Exploring the Metaorganism Frontier

The recent KAUST Metaorganism Frontier research workshop brought together experts in microbial ecology and metaorganism evolution to discuss the current state of microbial ecology knowledge. Photo by Andrea Bachofen-Echt.

-By David Murphy, KAUST News

The recent KAUST metaorganism frontier research workshop brought together experts in microbial ecology and metaorganism evolution to explore the current state of microbial ecology knowledge. KAUST researchers and their overseas peers also discussed future research directions with an emphasis on how to address issues of animal and plant health through the lens of the metaorganism. The event consisted of a one-day open research conference held on February 19 and a two-day participants-only research workshop held from February 20 to 21.

Christian Voolstra, associate director of the Red Sea Research Center, opened the workshop by running through some of the event's goals, including shining a greater light on metaorganism research within KAUST.

"In recent years, there has been a changing imperative in life sciences sparked by advances in the genomic 'tools' used to study the molecular setup of organisms. In particular, the development of next-generation sequencing has changed our understanding of microbial diversity associated with organisms and their environments," Voolstra noted.

"There is now a multitude of research to support the notion that a host-specific microbiome provides functions related to metabolism, immunity and environmental adaptation to their animal and plant hosts. These studies also open new channels to understanding organismal health and environmental adaptation," he added.

"The overarching goal of this conference is to present to KAUST that metaorganisms are awesome," Voolstra continued. "A metaorganism is not a bug, it's a feature. Any microbial niche we humans inherited was long occupied by bacteria—archaea and bacteria have been here a lot longer than us. The intertwining of bacterial and eukaryotic genomes is not just historical but rather functional—we are metaorganisms, and bacteria matter."

The microbial community

The diverse subject matter of the workshop was reflected in the lineup of international universities and institutions represented, including the University of MelbourneUniversity of FreiburgUniversity of JenaLudwig Maximilian University of MunichCentre Scientifique de Monaco and the University of Kiel. Supplementing the international attendees were a broad range of researchers from the University's Red Sea Research Center (RSRC), the Desert Agriculture Initiative Research Laboratory (CDA) and the Biological and Environmental Science and Engineering Division (BESE).

In the opening keynote of the conference, Geoffrey McFadden, a professor at the School of BioSciences at the University of Melbourne, delivered a presentation entitled "Malaria versus Symbiodinium: similarities, differences & opportunities." McFadden and his team have made significant progress in malaria research in recent years. During his keynote address, McFadden, who was awarded an Australian Laureate Fellowship from the Australian Research Council in 2017, discussed his research, which includes the origin of mitochondria, plastids, parasitology, endosymbiosis and molecular evolution.

"Malaria is still a major global health problem. It is now eradicated in Australia, but it still persists in Saudi Arabia. Here in Saudi Arabia, you are in a major mosquito carrier zone. Malaria can only spread by mosquito bite. It cannot be spread in any other way," McFadden said.

Conference attendees listen to presentations at the KAUST Metaorganism Frontier research workshop recently held on the University's campus. Photo by Andrea Bachofen-Echt.

"Azithromycin-resistant parasites produce very few sporozoites and cannot infect a naïve host, and azithromycin-resistant lines are non-transmissible. Malaria parasites actively invade host cells and they pull the host cell membrane around themselves to create a parasitophorous vacuole," he stated.

Daniele Daffonchio, professor of bioscience in the University's BESE division, spoke on the microbial continuity (and discontinuity) within and around a mangrove crab. He described how, due to their industrious nature, the mangrove crabs are the "engineers" of the mangrove ecosystem, and they continuously contribute to sustaining the environment around them.

"Tens of crab species live in the mangrove ecosystem at the fringe of land and sea. Crabs densely colonize mangrove sediments. The crabs reshape the sediment's bacterial assemblages and they rework the sediment. Bacterial communities are stratified but yet connected following the crab bioturbation and reworking," Daffonchio said.

"Microbial activities contribute to reshape the sediment biogeochemistry. At an ecosystem scale, we have estimated, based on crab density data, that the influence of crabs on the sediment conditions range from 20 to 78.5 percent of mangrove sediment surface along the Red Sea/East African longitudes," he added.

Building towards a sustainable future

Research Scientist Maged Saad and Professor Heribert Hirt from the University's CDA both highlighted how KAUST is trying to find a solution to increase global sustainable food production to alleviate food shortages worldwide.

"Global warming and climate change are continuing to affect global agriculture. Hunger is a big problem worldwide, and at KAUST, we are trying to find a solution for humanity to increase sustainable food production," Saad said.

Professor Heribert Hirt from the University’s Desert Agriculture Initiative Research Laboratory (CDA) delivers his presentation during the KAUST Metaorganism Frontier research workshop. Photo by Andrea Bachofen-Echt.

The CDA's fieldwork studies have shown that plant root endospheres display a limited microbial diversity when compared to soil and rhizosphere microbiomes. Results have also shown that the primary determinant of the rhizosphere bacterial community is the soil type and that the plant genotype plays a more important role in microbiome composition.

"We want to decipher molecular linguistics in the communication of beneficial bacteria and plants—we want to decode the molecular 'language' of plants. Plant ethylene signaling is essential for induced stress tolerance. If you put a plant under abiotic stress, it 'cries out' for help," Hirt noted.

The foundations of metaorganisms

Voolstra delivered a presentation entitled "Microbiome Structure and Function of Coral holobionts." In his talk, Voolstra detailed how the metaorganism network extends our ability to understand the ecology and evolution of animals and plants. He also outlined the local and global threats to what he dubbed the "rainforest of the ocean," or reef ecosystems and how coral holobionts are the foundation metaorganisms of coral reef ecosystems.

"The metaorganism network extends our ability to understand ecology and evolution of animals and plants. The diversity and function of microbes needs to be incorporated when assessing adaptation of multicellular organisms to environmental change. The bacterial community structure responds in a host-specific manner. There is a no 'one size fits all' manner," Voolstra said.

Neus Garcias Bonet, a postdoctoral fellow in the Tarek Ahmed Juffali Research Chair in Red Sea Ecology group, presented on the Red Sea seagrass microbiome. She outlined how seagrasses are one of the largest carbon sinks on Earth and how they protect coastlines from erosion while supporting a large fraction of subsistence fisheries, ensuring food security for many countries.

Sustaining global ecosystems

Jeroen van de Water, a postdoctoral scientist at the Scientific Center of Monaco (CSM), France, identified how nature can be used to alter pathogens and how seagrass ecosystems moderate pathogens of marine animals. He described his team's research focus at CSM, and specifically their focus on filtration and microbial filtration in coastal ecosystems.

During his presentation, van de Water highlighted some of the many benefits of seagrasses, which are believed to be the third most valuable ecosystem in the world. He expanded on the seagrasses ability to provide natural filtration in our oceans; how seagrass leaf extracts are known to kill human pathogens; how seagrasses are the foundation of coastal food webs while providing a nursery habitat for sea creatures; and how seagrass meadows moderate levels of pathogens in heavily contaminated seawater.

David Kamanda Ngugi, a research scientist based in the KAUST Red Sea Research Center, asks a question during a post-presentation Q&A session. Photo by Andrea Bachofen-Echt.

Linda Blackall from the School of BioSciences and School of Earth Sciencesat the University of Melbourne rounded the workshop with the final keynote lecture of the day entitled "Microbial composition and some functions of the anemone holobiont." Blackall, who is an environmental microbial ecologist, expanded on her team's research with the microbiota of non-mammals, including corals and sponges.

The KAUST metaorganism frontier research workshop was organized by Professors Christian Voolstra, Maren ZieglerBenjamin Hume, Heribert Hirt and Carlos Duarte, director of the Red Sea Research Center and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology, with financial support from the KAUST Office of Sponsored Research (OSR).

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