This work was led by the fantastic Dr. Lauren Krausfeldt, who is currently working with NIAID. This field-to-lab project was challenging and required a ton of perseverance on her part, especially during the social distancing era. I was just happy to be along for the ride.

Overall, these shifts in transcriptome provide us critical information on the activities of Microcystic during bloom and may hint at ways to disrupt bloom intensification and persistence.

Later in the bloom, we found that genes involved in phage protection and toxin production were upregulated. Here, we think Microcystis is activating genes that protect itself against microbial competitors and phage, which may be critical to promoting bloom stability and persistence.

When fed nitrogen, we first saw an increased transcription of genes involved in photosynthesis and nitrogen import. Here, we think Microcystis is working hard to consume as much nitrogen and sunlight as possible to drive the bloom.

We found striking temporal shifts in the transcriptome of Microcystis, which provide insight into how it intensifies and sustains the bloom.

Blooms can often appear ‘out of nowhere’, making the understanding of the transcriptional changes that drive them hard to study. To meet this challenge, we created mesocosms in a river undergoing a bloom. We fed the mesocosms nutrients that drive blooms and measured the transcriptome daily.

In freshwater lakes, the cyanobacteria Microcystis sp. can cause toxic algal blooms that can kill off wildlife, contaminate drinking water, and injure humans. The intensity and frequency of these blooms have been increasing, driven by anthropogenic factors and climate change.

This study was led by the fantastic undergraduate student Daniella Hernandez, along with an all-star cast of undergraduates, graduates, post-docs, and collaborators, including @ajlopatkin.bsky.social and her team. Congrats to everyone involved!!!

Why this occurs, we don’t know yet, but we are eager to find out. Nevertheless, this work underscores the importance of nucleotide synthesis in determining density-dependent antibiotic resistance

Surprisingly, we found pyrimidine synthesis activity predicts the inoculum effect for aminoglycoside antibiotics, while purine synthesis activity predicts the inoculum effect for B-lactam antibiotics.

We also found that these changes were highly correlated to the strength of the inoculum effect for multiple antibiotics. To develop this further, we examined transcription in purine and pyrimidine synthesis pathways and asked how they could predict changes in the inoculum effect.

This alluded to the role of nucleotide synthesis in the inoculum effect. To test this, we experimentally perturbed nucleotide synthesis in E. coli. We found that this increases bacterial metabolism and reduces growth rate, as predicted in our model.

However, we didn’t know what pathways were responsible. To answer this question, we used an E. coli metabolic model and individually knocked out all of the genes in silico. We found that removing genes in nucleotide synthesis increased metabolism while reducing growth.

Our previous work showed that interactions between bacterial metabolism and growth can explain density-dependent antibiotic resistance, also known as the inoculum effect. When metabolism is greater than growth, bacteria can no longer resist antibiotics using their density.

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