotiable.

Location

This job is located on the main campus of the University of Florida in Gainesville, FL, and though remote work may be acceptable at certain times, applicants should expect to spend the majority of their week on-site.

Applying

Please note that international applicants must have a valid US visa and be able to work in the United States. International applicants who are ALREADY approved to work in the US are welcome to apply.

Email 1) your CV, 2) a short statement of interest, and 3) a list of your hobbies to ForestEntomology@ifas.ufl.edu with the subject line “Beetle samples 2024”.

New Experiment to Study Introduced Wood Decay Fungi

Posted on May 30, 2019 by jirihulcr in Uncategorized

The UF Forest Entomology Lab is embarking on a new set of experiments to better understand a recent pair of invaders that could potentially have an outsized impact on the environment. The ambrosia beetle Ambrosiodmus minor and its fungal symbiont Flavodon ambrosius are a pair of introduced species from Southeast Asia which are unusual because unlike most beetle-borne fungi, F. ambrosius is a wood-decaying fungus.

Among approximately 3,000 species of ambrosia beetles, which transport and cultivate specific fungi that serve as their sole source of food, only five are currently known to carry fungi that decay wood (though it is likely that there are more to be identified). Flavodon‘s ability to decay wood could have a broader effect in its introduced environment, impacting the forest microbiome.

“Flavodon offers an example of how [introduced beetles] might be kind of quietly changing ecosystem dynamics,” says Dr. James Skelton, part of the team researching the invasion, “introducing a fungus that is breaking down wood, getting there faster than other decay fungi, perhaps competing with native fungi and excluding native biodiversity.”

“Flavodon seems to out-compete other decay fungi,” says Demian Gomez, a PhD candidate leading the new study. “This fungus can grow really fast and outpace the other decay fungi.”

The first specimens of A. minor and Flavodon in North America were found in Jacksonville, Florida in 2011. Since then, the symbionts and their hosts have spread rapidly and become one of the most common species of ambrosia beetles in Northern Florida. They have also been collected in Georgia, Alabama and Mississippi. Analysis of their native range in Asia suggests that the beetles and fungi will probably be able to tolerate cold weather well enough to continue moving north into the forests of the mid-Atlantic.

A. minor can colonize many species of tree and is not specific to any particular clade of host plants. Even pine trees, with their unique set of chemical defenses, can be colonized. However, the beetles have not yet been observed attacking healthy trees. They target dead and dying hosts.

The experiment beginning this month involves inoculating 21 wooden logs with Flavodon. A control group of 21 identical logs were not inoculated. Innoculation was accomplished by drilling out a dozen holes in each log and filling them with wooden pegs pre-colonized in the lab with Flavodon. The control group received sterilized wooden pegs. The logs will be left in a forest for approximately seven months and then sampled to determine the composition of their respective fungal communities.

“We’ve seen that Flavodon is pretty aggressive,” Gomez says. “We’re going to test how it actually effects the natural communities of fungus. We want to quantify exactly how aggressive it is competing against other species in the fungal community.”

“These beetles are very abundant, they’re infesting a lot of trees and they are bringing in a novel fungus that is capable of doing pretty extensive decay,” says Skelton. “And that entry into the wood that Flavodon has is pretty unique among decay fungus. Most of them have to get in through wind blown spores, or wait for a limb to break… but having a beetle to fly you around and bore a hole through the bark and innoculate that fungus into freshly dead wood is an advantage that pretty much no other decay fungus has.”

“We might see increased decomposition rates and consequently more carbon released as CO2 as the wood decomposes,” Skelton says.

Sentinel Garden Project Set to Start in China

Posted on May 8, 2019 by jirihulcr in Uncategorized

With the coming of summer, the UF Forest Entomology Lab has two big things to look forward to. An increase in observable beetle activity, and the opportunity to step away from the classroom and lab to find out what’s happening in the field.

PhD candidate A. Simon Ernstsons will spend three months organizing field work in China that is critical to the future of the lab and for establishing a better way of preventing destructive outbreaks of forest pests. Ernstsons will be spearheading the lab’s new sentinel garden project aimed at identifying future pests before they even arrive in the US.

Ernstsons must find his way around several regions of rural China, obtain hundreds of trees of American commodity species that are rare in Asia, transport them to remote planting sites, then monitor them for damage by local insects. Some of the trees will be deliberately stressed to simulate the effects of flooding and drought.

“Then we have a really important data point where we know something potentially dangerous is in a certain area,” Ernstsons says. “We can then feed back that information back to USDA [division of Animal and Plant Health Inspection Service] and it can influence things like bio-security measures, phytosanitary control, that sort of thing.”

Sentinel gardens are a relatively new concept already being explored between France and China by Dr. Alain Roques and his team at the French National Institute for Agricultural Research. There is currently no equivalent involving the United States, though botanical gardens may notify one another when they notice a new pest on an exotic tree.

Organizing an experiment like this is not an easy task. Layers of government bureaucracy, cultural differences, and language barriers make it difficult to design and monitor an experiment involving hundreds of trees that are scarce in China. Fortunately, Ernstsons (who speaks five languages, including Mandarin), has experience with a small-scale pilot project for the lab last summer.

“Imagine trying to arrange two hundred trees to be delivered to a village on the side of a mountain in the middle of rural China, how would you go about doing that and how difficult do you think would that be?” Ernstsons asks. “That’s my experience. Going out and doing those kinds of things with local scientific collaborators, but also collaborators for logistics, things like sourcing and buying the trees.”

The work is funded by grants from USDA’s APHIS through the Plant Protection Act, section 7721.

As invasive beetles including the emerald ashborer and the Asian long-horned beetle continue to destroy American trees, could those infestations have been prevented by sentinel gardens? Ernstsons believes so.

“We certainly could have known well in advance and tried to put measures in place. Once it’s arrived we’ve seen again and again that ninety nine percent of the time it’s a losing battle.”

AI Bark Beetle Identifier

Posted on July 14, 2023 by Lauren Nigri in Announcements

Our Sentinel Gardens in Asia

Posted on July 14, 2023 by Lauren Nigri in Announcements

ERUDITUS bark beetle identification training app

Posted on June 19, 2023 by jirihulcr in Announcements

Need to train your bark beetle identification skills? Do you want to skip character-based keys and practice your “gestalt” (identification by the overall morphology using your expertise)? Try the new app ERUDITUS, available for download on your smartphone from Apple Store and Google Play.

It is not an Artificial Intelligence-based app for beetle identification magic. It trains YOU! Your human intelligence :). The Entomology Today newsletter describes it here: https://entomologytoday.org/2020/10/07/bark-beetle-identification-app-for-that-eruditus/

New Geosmithia review

Posted on June 19, 2023 by jirihulcr in Announcements

Discovered relatively recently, these bark beetle-associated fungi are ubiquitous in the scolytine realm. But not where the Ophiostomatoid fungi reign. https://link.springer.com/article/10.1007/s11557-023-01880-x

The Spruce Bark Beetle versus the People

Posted on May 14, 2023 by jirihulcr in Announcements

PhD in quantitative biology focused on bark beetles

Posted on August 17, 2022 by jirihulcr in Announcements

Join the Forest Entomology team at the University of Florida (www.ambrosiasymbiosis.org) on our quest to understand forest insects and their evolution, ecology and systematics using cutting-edge biology methods.

This position can be focused on several topics:

systematics and phylogenetics
artificial intelligence (machine learning) in beetle identification
genetics, genomics or transcriptomics of the beetles
biodiversity information management

We appreciate previous experience with some of these fields, but it is not required. What we value the most is a commitment to rigorous science, love for numbers and data, good writing skills, and some biology nerdiness.

Dates

Applications are due on February 20, 2022.
Start: ideally in the Fall 2023.

Salary

The fully-funded PhD student position includes a $30,000 annual stipend, University of Florida tuition, health insurance, and research expenses (the total value of this position is over $200,000). Opportunities for international travel, conference visits and collaborations will be regularly available. International students are encouraged to apply.

Location

The main campus of the University of Florida in Gainesville, FL. Gainesville is one of the best college towns in the U.S.

How to apply

Email 1) your CV, 2) a short statement of interest and 3) a list of your hobbies to hulcr@ufl.edu with subject line “Beetle data science 2023”.

POSTDOC: Ambrosia symbiosis transcriptome

Posted on August 12, 2022 by jirihulcr in Announcements

The University of Florida Forest Entomology Lab is offering a postdoc position to study the molecular interactions between the insect tissue and the fungus in the ambrosia symbiosis.

We have the data; we need you to analyze them!

We have several transcriptome sequence datasets for the different tissues (fungus-free beetle, pure fungus, and the mycangium where the two unite) and we need a smart molecular biologist or bioinformatician to interpret what makes the two organisms talk. We also have a genome sequence of the beetle.

Previous experience with transcriptomics, insect of fungus molecular physiology, or other fields of bioinformatics and molecular biology will obviously be a bonus. Independent publication experience is required (the output of the project is not just the analysis, but a paper). Innovative interdisciplinary ideas about symbiosis functioning are welcome.

The position includes annual stipend of $60,000 and health insurance. The initial contract is for one year with high likelihood of extension to multiple years depending on productivity. The position is based at the University of Florida, Gainesville, FL. Partial remote work is acceptable, but is not a complete home office; we do need the postdoc to appear in the lab at least sometimes. International applicants are welcome.

NEW Application deadline: September 15, 2022.

Start date: ideally in the fall of 2022 or early 2023.

To apply

Send an email to hulcr@ufl.edu and include 1) Cover Letter, 2) your CV, and 3) a list of hobbies and interests.

Beetle-fungus postdoc

Posted on March 30, 2021 by jirihulcr in Uncategorized

The University of Florida Forest Entomology Lab is offering a postdoc position to study various aspects of the bark beetle-fungus symbiosis and its effect on trees.

The topic is open-ended

The applicant will decide, together with our team, the topic they will pursue. It should be related to the relationship between bark/ambrosia beetles and fungi, ideally using molecular biology or quantitative/statistical methods. Previous experience with molecular biology or statistical ecology experience would be a bonus.

Topics that we are seeking to develop include:

DNA or RNA metabarcoding of fungal communities
the transcriptome of the mycangium
genome features in the beetles and/or the fungi related to the symbiosis
fungus community analysis, network analysis or modeling
physiology of trees under attack
pest and disease diagnostic tools
invasive beetle/fungus assessment
forest pests in Asia
policy and regulation of threats to forest health

Other topics are available, and we welcome the candidate’s personal research preferences.

Includes annual stipend of $50,000 and health insurance. The initial contract is for one year with high likelihood of extension to multiple years depending on productivity. The position is based at the University of Florida, Gainesville, FL, but can include cooperation with colleagues at other institutions. International applicants are welcome.

Application deadline: Until filled.

Start date: any time during 2021 or early 2022.

To apply

Send an email to hulcr@ufl.edu and include 1) Cover Letter, 2) your CV, and 3) a list of hobbies and interests. Specify which of the two positions you are interested in.

POSTDOC or PhD: invasive wood borers

Posted on February 3, 2021 by jirihulcr in Uncategorized

Interested in invasive species and international field work? Join our team in an exciting project:

Pre-invasion assessment of Asian wood borers by sentinel gardens

We are looking for a PhD STUDENT or a POSTDOC to manage existing sentinel gardens in China and to collect unique data on high-priority, potentially invasive wood boring insects. What is a sentinel garden? See the coverage of our project in Science: Scientists plant ‘sentinel trees’ to warn of devastating pests.

Our first round of results is very promising, see the video below:

The position is fully-funded, and includes annual stipend ($26,000 for a student, $50,000 for a postdoc), health insurance, research expenses, and visa assistance.

The PhD graduate assistant contract is for 4 years. Postdoc contract is for one year with high likelihood of extension to multiple years depending on productivity. The positions are based at the University of Florida, Gainesville, FL, but will include substantial field work in Asia, most likely China. Opportunities in cutting-edge research technology, conferences and collaborations are regularly available. International applicants are welcome.

Colleagues from China are welcome to apply for this position. We completely understand the difficulties with current visa policy and travel. If you are interested in working with us but are concerned about your ability to join an American institution, let’s get in touch to start the conversation.

The project will focus on one main research direction:

Interactions between Asian wood borers and American trees in our network of sentinel gardens in China.

Additional topics that the applicant is welcome to develop include:

Beetle or fungus molecular and traditional systematics or ecology.
Host tree physiology and response under stress.
Translation of invasion science to policy, collaboration with agencies.

Previous experience with beetle research is not necessary. Experience with invasion ecology, systematics, tree physiology or statistics is a bonus.

Application deadline

March 12, 2021.

Start date

Any time during 2021, the earlier the better.

To apply or to inquire, send an email to hulcr@ufl.edu and include 1) Cover Letter, 2) your CV, and 3) a list of your interests and hobbies.