Here’s a fact: there are a lot of bacteria and fungi on our planet. You’re probably used to hearing about these mighty microorganisms in terms of their interactions with us: they give us food like bread, cheese, and beer, help digest these foods, and occasionally get out of hand and make us sick, among many other things. However, this anthropocentric view often ignores the fact that these microorganisms spend a lot more time interacting with each other than they do with us—and down in their world, the competition can be fierce.
Phoebe Hsieh, a postdoctoral fellow in the Malik Lab at Fred Hutch, spends a lot of her time thinking about how microbes interact and evolve. “We know a good bit about how different bacterial species compete with each other for limited resources, and we know some about how different fungal species do the same. But we know much less about how bacteria and fungi interact with each other, even though they often coexist in polymicrobial communities, including in contexts important to human health like the gut or certain infections.” To fill this knowledge gap, Hsieh took two common model organisms—a bacterium called Pseudomonas aeruginosa and a fungus called Candida albicans—and performed a fairly straightforward experiment: she cultured each separately, cultured the two together, and compared their growth in each case.
Right away, these experiments revealed an interesting phenomenon: while C. albicans was just as happy growing by itself or with its bacterial counterpart, P. aeruginosa grew at least an order of magnitude slower in the co-culture setting. To figure out which P. aeruginosa genes may be involved in competition with C. albicans, the team implemented a genetic loss-of-function screen in which transposons targeting every P. aeruginosa gene were inserted into the bacterial genome (one transposon per cell) before they were grown alone or with C. albicans and the resulting population transposon frequencies were determined using sequencing. In this way, transposons targeting genes that protect P. aeruginosa from C. albicans antagonism would become underrepresented in the population. Strikingly, this experiment revealed eight genes uniquely required for P. aeruginosa growth in the co-culture setting—even more surprisingly, three of these genes are genomic neighbors. “Of these three genes, the only one which has been characterized to date, MgtA, encodes a transporter for magnesium,” notes Hsieh.
Could it be that P. aeruginosa competes with C. albicans for magnesium? After confirming that P. aeruginosa lacking MgtA grew slower in the presence of C. albicans, and that P. aeruginosa grown in ‘spent media’ from C. albicans had lower magnesium levels, they performed another relatively simple but telling experiment: they co-cultured these two organisms in media supplemented with extra magnesium. Indeed, boosting magnesium levels rescued the harmful effect that C. albicans had on growth of most P. aeruginosa mutants—after repeating their genome-wide screen above in magnesium-supplemented media, Hsieh and colleagues were surprised to find that most of their previous gene hits (genes which were important to maintain P. aeruginosa growth in the presence of C. albicans) were no longer deleterious in magnesium-replete conditions! Finally, Hsieh and colleagues showed that competition for magnesium occurred between several other bacteria-fungal species pairs, suggesting magnesium as a generalizable axis of nutritional competition between these two microbes. “While competition for other essential metal ions in the microbial world has been studied before,” notes Hsieh, “this work is the first to demonstrate that magnesium can be a growth-limiting nutrient source in co-culture settings.”
What might this fierce competition for magnesium between bacteria and yeast mean for human health? When Hsieh and colleagues took a closer look at the roles of magnesium in bacterial biology, they were interested to find that one specific class of bacteria (called ‘Gram-negative bacteria’) use magnesium to stabilize their protective outer membranes—structures which are targeted by a class of last-resort antibiotics called polymyxins. “Previous work has discovered bacterial signaling pathways which respond to magnesium limitation and foster resistance to polymyxin and similar antibiotics,” notes Hsieh, “so we wondered whether magnesium depletion by fungi in the co-culture setting might therefore promote bacterial polymyxin resistance.”
They showed that this was indeed the case, but they took it a step further—they co-cultured their two model microbes for 90 days while steadily ramping up the dose of polymyxin E in their media. As expected, P. aeruginosa grown this way showed markedly increased polymyxin resistance at the end of this experiment, but the real surprise came when they separated the bacteria from their C. albicans roommates—their polymyxin resistance disappeared (in a magnesium-dependent manner)! “These were pretty surprising results, suggesting that in long-term polymicrobial communities, fungi may modulate the antibiotic resistance of their bacterial counterparts, in part through sequestering magnesium,” says Hsieh.
“Of course, there’s still plenty that we don’t know about how this interaction works—we’re currently looking into the functions of the uncharacterized bacterial genes that came up in our screen, and we’re studying how exactly fungal magnesium sequestration alters the trajectory of evolving polymyxin resistance in bacteria. Considering the increasing threat of antibiotic resistance in polymicrobial infections, we think investigating this novel axis of inter-species nutritional competition may bring new strategies to overcome antibiotic resistance and better understand microbial evolution,” says Hsieh. So, the next time you’re arguing with your roommates about who ate the last frozen pizza, consider that this concept may have far-reaching implications for the structure and evolution of the rich microbial ecosystems that surround us, feed us, hurt us, and everything in between.
The spotlighted work was funded by the National Institutes of Health, the Cystic Fibrosis Foundation, Howard Hughes Medical Institute, and the Burroughs Wellcome Fund.
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium members Dr. Harmit Malik and Dr. Ajai Dandekar contributed to this study.
Hsieh Y-YP, Sun W, Young JM, Cheung R, Hogan DA, Dandekar AA, et al. (2024) Widespread fungal–bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLoS Biol 22(6): e3002694.
Science Spotlight writer David Sokolov is a graduate student in the Sullivan Lab at the Fred Hutch. He studies how cancer cells modify their metabolism to facilitate rapid proliferation and accommodate tumor-driving mitochondrial defects. He's originally from the east coast and has bachelors' and masters' degrees from West Virginia University. Outside of the lab, you'll find him enjoying the outdoors, playing music, or raising composting worms in his front yard.
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