A trait-based framework for linking microbial communities with carbon transformations under precipitation change
Droughts are common throughout the world. As the climate changes, droughts may become more frequent and intense. Still, scientists are uncertain about how drought will affect the natural world, particularly the bacteria, fungi, and other microbes that live in soils. These tiny life forms are crucial because they control the Earth’s flows of carbon and essential nutrients. Researchers at the University of California, Irvine, and Lawrence Berkeley National Laboratory teamed up to study how the microbiome, or collection of bacteria and fungi in the soil, deals with drought. Since 2007, the researchers have used shelters with retractable roofs to prevent nearly half of normal rainfall from reaching grass and shrub ecosystems, and their soil microbiomes, in Southern California. The study team discovered that microbes have some clever tricks up their sleeve for surviving drought. When growing on dead grass as a food source, microbes ramp up production of specialized chemicals called osmolytes that keep their cells from drying out. But microbes growing on dead shrubs face another problem. Unlike grass, shrub leaves are a lousy food source. To digest and consume shrub leaves, microbes have to exude more enzymes, which act like biochemical chef knives that chop complex leaf molecules into bite-sized pieces. Carbon is the coin of the microbial realm, earned via enzyme action or slurping up dead plant juices. Microbes growing under normal conditions on tasty dead grass have it easy: they can spend most of their carbon currency on growth. With drought, life gets harder as microbes need to pay up for osmolytes and ramp down their growth. It gets worse with shrub leaves because microbes have to multi-task among growth, enzyme secretion, and osmolyte production. When drought hits, microbes on shrub leaves forgo the osmolytes, probably because losing the carbon revenue from enzyme investment would be a deal-breaker for survival. The next question tackled by the researchers asked how the genes controlling microbial lifestyles sort out across the tree of life. Most microbiologists thought these lifestyles would correspond to rather large branches on the tree. But the study team found that in fact, very closely related microbes differ in important and interesting ways. For example, bacteria that have nearly identical housekeeping genes respond distinctively to warming, rainfall, and plant chemistry. As a result, soil microbiomes are much richer in diversity than originally thought. And studying microbial diversity in much greater detail could open up many more possibilities for how microbial life deals with changing environmental conditions. Trying to understand microbial life without the fine details of genetic diversity is like trying to stream Netflix on a dial-up connection. By looking across the landscape, the researchers revealed that microbial diversity is absolutely critical for maintaining the planet’s flows of carbon and nutrients. The study team designed a new technology—microbial cages—for transplanting intact microbiomes. With the cages, the researchers could move microbiomes to novel environments and compare their ability to cycle carbon and nutrients. In some cases, performance tailed off when microbiomes found themselves in a new environment, but in other cases, performance rivaled or even exceeded that of the resident microbiome. And even the low performers eventually caught up to the native microbiomes if given sufficient time. These findings mean that microbiomes—at least in Southern California—may be resilient to climate shifts due to a high diversity of microbial lifestyles. Coping with heat and drought may literally be in their DNA. The last piece of the research puzzle, and a “Holy Grail” for microbial ecologists, is to forecast the behavior of diverse microbiomes. To meet this challenge, the study team developed new theory and computer models. For the first time, these models account for hundreds of different microbes and how their intricate lifestyles cope with drought. The models are starting to connect the tiniest microbes with the global cycles that sustain Earth’s farms, fields, and forests. With that connection, it will be easier for society to plan for a world with more droughts and other climate disruptions.