Summer Science Book Club

This website serves as the homepage for #microjc, a summer science book club. Each summer, we select a theme and read three books on that theme: one in June, one in July, and one in August. See the menu for archive pages of past book clubs. Our online discussions bring together scientists of different fields from across the globe. All are welcome to join us. Please contact Laura Williams via Twitter (@MicroWavesSci) or email (lwillia7 at providence dot edu) with any questions.

Below is the archive for a monthly journal club that ran from 2015 to 2018 (until my professoring duties made it too difficult to keep up!). All of our past book club and journal club discussions are available on our YouTube channel.

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Thursday, March 29 at 3 pm ET: Attack of the giant viruses!

Whenever I teach a microbiology course, we always spend a bit of time at the beginning of the semester discussing whether or not viruses are alive. Most of the time, we’re focused on familiar viruses such as influenza and rhinovirus. But giant viruses such as Mimivirus challenge some of our assumptions about viruses. Their genomes are often much larger than typical viruses and encode multiple functions. In this paper, the authors describe the discovery of Tupanvirus, a giant virus with many translation-related genes. What does this mean for viral evolution? Does this change whether or not we consider viruses as living organisms? Join us for the attack of the giant viruses!

Link to paper: https://www.nature.com/articles/s41467-018-03168-1

Link to join Hangout: https://hangouts.google.com/hangouts/_/qnobxu2ixzhfthnpga5snzybzie

Thursday, February 22 at 3 pm ET: Horizontal gene transfer and bacterial evolution

Horizontal gene transfer (HGT) occurs when one bacterial cell “donates” DNA to another bacterial cell. This phenomenon is a contributor to the growing problem of antibiotic resistance, in that bacteria are not constrained to de novo mutations in order to become resistant, but can also acquire genes encoding antibiotic resistance via HGT. How the process of HGT impacts bacterial evolution is a complex question. In this paper, Rohan Maddamsetti and Richard Lenski use experimental populations from Lenski’s long-term evolution experiment with E. coli to investigate how HGT affects genome evolution. What is the impact of HGT on population variation? How does selection act on the “donated” sequences? As the 30th anniversary of the LTEE approaches, join us to discuss this paper!

Link to paper: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007199

Link to join Hangout: https://hangouts.google.com/hangouts/_/euxytatgwjbijpcm5m4e4nycdee

Thursday, January 25 at 3 pm ET: Genomic view of population-level heterogeneity

We know that bacteria are important members of ecosystems, but we don’t have a good handle on the population structure of bacterial communities in different ecosystems. How should we define genetically and ecologically distinct populations? How do these populations vary over time? In this paper, researchers use single-cell genomics and metagenomics to investigate bacterial population structure in four freshwater lakes. They specifically focus on particular lineages of Actinobacteria and Alphaproteobacteria. First, they compare single-cell genomes from these lineages and assess sequence similarity across the genomes. Then, they use these genomes as references to recruit reads from a metagenome time series. They find “sequence-discrete populations”, some of which appear to be ecologically distinct as well. These findings and methods contribute to our understanding of bacterial communities and microbial ecology in general.

Join us to discuss the paper! Link to paper: https://www.nature.com/articles/s41396-017-0001-0

Link to join our Hangout: https://hangouts.google.com/hangouts/_/rgthozwe3nfmjd6br5xgob3hbie

Thursday, November 30 at 3 pm ET: Phage and cheating in Pseudomonas

Some bacteria can detect the numbers of their neighbors using a mechanism called quorum sensing. When bacteria reach certain cell densities, quorum sensing signals can turn on or change expression of particular genes. In Pseudomonas aeruginosa, this includes expression of virulence factors, which impact the bacterium’s ability to cause disease. Not all Pseudomonas cooperate, though. Some bacterial cells are “cheaters”. Their quorum sensing systems are deficient, so they don’t turn on expression of the virulence genes. Instead, they use the secreted virulence factors produced by their neighbors.

So why don’t cheaters take over? In this paper, a group of researchers from Mexico, Germany, Japan and the U.S. studied the role of lysogenic bacteriophage in controlling cheaters. For the phage they tested, they found that phage infection can reduce the proportion of cheaters in a population. The phage attach preferentially to Pseudomonas mutants that are deficient in their quorum sensing systems.

What does this mean for understanding the sociality of Pseudomonas? Does this have implications for phage therapy as a treatment for bacterial infections? Join us on Thursday, November 30 at 3 pm ET to discuss!

Link to paper: https://www.frontiersin.org/articles/10.3389/fmicb.2017.01669/full

Join our Hangout by clicking this link: https://hangouts.google.com/hangouts/_/yn2fd3igl5brzpngkfi5m53mome

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