The lab under the sea

By Jennifer Racz

The study of bacteria has revolutionized our understanding of health and disease, and has led to significant advancements in medical treatments, nutrition and food technology, and biotechnological applications. However, this research has mostly centered on bacteria in living organisms, such as E. coli, studied under conditions found in the human body. For scientists interested in other ecosystems, like the ocean, these human-based bacterial models are less useful.

While bacteria in the body have plenty to feast on, those in the sea are starving due to an almost complete lack of food. In addition, compared to the balmy 37⁰C (98.6⁰F) temperatures in the human body, bacteria in the sea live in a much colder environment ranging from 4-18⁰C (39-64⁰F). Given the critical role that bacteria play in marine environments and the environmental chaos plaguing our world, new models are needed to understand their role in environmental processes and the underlying mechanisms, especially under conditions of climate change.

Replicating nature

Given the multitude of interfering factors that make studying microscopic organisms in their natural surroundings too complicated, Dr. Einat Segev, in the Department of Plant and Environmental Sciences, has invited the sea into her lab, where she has created highly monitored systems that mirror the natural conditions in marine environments. These models allow microbes—specifically bacteria and their algal hosts—to live and function the way they do at sea, providing ecologically relevant information about their internal mechanisms and their interactions with each other.

Like the natural sea environment, Dr. Segev’s systems contain no external food source, obligating starving bacteria to rely on their algal partners to secrete food. The water temperature is also a cool 18⁰C (64⁰F) and light conditions are replicated to reflect intensity and daily cycles found in the sea (case in point, when taking pictures of the Segev lab, the photographer could not use a flash, as not to add light to the perfectly tuned sea environment). Thanks to its incredible precision, Dr. Segev’s new model allows her to study how bacteria operate in their real-life environment and reveal new bacterial behaviors that would otherwise be overlooked.

Recognizing that there is not a one-size-fits-all model representing every condition and microbe in the ocean, the Segev group has diversified their model systems to capture different levels of complexity. In their most simple system, they are studying one species of bacteria with one kind of algae. In a more complex synthetic community, they partnered several bacterial species together with an algal host to study how microbial communities function together in the ocean. Finally, their most complex system contains a natural microbial population in vessels that are submerged “at sea.” Thanks to these increasing levels of biological and ecological complexity in-house marine systems, the team is able to take a comprehensive look at microbes and their interactions with each other and with their environment.

Dr. Segev’s controlled microbial ecosystems have also allowed her group to develop genetic tools for marine bacteria, and thus gain a greater understanding of the genes that drive functions and processes within and between the microbes. Using this information, the scientists are able to go beyond general correlations—observations that two factors may be linked or related—and gain a deep understanding of how things actually work.

“Developing these tools is crucial as it helps us unlock the vast potential of marine bacteria to drive environmental processes and understand the bacterial role in global biogeochemical cycles,” Dr. Segev elaborates.

Bacterial bounty

These days, she is using her model to address a problem commonly known as “sea snot”—particles of microalgae and bacteria held together by an extracellular matrix (similar to a scaffold that holds everything in place) that, in significantly altered, unbalanced environments, forms a thick layer on the surface of water in coastal regions around the world. These layers of “slime,” occurring more and more in the Mediterranean Sea, have harmful effects on their surroundings, including suffocating the marine life below them.

Searching for answers as to what is causing microbes to aggregate and form sea slime, the members of the Segev group recreated the conditions to promote microbial aggregation right inside their lab. The resulting slime model system allowed them to dive deep into the mechanisms behind this thick sludge and discover that bacteria and algae manufacture the extracellular matrix.

Taking their analysis a step further, the group identified and analyzed the genes in environmental samples. Here they observed a very interesting phenomenon: in vast areas at sea where microbial aggregation was dominant and algae were abundant, the bacterial genes responsible for matrix production were expressed in extremely high levels. This finding suggests an important mechanism, hidden until now, behind the formation of sea slime and reveals bacteria’s central role in microbial aggregation. Their new discovery, along with the identification of the genes that encode the aggregating matrix, offers a possible target for degradation or prevention of this destructive phenomenon.

Pieces of the puzzle

The interdisciplinary and collaborative spirit of the Weizmann Institute and its scientists played an essential role in Dr. Segev’s achievements. Trained as a geochemist and a microbiologist, she can see the need to consider both microbial and the chemical worlds to get the complete picture.

“I have a strong belief that you have to merge the understanding of the environment and microorganisms within it to tap into the full potential of microbial metabolism and their physiology to address problems that arise due to climate change,” she says. “Otherwise you’re missing a big part of the picture.”

Her unique lab models are instrumental in helping her achieve her ultimate goal: to understand how tiny microbes and their cellular processes affect the environment on the global scale, especially in the context of climate change.

These microscopic-scale phenomena could hold the key to bacterial interventions in polluted environments and shine light on the path to a healthier planet.

EINAT SEGEV IS SUPPORTED BY:

• de Botton Center for Marine Science