A microbiome is the assemblage of microorganisms — bacteria, archaea, fungi, algae, small protists and viruses — that exist in a given environment, and increasingly these microbiomes have the attention of an assemblage of many scientists working in diverse fields.
Microbial communities are vital to all ecosystems, from desert sediments to the human gut. “We live in a golden age of microbiology, thanks to advances in next generation multiomics technologies and imaging techniques,” says bioscientist Alexandre Rosado. Rosado works across disciplines on an array of microbial studies, from plant science and human health to the microbes living on the international space station.
“These microbes assemble themselves, following a set of ecological rules, into a functioning microbial community. These same rules apply to any microbiome in any ecosystem,” Rosado continues. “A precise definition of a microbiome remains tricky due to their extraordinary complexity, and how little we know about these incredible communities.”
The expanding influence of microbes
Using genomics, metabolomics and proteomics approaches, scientists are beginning to understand the different roles played by different species of microbes and their interactions within these communities. Often the microbe-host relationship is so entwined that it is impossible to separate them. Each depends on the other to survive, and they live as a symbiotic unit or “holobiont,” where the microbes and host continuously communicate with one another and share resources.
“In humans, the microbiome could be seen as an entire second genome, given that it hosts more cells than the human body itself,” says Rosado.
Moreover, at least in plants, there is evidence now that entire microbiomes are inherited by the next generation via the seeds. In other words, plant genomics has come of age and should be replaced by a true plant-microbe (holobiont) genomics.
Microbiomes enable complex lifeforms to survive and thrive in all manner of challenging conditions. Boosting the human gut microbiome can help tackle and even prevent disease. Giving a plant the right dose of the right microbes can transform its growth and overall health.
Saudi Arabia is home to multiple extreme environments where life is sustained under harsh conditions, from arid deserts to coastal mangroves and coral reefs in the Red Sea. The microbiomes underpinning these environments are better understood through investigations by KAUST researchers.
A microbial boost to regreen the desert
“The desert is full of surprises,” says plant scientist Heribert Hirt. “We have missed many important features in plants from arid regions, largely because these areas are not used for growing crops and are under-researched. It is exciting to see desert plant science taking root in Saudi Arabia.”
At present, the primary goal for Hirt and his team is to learn how to successfully regenerate and support ecosystems in extreme environments like the Saudi desert.
“The plant-soil-microbe nexus is vital. You cannot boost just one of these because they all depend upon one another,” says Hirt. “If you want to add or reinstate plants in a specific place, you have to understand the soils — and the microbes that those plants rely on — to build a stable, sustainable ecosystem.”
Hirt’s team recently created the Saudi soil bio-atlas, the first database of its kind to include all biological components of soils across Saudi Arabia. They isolated thousands of microbial strains from the soils and will use this knowledge to boost desert regreening and enhance agricultural lands in line with Saudi’s Vision 2030.
Every desert location has a subtly different microbiome. Hirt and co-workers have developed a method to naturally restore beneficial microbes to two common desert plant species, the Acacia tree and the shrub Haloxylon. To do this, before planting, they coat the seeds with specific endophytes or naturally occurring bacteria selected from local soils. These beneficial bacteria boost the plants before they interact with the rest of the soil microbiome.
In arid climates like Saudi Arabia, millions of hectares of arable land have been degraded through overgrazing, industrial exploitation, water-resource mismanagement, urbanization and climate change.
However, desert plants have developed beneficial relationships with microbiomes to boost their ability to survive in extreme environments.
Microorganisms in soil form mutually beneficial symbiotic relationships with plants. The plant microbiome helps the roots to absorb nutrients from the soil while boosting plant immunity from pathogens and providing resistance to stressors such as drought. Microbiomes also help to mitigate against climate change by sequestering and storing carbon in the soil.
An unexpected carbon store
The research by Hirt and co-workers has produced exciting discoveries. Like animals that hibernate through the winter, desert plants have an extraordinary ability to withstand lengthy droughts; Hirt calls this “summernating.”
Hirt’s team found that some of the organic acid oxalate that is produced by desert plants filters into the soils where microbes take it up. They discovered that desert soils hold many microbes that utilize oxalate as a carbon source. The microbes turn the oxalate into carbonate; in arid soils, carbonates are a highly stable carbon store that can keep carbon locked away for centuries. Their bioengineering plans could therefore hold double benefits by regreening and removing excess carbon from the atmosphere. The team will conduct their first field trials at the NEOM city project, following successful initial greenhouse experiments. If successful, similar projects could be rolled out across other arid regions.
The secrets of the mangrove microbiome
Mangroves are another important carbon sink and host a wide diversity of species. Saudi Arabia is one of few remaining strongholds of this ecosystem, and so scientists want to learn how to protect existing mangroves and help them to flourish.
For Rosado, the microbiome that underpins mangroves is one of the most fascinating microbial communities.
“These mangroves flourish in extreme circumstances, with high heat and salinity tolerances,” says Rosado. “The microbes that live there are specialized and unique and can withstand extraordinary stressors — they thrive on these pressures. We’ve only begun to scratch the surface of traits of the mangrove microbiome and the benefits they confer to their plant hosts and other organisms.”
Pressures from both sea and land can impact the health of mangroves. One example is the threat from oil spills; this contamination can cause irreparable damage. Before she moved to KAUST, Raquel Peixoto was tasked with finding ways to use microbes to clean up mangroves following oil contamination.
“We identified microbes that were capable of degrading crude oil, and we experimented with certain species that could degrade the oil, but also enhance the regrowth of mangrove plant species,” says Peixoto. “It’s astonishing what these tiny powerful microorganisms can do.”
Now Peixoto investigates whether these same microbial boosts could be given to corals.
Microbiome and the nitrogen cycle
Microbes in mangrove sediments break down nitrogen molecules under anaerobic conditions to produce nitrogen based nutrients such as ammonia, nitrates and nitrites. These are then taken up by the mangroves, providing essential nutrients in an otherwise low-nutrient environment.
The consumption of oxygen and reduction of sulfate by bacteria in mangrove sediment contributes to the anoxic environment that slows the decomposition of organic matter. This helps the sediments to store sequestered carbon for longer and reduce CO2 concentrations in the atmosphere.
Mangrove sediments are powerful carbon sinks, storing up to 10 times more carbon than terrestrial forests. The microbes in mangrove soils help to absorb carbon from the atmosphere and store it in the sediment.
A probiotic pick-me-up for coral reefs
Peixoto identified that nobody had researched probiotics for corals. Corals are symbiotic organisms: they partner with specific algae species to share resources and trade nutrients. Without their algal symbionts, corals die within a few weeks. These algae are part of the wider microbiome associated with corals, and although the science of reef microbiomes is in its early days, Peixoto and her team are pioneering novel techniques that might help address threats to reefs.
“Coral reefs are highly sensitive to climate change,” says Peixoto. “Corals take hundreds of years to grow, so it is crucial to protect existing ones, alongside supporting new coral nurseries.”
When water temperature increases, the algae symbionts compete with the corals for resources, so the corals expel them, also known as “coral bleaching.“ The corals are still alive, but without the algae, they may soon die.
Peixoto and her team are the proud custodians of a coral village — a reef in the Red Sea just off the coast of KAUST — that operates as a vast, natural laboratory where they also regularly host educational outreach events.
Peixoto’s team have successfully inoculated corals in the lab with beneficial bacteria, sourced from the reef, to boost their microbiome — these are also known as beneficial microorganisms for corals. The trials proved so successful that the team have since moved their experiments out into the coral village where they inoculate specific corals with probiotics and then track their health over time.
“This year, for the first time, we collected the offspring from inoculated corals to see if their microbiome is naturally more resilient. We are tracking their epigenetic changes, which is completely new research for this field,” says Peixoto.
Sea temperature increases due to climate change contribute to the breakdown of the symbiotic relationship between corals and the microbiome. When this breakdown becomes widespread and chronic, it can lead to extensive coral mortality.
Coral reefs are inoculated with BMCs specially selected and prepared in the laboratory. The inoculated BMCs are then spread over the test coral in a controlled way to boost the microbiome abundance inside the coral.
BMCs help corals to grow by promoting nutrient uptake and mitigate stress while increasing resilience to pathogens, pollution and temperature fluctuations. They are also important in coral early-stage life development.
The beneficial bacteria that coexist with corals are crucial for energy production, nutrient acquisition, reproduction, resistance to toxic pollutants and resilience against pathogens. Disrupting this symbiotic relationship is a major cause of widespread coral reef deterioration.
Art: Ana Bigio. Scientific review: Raquel Peixoto, Red Sea Research Center; Alexandre Rosado; Heribert Hirt, Center for Desert Agriculture; KAUST