the goal, peixoto later explains, is to restore a healthy microbiome to a reef thrown out of whack by coral diseases, triggered by pollution, ocean acidification, and warming waters. 

“we are causing the problem [that is] affecting these microbiomes,” says peixoto, of the king abdullah university of science and technology in thuwal, saudi arabia. “so we need to try to restore it, or at least to protect it to be as similar as what it was before.”

the potential of probiotics

in the coral village, peixoto is testing to see if a carefully curated dose of probiotics – bacteria that are beneficial to its host – could help reduce the bleaching diseases that are killing tropical reefs from the caribbean to australia at an alarming rate. a growing cohort of microbiologists believe that beneficial bacteria, already commonly used as nutritional supplement and agricultural fertilizer, might help not just corals but also many other at-risk animals and plants. led by peixoto, a global group of 25 experts made the argument in a perspective piece published in nature microbiology last year.

the concept of probiotics for wildlife has only been around for roughly a decade, so scientists are still teasing out which bacteria to use as they study the cascades of microbial interactions in both the host species and environment. but with extinctions looming, researchers are hurrying to test probiotics on everything from farmed norwegian salmon to honeybees. so far, most of the tests have been confined to labs, though there have been some small-scale field tests, too. 

in 2019, for example, probiotic expert gregor reid mixed sugar and three strains of lactobacillus bacteria to treat diseased honey bees in ontario, canada. a couple weeks later, larvae from treated hives had significantly fewer pathogens than those from untreated hives. he thinks other combinations of probiotics may be even more effective and is eager to explore the possibilities at a time when bee populations are declining.

“the bees are dying off,” says reid. “and the day they die off, we’re toast as a species.”

frogs are in a similar boat: in recent years, hundreds of frog species around the world have been ravaged by the batrachochytrium dendrobatidis (bd) fungus. in 2011, scientists caught frogs in the sierra nevada mountains that hadn’t yet been exposed to bd and bathed some in water with a naturally-occurring bacteria, and the rest in pond water. a year later, they returned to the site and couldn’t find any of the untreated frogs, but 39 percent of probiotic-treated individuals were recovered, indicating that the probiotics had at least some effect. 

disease ecologist molly bletz of the university of massachusetts at amherst, who studies frogs from madagascar, has also shown that some microbes resist bd in the lab. “it’s complicated,” she sums up, “but with glimmers of hope.” 

one complication is that there are so many potentially beneficial bacteria to choose from, depending on the species being treated and its particular environmental risks. bletz has cataloged over 7,000 amphibian microbes – and scientists aren’t limiting themselves to just the host’s resident microbes. “if it’s a species that is super-susceptible to the disease, maybe they just don’t have the right bacteria,” says bletz. so in other cases – like reid’s bees, which received bacteria harvested from a healthy woman’s urethra way back in 1980 – scientists are experimenting with foreign strains. 

despite all the potential treatment variations, biotechnologist gabriele berg, a coauthor of the nature microbiology piece, says the fundamental practices for microbial interventions are similar. “if it is in our gut, or if it is in the rhizosphere [plant roots], or if it is on the nose of a bat,” she says, “the rules and the principles are the same.” 

recognizing these commonalities, peixoto, berg, and other microbial researchers have joined forces to outline safe steps for any probiotic intervention, whether it be in corals or frogs. their framework, included in the 2022 paper, calls for careful selection of probiotic strains and consideration of environmental impacts, among other recommendations. 

a carefully considered call to action

it’s essential that experts reach a consensus on ethical and safety considerations of these treatments before the technologies are widely used, says rachel backer, an independent scientific consultant based in vancouver who has researched plant-microbe interactions in hops and cannabis. 

what could go wrong if probiotics are let loose in an ecosystem is the kind of question that keeps her up at night, she says.

“these are complex products to regulate, because they’re just inherently complex,” says backer, who was not a signatory on the paper. she argues that the indiscriminate use of antibiotics in agriculture is a precedent to consider. antibiotics were initially seen as a miracle for livestock farmers, backer says, but their overuse has led to pollution and antimicrobial resistance.  “if we keep making the same mistake over and over of not considering these things, it becomes pretty indefensible,” she says. 

peixoto notes that probiotics typically don’t last forever (unless they colonize a host, which can happen). and though she acknowledges the risks, she argues that doing nothing is also indefensible. corals, for instance, have an alarming prognosis; a recent report projected that 70 to 90% of live coral would disappear by 2050. her team is working tirelessly, applying probiotics three times a week to the underwater coral village, while developing an automatic dispenser that can spray probiotics from the comfort of home. peixoto knows that it’s optimistic to be already increasing the efficiency of various treatments when there has been so little field testing. but she sees no other option. 

“we don’t have time. we can’t develop these things one at a time,” peixoto says. “when you’re talking about terminal patients… this is urgent.”

“it looks just like this,” fresno rueda said, displaying the spinach smoothie at her workbench.  

the belly of the beast: studying bison gut bacteria

on the ranch, home to the turner institute for ecoagriculture, fresno rueda is studying the nutrient-processing genetics of bacteria in bison rumen. the rumen is the largest compartment of the bison’s gut. it contains bacterial colonies in its fluid, which break down the animal’s natural diet of prairie grasses and vegetation. 

a symbol of america’s past, the bison is gaining interest from livestock researchers as they look toward a future of declining grassland. 

since the turn of the century, extreme heat and lacking rainfall have ravaged the great plains. as of late september, 50% to 80% of pasture and rangeland in the plains is rated poor- to very poor-quality as a result of drought. two-thirds of regional cattle ranchers have reported selling parts of their herd due to inadequate feed, according to an american farm bureau survey. 

bison, meanwhile, demonstrate a unique resilience to climate change’s effects on their diet. 

the animal belongs to a family of herbivorous mammals with multi-part stomachs, known as ruminants. cows, sheep, goats, and yaks are also in the ruminant family. species in this family lack the gut enzymes necessary to break down grass and instead rely on internal colonies of bacteria to aid in the process.

bison are supported by the work of more than 116,000 kinds of bacteria, many of which are not found in other ruminants. researchers believe genes in these microbes allow bison to digest starchy, low-nutrient plants better, and maintain weight in drought conditions for longer periods of time.  

“they seem to not lose condition as quickly as other domesticated ruminants will when they’re on poor-quality forage,” said carter kruse, director of science and conservation with the turner institute for ecoagriculture. “we think there’s some key in the bison rumen that allows them to process this forage, which could have huge implications for how we manage the animals out on the range.” 

finding helpful bacteria in this rumen would mean a higher-margin future for bison ranchers, as they spend less on supplemental feed. it may also help livestock ranchers across the industry. 

fresno rueda said transplanting rumen bacteria between ruminants has been done in prior study. so finding a key colony in bison could help other livestock survive on nutrient-poor grasses for longer periods of time, as well. 

“if we identify beneficial bacteria, some of the things we can do with them are create products, or prebiotics, or probiotics,” the research assistant said. “it’s not just going to be for the bison. these will be for goats, and sheep, and cattle.”

a dirty job

according to fresno rueda, bison rumen bacteria have less than 90% genetic resemblance to bacteria from other ruminants.  

“we don’t really know what they are,” she said.

finding out is somewhat of a messy process. and it all happens in a white bison shed, the research team’s lab at mcginley ranch. 

inside is a maze of blue-painted gates and pens, with cut-up tire flooring and wooden platforms placed above them. on this mid-september sampling day, three bison had been wrangled into a holding chamber. they snorted and rattled barrier rails with their flanks. the shed smelled of manure, sulphuric bile, and wood chips.

a ranch technician led one bison through a corridor of pens with a flagpole until it arrived in the bison chute, a shipping container-like chamber. with the press of a button, the researchers applied gentle hydraulic pressure to hold the bison in place. 

at one end, kruse inserted a hand into the bison’s rectum for a fecal sample before bagging it and bringing it to fresno rueda. at the other, turner institute of ecoagriculture veterinarian tom bragg maneuvered a metal pipe into the bison’s mouth, before inserting a length of plastic tubing. 

“this tube is curved at the end,” bragg said. “so once we get it into their mouth, they swallow it, and it makes collection easy.”

on cue, the bison shook its head and olive-green rumen fluid flowed through the tube into a plastic bucket. fresno rueda paced the room with purpose, occasionally draining samples into test tubes and documenting them.

when work was complete, fresno rueda and kruse loaded their materials for a return trip to their lab in sdsu’s animal science department. they planned to break open the bacteria and extract the dna with a soap solution and high-speed test tube shaker. then, the research team would analyze bacterial dna chunks for their function. 

“right now, we’re just in the process of finding out what is there,” fresno rueda said.

while fresno rueda has two years left to complete her research, the promise of a viable probiotic is at least three years down the road. 

still, initial findings have the researchers hopeful for a more robust grass-fed meat market.

“if we show producers that grass-fed animals are healthier, higher-profit, and better for the environment, they will market it better as an alternative,” fresno rueda said. “it’s a win-win.” 

the energy in wastewater treatment most commonly comes from carbon containing organic matter. bacteria convert organic matter into methane, a combustible fuel that can be burned to generate power. in addition to carbon containing organic matter, there is also nitrogen in wastewater. unfortunately, current treatment processes don’t recover energy from waste nitrogen. but what if we could convert waste nitrogen into a combustible gas, just like converting organic matter into methane? it turns out we can! that’s where the rockets come in. bacteria are capable of converting waste nitrogen into nitrous oxide… yeah, nitrous oxide. the same stuff your dentist gives you, although dentists usually call it “laughing gas”. it’s also the same gas racecar enthusiasts use to supercharge their engines, although they call it “nitrox”. it’s also the same gas that has been used for decades in rockets. in fact, space ship one, the first privately manned spaceplane that is paving the way for sub-orbital space flights open to the public, used nitrous oxide in its rocket motors. it’s powerful stuff and we can get it for free from wastewater! at stanford we are developing a way to get bacteria to convert waste nitrogen into nitrous oxide, thus enabling energy recovery from both waste carbon and nitrogen. by producing nitrous oxide, we could essentially “supercharge” wastewater treatment, kind of like a nitrox turbocharged racecar.

wastewater treatment may not take us to the moon, but it can provide a serious amount of free and clean energy. considering that the treatment of wastewater consumes 3% of u.s. energy supply and wastewater treatment plants are often the highest energy expenditure for cities, generating power from wastes seems like a really good idea.