Journal Club Announcements

This website serves as the homepage for #microjc, an online microbiology journal club hosted by Karen Lo and Laura Williams. Once a month, we discuss an interesting paper in microbiology, bringing together scientists of different fields from across the globe (one of the great strengths of online journal clubs!).

We are always glad for new people to join our discussions. Watch the space below for information on upcoming journal clubs. A few minutes before the discussion is set to start, we’ll update the relevant post with the link to join our online video chat (broadcast to YouTube). All you need to do is click on the link to join us. If you have questions or trouble connecting, feel free to contact Laura (@MicroWavesSci) or Karen (@kareynlo). You can check out our past discussions at our YouTube page.

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Thursday, October 26 at 3 pm ET: Mutation rate and population density

Mutation generates the raw material on which natural selection acts. The mutation rate of an organism reflects the balance between the occurrence of errors in DNA and the organism’s ability to repair these errors. In PLoS Biology this past August, a team of researchers in the UK investigated how population density affects the balance between error rate and repair, thereby influencing the mutation rate of an organism. In the paper, they describe a phenomenon called density-associated mutation-rate plasticity (DAMP), in which the mutation rate is inversely correlated with population density. They find this phenomenon in bacteria, eukaryotes and viruses, and they consider how DAMP might impact evolutionary trajectories.

Join us Thursday, October 26 at 3 pm ET to discuss mutation rate, what factors influence mutation rate, and how this might impact our models and tests of evolution. All are welcome!

Link to the paper: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002731

Link to join our Hangout: https://hangouts.google.com/hangouts/_/55ueq565rvh3ti57d2eha2nnwqe

Thursday, September 28 at 3 pm ET: Time to talk taxonomy

To steal a saying from Benjamin Franklin: nothing is certain in biology except death and taxonomy. For our first #microjc of fall 2017, we’ll tackle taxonomy. In particular, we’ll discuss two recent papers on taxonomy and systematics. For our first paper, Holly Bik argues in PLoS Biology for renewing our focus on taxonomy and partnering traditional approaches with -omics techniques. This perspective piece uses nematodes as a specific example, but the argument applies to the myriad microbes in the world, including the oft-overlooked protists. For our second paper, Dave Baltrus (a #microjc member!) considers the bacterial side of things in a Trends in Microbiology opinion piece, using the complicated case of Pseudomonas taxonomy to illustrate the challenges facing bacterial taxonomy in a time of rapidly multiplying genome sequences.

Join for us a lively discussion on Thursday, September 28 at 3 pm ET!

Link to Holly Bik’s PLoS Biology paper: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002231

PDF of Dave Baltrus’ Trends in Microbiology opinion piece baltrus_trends_2016

Friday, May 5 at 2 pm ET: Processes shaping microbiome of bromeliad plants

In microbiome studies, researchers often consider both taxonomic composition (what bacterial taxa are there?) and functional capacity (what can these bacteria do?). In this paper, researchers looked at the microbial communities in the “tanks” of bromeliad plants. These “tanks” are central cavities that collect rainwater and organic material. The researchers used 16S rRNA gene data to detect different types of bacteria and classified these bacteria into one of nine metabolic functional groups. They then examined the taxonomic composition within each of these groups. What processes, such as environmental filtering, random demographic drift or biotic interactions, affect the composition of these functional groups? Join us Friday May 5 to discuss!

Link to paper: https://www.nature.com/articles/s41559-016-0015

Link to join Hangout: https://hangouts.google.com/hangouts/_/dxrz43wldbeutbn2faynfr7uzme

Thursday, March 23 at 3 pm ET: Ancient genes in modern times

What happens when a time-traveling gene is plunked down into a modern bacterial genome? How does the ancient gene sequence evolve? What adaptations occur across the modern genome? In this week’s #microjc, we’ll discuss a paper in which the authors used phylogenetic inference to go back ~700 million years and reconstruct the gene sequence of a protein important for bacterial translation (EF-Tu). They then replaced the modern gene sequence in an E. coli genome with this ancient sequence and grew the hybrid over thousands of generations in the lab. Just like Sean Astin and Pauly Shore thawing out Brendan Fraser, we’ll discuss what happens when ancient and modern collide (yes, that was an Encino Man reference). Join us!

Link to paper (open access): http://link.springer.com/article/10.1007/s00239-017-9781-0

Link to join Hangout: https://hangouts.google.com/hangouts/_/lajut3szxfg7blnizwiivjr4iye

Thursday, February 23 at 2 pm ET: Modeling biotic interactions in soil biogeochemistry

In this edition of #microjc, we’ll discuss a recent review and synthesis paper exploring models of soil biogeochemistry. These models are valuable for understanding and predicting the outcomes of climate change and environmental disturbances. However, the authors of this paper argue that current models don’t adequately consider biotic interactions, such as predation and competition. What exactly is missing from these models, and how can we improve them? We’ll tackle this topic, and I will brush up on my Michaelis-Menten equations. Join us!

Link to paper: http://onlinelibrary.wiley.com/doi/10.1111/ele.12712/epdf

Link to join Hangout: https://hangouts.google.com/call/767gzerhvzcytj3qliggrh3lhae

Friday Feb 3rd at 3pm ET: Microbial metabolites modify fly manners

MicroJC is back from winter holiday! We’re kicking off with a bang, with what could be a landmark paper in host-microbe community interactions. Within a host’s microbiome, each constituent can produce a multitude of metabolites. These metabolites create a chemical mosaic that interacts with other members of the microbiome and the host, which ultimately affects host fitness in a positive, neutral, or negative manner.

If microbiome composition can have a large impact on host fitness, wouldn’t it make sense for the host to shape its own microbiome to maximize fitness? So any animal may change its behavior to acquire certain microbes, much like you or I may choose to eat fermented food or probiotic yogurt. How then specifically do interactions between microbes affect animal fitness? In Elife this month, a group of researchers examine these critical questions by looking at metabolite exchange between microbial species and fruit fly feeding/egg-laying behavior. Join us on Friday, February 3rd at 3PM ET as we look at the first paper to connect these dots.

Link to join our Hangout:
https://hangouts.google.com/call/nzrwwyxl7ff3tpzdpu6sgn2j4ee

Elife paper (open access):

https://elifesciences.org/content/6/e18855/article-data

Wednesday, Dec 21 at 1 pm ET: How bacteria affect multicellular development

How did multicellular life evolve? This is a fundamental question in biology. One way to investigate this question is to probe the developmental programs of organisms like choanoflagellates, protists that are considered the closest living relatives of animals. Some species of choanoflagellates alternate between a single-celled and a multicellular form, called a rosette. The formation of this colonial assemblage of individual choanoflagellates is prompted by cues from environmental bacteria. This system provides a fascinating glimpse into how our own microbial partners may have impacted our evolution as multicellular animals.

In this paper published earlier this year, Nicole King and her colleagues looked at one particular species of bacteria and analyzed how its lipids affect the development of rosettes. Join us on Wednesday 12/21 at 1 pm ET as we talk choanos, bacteria and multicellular life! (You know, just your typical holiday party topics.)

Link to paper (open access): http://www.pnas.org/content/113/28/7894.full

Link to join Hangout is here: https://hangouts.google.com/call/5n3nwj3tubbmnjud3putwlmoqee