Tag Archives: Marine Biology

Microbiology

Ancient viruses discovered in coral symbionts’ DNA

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An international team of marine biologists has discovered the remnants of ancient RNA viruses embedded in the DNA of symbiotic organisms living inside reef-building corals.

The RNA fragments are from viruses that infected the symbionts as long ago as 160 million years. The discovery is described in an open-access study published this week in the Nature journal Communications Biology, and it could help scientists understand how corals and their partners fight off viral infections today. But it was a surprising find because most RNA viruses are not known for embedding themselves in the DNA of organisms they infect.

The research showed that endogenous viral elements, or EVEs, appear widely in the genomes of coral symbionts. Known as dinoflagellates, the single-celled algae live inside corals and provide them with their dramatic colors. The EVE discovery underscores recent observations that viruses other than retroviruses can integrate fragments of their genetic code into their hosts’ genomes.

“So why did it get in there?” asked study co-author Adrienne Correa of Rice University. “It could just be an accident, but people are starting to find that these ‘accidents’ are more frequent than scientists had previously believed, and they’ve been found across all kinds of hosts, from bats to ants to plants to algae.”

That an RNA virus appears at all in coral symbionts was also a surprise.

“This is what made this project so interesting to me,” said study lead author Alex Veglia, a graduate student in Correa’s research group. “There’s really no reason, based on what we know, for this virus to be in the symbionts’ genome.”

The study was supported by the Tara Ocean Foundation and the National Science Foundation and led by Correa, Veglia and two scientists from Oregon State University, postdoctoral scholar Kalia Bistolas and marine ecologist Rebecca Vega Thurber. The research provides clues that can help scientists better understand the ecological and economic impact of viruses on reef health.

The researchers did not find EVEs from RNA viruses in samples of filtered seawater or in the genomes of dinoflagellate-free stony corals, hydrocorals or jellyfish. But EVEs were pervasive in coral symbionts that were collected from dozens of coral reef sites, meaning the pathogenic viruses were — and probably remain — picky about their target hosts.

“There’s a huge diversity of viruses on the planet,” said Correa, an assistant professor of biosciences. “Some we know a lot about, but most viruses haven’t been characterized. We might be able to detect them, but we don’t know who serves as their hosts.”

She said viruses, including retroviruses, have many ways to replicate by infecting hosts. “One reason our study is cool is because this RNA virus is not a retrovirus,” Correa said. “Given that, you wouldn’t expect it to integrate into host DNA.

“For quite a few years, we’ve seen a ton of viruses in coral colonies, but it’s been hard to tell for sure what they were infecting,” Correa said. “So this is likely the best, most concrete information we have for the actual host of a coral colony-associated virus. Now we can start asking why the symbiont keeps that DNA, or part of the genome. Why wasn’t it lost a long time ago?”

The discovery that the EVEs have been conserved for millions of years suggests they may somehow be beneficial to the coral symbionts and that there is some kind of mechanism that drives the genomic integration of the EVEs.

“There are a lot of avenues we can pursue next, like whether these elements are being used for antiviral mechanisms within dinoflagellates, and how they are likely to affect reef health, especially as oceans warm,” Veglia said.

“If we’re dealing with an increase in the temperature of seawater, is it more likely that Symbiodiniaceae species will contain this endogenous viral element? Does having EVEs in their genomes improve their odds of fighting off infections from contemporary RNA viruses?” he said.

“In another paper, we showed there was an increase in RNA viral infections when corals underwent thermal stress. So there are a lot of moving parts. And this is another good piece of that puzzle.”

Correa said, “We can’t assume that this virus has a negative effect. But at the same time, it does look like it’s becoming more productive under these temperature stress conditions.”

Thurber is the Emile F. Pernot Distinguished Professor in Oregon State’s Department of Microbiology.

The study included more than 20 co-authors from the University of Konstanz, Germany; the Institute of Microbiology and Swiss Institute of Bioinformatics, Zürich; the University of Perpignan, France; the Scientific Center of Monaco; the Université Paris-Saclay, Evry, France; the Tara Ocean Foundation, Paris; the University of Maine; Sorbonne University, France; the University of Tsukuba, Japan; Paris Science and Letters University, France; the University of Paris-Saclay; the Weizmann Institute of Science, Rehovot, Israel; Côte d’Azur University, Nice, France; the European Bioinformatics Institute, University of Cambridge, England; Ohio State University; and the National University of Ireland, Galway.

National Science Foundation support was provided by three grants (2145472, 2025457, 1907184).

  • Alex J. Veglia, Kalia S. I. Bistolas, Christian R. Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Vargas, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre E. Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Shinichi Sunagawa, Olivier P. Thomas, Romain Troublé, Didier Zoccola, Adrienne M. S. Correa, Rebecca L. Vega Thurber. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Communications Biology, 2023; 6 (1) DOI: 10.1038/s42003-023-04917-9

    • Rice University
    Microbiology

    Why do some people live to be 100? Intestinal bacteria may hold the answer

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    We are pursuing the dream of eternal life. We fast to stay healthy. And each year, we spend billions of kroner on treatment to make sure we stay alive. But some people turn 100 years old all by themselves. Why is that?

    Researchers from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen have set out to find the answer.

    Studying 176 healthy Japanese centenarians, the researchers learned that the combination of intestinal bacteria and bacterial viruses of these people is quite unique.

    “We are always eager to find out why some people live extremely long lives. Previous research has shown that the intestinal bacteria of old Japanese citizens produce brand new molecules that make them resistant to pathogenic — that is, disease-promoting — microorganisms. And if their intestines are better protected against infection, well, then that is probably one of the things that cause them to live longer than others,” says Postdoc Joachim Johansen, who is first author of the new study.

    Among other things, the new study shows that specific viruses in the intestines can have a beneficial effect on the intestinal flora and thus on our health.

    “Our intestines contain billions of viruses living of and inside bacteria, and they could not care less about human cells; instead, they infect the bacterial cells. And seeing as there are hundreds of different types of bacteria in our intestines, there are also lots of bacterial viruses,” says Associate Professor Simon Rasmussen, last author of the new study.

    Joachim Johansen adds that aside from the important, new, protective bacterial viruses, the researchers also found that the intestinal flora of the Japanese centenarians is extremely interesting.

    “We found great biological diversity in both bacteria and bacterial viruses in the centenarians. High microbial diversity is usually associated with a healthy gut microbiome. And we expect people with a healthy gut microbiome to be better protected against aging related diseases,” says Joachim Johansen.

    Once we know what the intestinal flora of centenarians looks like, we can get closer to understanding how we can increase the life expectancy of other people. Using an algorithm designed by the researchers, they managed to map the intestinal bacteria and bacterial viruses of the centenarians.

    “We want to understand the dynamics of the intestinal flora. How do the different kinds of bacteria and viruses interact? How can we engineer a microbiome that can help us live healthy, long lives? Are some bacteria better than others? Using the algorithm, we are able to describe the balance between viruses and bacteria,” says Simon Rasmussen.

    And if the researchers are able to understand the connection between viruses and bacteria in the Japanese centenarians, they may be able to tell what the optimal balance of viruses and bacteria looks like.

    Optimising intestinal bacteria

    More specifically, the new knowledge on intestinal bacteria may help us understand how we should optimise the bacteria found in the human body to protect it against disease.

    “We have learned that if a virus pays a bacterium a visit, it may actually strengthen the bacterium. The viruses we found in the healthy Japanese centenarians contained extra genes that could boost the bacteria. We learned that they were able to boost the transformation of specific molecules in the intestines, which might serve to stabilise the intestinal flora and counteract inflammation,” says Joachim Johansen, and Simon Rasmussen adds:

    “If you discover bacteria and viruses that have a positive effect on the human intestinal flora, the obvious next step is to find out whether only some or all of us have them. If we are able to get these bacteria and their viruses to move in with the people who do not have them, more people could benefit from them.”

    Even though this requires more research, the new insight is significant, because we are able to modify the intestinal flora.

    “Intestinal bacteria are a natural part of the human body and of our natural environment. And the crazy thing is that we can actually change the composition of intestinal bacteria. We cannot change the genes — at least not for a long time to come. If we know why viruses and intestinal bacteria are a good match, it will be a lot easier for us to change something that actually affects our health,” says Simon Rasmussen.

  • Joachim Johansen, Koji Atarashi, Yasumichi Arai, Nobuyoshi Hirose, Søren J. Sørensen, Tommi Vatanen, Mikael Knip, Kenya Honda, Ramnik J. Xavier, Simon Rasmussen, Damian R. Plichta. Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nature Microbiology, 2023; DOI: 10.1038/s41564-023-01370-6

    • University of Copenhagen – The Faculty of Health and Medical Sciences
    Microbiology

    Scientists Discover New Probiotic That Could Protect Corals From a Mysterious and Devastating Disease

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    Scientists from the Smithsonian’s National Museum of Natural History have discovered the first effective bacterial probiotic capable of treating and staving off stony coral tissue loss disease (SCTLD). This enigmatic disease has wreaked havoc on Florida’s coral reefs since 2014 and is swiftly permeating the Caribbean region.

    The researchers’ findings were published in the journal Communications Biology. It presents a promising alternative to the currently used broad-spectrum antibiotic, amoxicillin. While amoxicillin is the only verified treatment for the disease so far, and it carries the potential risk of fostering antibiotic-resistant bacteria.

    SCTLD afflicts at least two dozen species of so-called hard corals, which provide essential habitats for innumerable fishes and marine animals of economic and intrinsic value while also helping to defend coastlines from storm damage. Since its discovery in Florida in 2014, cases of SCTLD have been confirmed in at least 20 countries. The precise cause of the malady remains unknown but once a coral is infected, its colony of polyps can die within weeks.

    “It just eats the coral tissue away,” said Valerie Paul, head scientist at the Smithsonian Marine Station at Fort Pierce, Florida, and senior author of the study. “The living tissue sloughs off and what is left behind is just a white calcium carbonate skeleton.”

    Paul has been studying coral reefs for decades, but she said she decided to go “all in” on SCTLD in 2017 because it was so deadly, so poorly understood, and spreading so fast.

    While probing how the disease is spread, Paul and a team including researchers from the University of Florida discovered that some fragments of great star coral (Montastraea cavernosa) swiftly developed SCTLD’s characteristic lesions and died, but other pieces never got sick at all.

    Though the precise cause of SCTLD is unknown, the efficacy of antibiotics as a treatment suggested pathogenic bacteria were somehow involved in the progression of the disease.

    For this reason, the researchers collected samples of the naturally occurring, non-pathogenic bacteria present on a pair of disease-resistant great star coral fragments for further testing. With these samples, the research team aimed to identify what, if any, naturally occurring microorganisms were protecting some great star corals from SCTLD.

     

    First, the team tested the 222 bacterial strains from the disease-resistant corals for antibacterial properties using three strains of harmful bacteria previously isolated from corals infected with SCTLD. Paul and Blake Ushijima, lead author of the study and an assistant professor at the University of North Carolina Wilmington who was formerly a George Burch Fellow at Smithsonian Marine Station, found 83 strains with some antimicrobial activity, but one in particular, McH1-7, stood out.

    The team then conducted chemical and genetic analyses to discover the compounds behind McH1-7’s antibiotic properties and the genes behind those compounds’ production. Finally, the researchers tested McH1-7 with live pieces of great star coral. These lab trials provided the final bit of decisive proof: McH1-7 stopped or slowed the progression of the disease in 68.2% of 22 infected coral fragments and even more notably prevented the sickness from spreading in all 12 transmission experiments, something antibiotics are unable to do.

    Going forward, Paul said there is a need to work on improved delivery mechanisms if this probiotic is going to be used at scale in the field. Currently, the primary method of applying this coral probiotic is to essentially wrap the coral in a plastic bag to create a mini aquarium and then inject the helpful bacteria. Perhaps even more importantly, Paul said it remains to be seen whether the bacterial strain isolated from the great star coral will have the same curative and prophylactic effects for other species of coral.

    The potential of this newly identified probiotic to help Florida’s embattled corals without the danger of inadvertently spawning antibiotic-resistant bacteria represents some urgently needed good news, Paul said.

    “Between ocean acidification, coral bleaching, pollution and disease there are a lot of ways to kill coral,” Paul said. “We need to do everything we can to help them so they don’t disappear.”

    Reference: “Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease” by Blake Ushijima, Sarath P. Gunasekera, Julie L. Meyer, Jessica Tittl, Kelly A. Pitts, Sharon Thompson, Jennifer M. Sneed, Yousong Ding, Manyun Chen, L. Jay Houk, Greta S. Aeby, Claudia C. Häse and Valerie J. Paul, 6 April 2023, Communications Biology.
    DOI: 10.1038/s42003-023-04590-y

    This interdisciplinary research is part of the museum’s new Ocean Science Center, which aims to consolidate museum’s marine research expertise and vast collections into a collaborative center to expand understanding of the world’s oceans and enhance their conservation.

    The study was funded by the Smithsonian, the Florida Department of Environmental Protection, the National Science Foundation, the National Oceanic and Atmospheric Administration and the National Institutes of Health.

    Smithsonian

    Microbiology

    Illuminating the Carbon Cycle: Coccolithophores’ Ability To Absorb Organic Carbon

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    In recent research from Bigelow Laboratory for Ocean Sciences, it’s revealed that coccolithophores, a type of phytoplankton crucial to the ocean-atmosphere carbon cycle, can survive in low-light conditions by absorbing dissolved organic forms of carbon, a process known as osmotrophy. Even though the absorption rate was slow, it offers a new understanding of the role these organisms play in the sequestration of carbon in the ocean floor and redefines our perception of the global carbon cycle.

    Coccolithophores, a globally ubiquitous type of phytoplankton, play an essential role in the cycling of carbon between the ocean and atmosphere. New research from Bigelow Laboratory for Ocean Sciences shows that these vital microbes can survive in low-light conditions by taking up dissolved organic forms of carbon, forcing researchers to reconsider the processes that drive carbon cycling in the ocean. The findings were published this week in the journal Science Advances.

    The ability to extract carbon from the direct absorption of dissolved organic carbon is known as osmotrophy. Though scientists had previously observed osmotrophy by coccolithophores using lab-grown cultures, this is the first evidence of this phenomenon in nature.

    The team, led by Senior Research Scientist William Balch, undertook their experiments in populations of coccolithophores across the northwest Atlantic Ocean. They measured the rate at which phytoplankton fed on three different organic compounds, each labeled with chemical markers to track them. The dissolved compounds were used by the coccolithophores as a carbon source for both the organic tissues that comprise their single cells as well as the inorganic mineral plates, called coccoliths, which they secrete around themselves. Uptake of the organic compounds was slow compared to the rate at which phytoplankton can take up carbon through photosynthesis. But it wasn’t negligible.

    “The coccolithophores aren’t winning any ‘growth race’ by taking up these dissolved organic materials,” Balch said. “They are just eking out an existence, but they can still grow, albeit slowly.”

    Plants, like coccolithophores, typically acquire their carbon for growth from inorganic forms of carbon extracted from the atmosphere like carbon dioxide and bicarbonate through photosynthesis. When coccolithophores die, they sink, carrying all that carbon down to the ocean floor where it can be remineralized or buried, effectively sequestering it for millions of years. This process is called the biological carbon pump.

    As part of a parallel process called the alkalinity pump, coccolithophores also convert bicarbonate molecules in surface water into calcium carbonate — essentially limestone — that forms their protective coccoliths. Again, when they die and sink, all that dense inorganic carbon is ballasted to the seafloor. Some of it then dissolves back into bicarbonate, thus ‘pumping’ alkalinity from the surface to depth.

    But the new evidence suggests that coccolithophores aren’t just using these inorganic forms of carbon near the surface. They’re also taking up dissolved organic carbon, the largest pool of organic carbon in the sea, and fixing some of it into their coccoliths, which ultimately sink into the deep ocean. This suggests that the uptake of these free-floating organic compounds is another step in both the biological and alkalinity pumps that drive the transport of carbon from the ocean surface to depths below.

    “There’s this big dissolved organic carbon source in the ocean that we always assumed wasn’t really related to the carbonate cycle in the sea,” Balch said. “Now we’re saying that some fraction of the carbon that is going to depth is really coming from that enormous pool of dissolved organic carbon.”

    This is the third and final paper published as part of a three-year National Science Foundation-funded project. The overall effort was inspired by a decades-old dissertation by William Blankley, a graduate student at Scripps Institution of Oceanography, Balch’s alma mater. In the 1960s, Blankley was able to grow coccolithophores in the dark for 60 days feeding them glycerol, one of the organic compounds used in the present study. Unfortunately, he died before his research could be published. The fact that Blankley’s findings could be reproduced all these years later with new technology, Balch said, is credit to the quality of that early work.

    The real challenge of the most recent study, though, was to undertake that research outside of a controlled lab environment. The team had to devise a method to measure these organic compounds in seawater — at ambient concentrations orders of magnitude lower than the Blankley experiments — and then track how they were being taken up by wild coccolithophores.

    “When you culture phytoplankton in the lab, you can grow as much as you want. But in the ocean, you take what you get,” Balch said. “The challenge was finding a signal in all the noise to say, proof positive, that it was coccolithophores taking up these organic molecules into their coccoliths.”

    Though the current project is complete, Balch said the next step is to examine whether coccolithophores are able to take up other organic compounds found in seawater at the same rate as the three tested thus far. Though the coccolithophores were using the three dissolved compounds at slow rates in these experiments, there are thousands of other organic molecules in seawater that they could potentially absorb. If they are using more of them, this finding may prove to be an even more significant step in understanding the global carbon cycle.

    Reference: “Osmotrophy of dissolved organic compounds by coccolithophore populations: fixation into particulate organic and inorganic carbon” 24 May 2023, Science Advances.
    DOI: 10.1126/sciadv.adf6973

    Bigelow Laboratory for Ocean Sciences

    Microbiology

    The Perfect “Pathogen” Storm – Deadly Bacteria Is Adapting to Plastic

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    Recent research has unveiled how the interaction among Sargassum species, plastic marine waste, and Vibrio bacteria creates the perfect “pathogen” that poses threats to marine biodiversity and public health. Vibrio bacteria, commonly found in global waters, are the leading cause of marine-related human fatalities. For instance, Vibrio vulnificus, often known as the flesh-eating bacteria, can cause severe foodborne illnesses from consuming seafood and can lead to infections and death from open wounds.

    From 2011 onwards, there’s been a notable increase in the presence of Sargassum, a type of free-living brown macroalgae, in the Sargasso Sea and other open ocean areas like the Great Atlantic Sargassum Belt, with regular and unusual seaweed accumulation events occurring on beaches. Additionally, plastic marine waste, initially discovered in the surface waters of the Sargasso Sea, has emerged as a global concern due to its longevity, persisting for decades longer than natural substrates in the marine ecosystem.

    Currently, little is known about the ecological relationship of vibrios with Sargassum. Moreover, genomic and metagenomic evidence has been lacking as to whether vibrios colonizing plastic marine debris and Sargassum could potentially infect humans. As summer kicks into high gear and efforts are underway to find innovative solutions to repurpose Sargassum, could these substrates pose a triple threat to public health?

    Researchers from Florida Atlantic University and collaborators fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris, Sargassum, and seawater samples collected from the Caribbean and Sargasso seas of the North Atlantic Ocean. What they discovered is Vibrio pathogens have the unique ability to “stick” to microplastics and that these microbes might just be adapting to plastic.

    “Plastic is a new element that’s been introduced into marine environments and has only been around for about 50 years,” said Tracy Mincer, Ph.D., corresponding lead author and an assistant professor of biology at FAU’s Harbor Branch Oceanographic Institute and Harriet L. Wilkes Honors College. “Our lab work showed that these Vibrio are extremely aggressive and can seek out and stick to plastic within minutes. We also found that there are attachment factors that microbes use to stick to plastics, and it is the same kind of mechanism that pathogens use.”

    The study, published in the journal Water Research, illustrates that open ocean vibrios represent an up-to-now undescribed group of microbes, some representing potential new species, possessing a blend of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize. Utilizing metagenome-assembled genome (MAG), this study represents the first Vibrio spp. genome assembled from plastic debris.

    The study highlighted vertebrate pathogen genes closely related to cholera and non-cholera bacterial strains. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic and lipophospholytic activities, consistent with pathogenic potential.

    Researchers also discovered that zonula occludens toxin or “zot” genes, first described in Vibrio cholerae, which is a secreted toxin that increases intestinal permeability, were some of the most highly retained and selected genes in the vibrios they found. These vibrios appear to be getting in through the gut, getting stuck in the intestines, and infecting that way.

    “Another interesting thing we discovered is a set of genes called ‘zot’ genes, which causes leaky gut syndrome,” said Mincer. “For instance, if a fish eats a piece of plastic and gets infected by this Vibrio, which then results in a leaky gut and diarrhea, it’s going to release waste nutrients such nitrogen and phosphate that could stimulate Sargassum growth and other surrounding organisms.”

    Findings show some Vibrio spp. in this environment have an ‘omnivorous’ lifestyle targeting both plant and animal hosts in combination with an ability to persist in oligotrophic conditions. With increased human-Sargassum-plastic marine debris interactions, associated microbial flora of these substrates could harbor potent opportunistic pathogens. Importantly, some cultivation-based data show beached Sargassum appear to harbor high amounts of Vibrio bacteria.

    “I don’t think at this point, anyone has really considered these microbes and their capability to cause infections,” said Mincer. “We really want to make the public aware of these associated risks. In particular, caution should be exercised regarding the harvest and processing of Sargassum biomass until the risks are explored more thoroughly.”

    Reference: “Sargasso Sea Vibrio bacteria: underexplored potential pathovars in a perturbed habitat” by Tracy J. Mincer, Ryan P. Bos, Erik R. Zettler, Shiye Zhao, Alejandro A. Asbun, William D. Orsi, Vincent S. Guzzetta and Linda A. Amaral-Zettler, 3 May 2023, Water Research.
    DOI: 10.1016/j.watres.2023.120033

    Study co-authors represent the NIOZ Royal Netherlands Institute for Sea Research, the Japan Agency for Marine-Earth Science and Technology, the Ludwig Maximilian University of Munich, Germany, Emory University, the University of Amsterdam and the Marine Biological Laboratory.

    This research was supported by the National Science Foundation (NSF) (grant OCE-1155671 awarded to Mincer), FAU World Class Faculty and Scholar Program (awarded to Mincer), NSF (grant OCE-1155571 awarded to Linda A. Amaral-Zettler, Ph.D., corresponding author, NIOZ), NSF (grant OCE-1155379 awarded to Erik R. Zettler, Ph.D., co-author, NIOZ), NSF TUES grant (DUE-1043468 awarded to Linda Zettler and Erik Zettler).

    Florida Atlantic University

    Microbiology

    Concerning – Popular Hawaiian Tourist Spot Is Being “Overused”

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    In August 2019, Hawaii’s Molokini island attracted over 40,000 tourists for snorkeling and diving. However, in March 2020, the global COVID lockdown brought that number down to nearly zero.

    The sudden and prolonged decrease in visitors to one of the world’s most renowned snorkeling destinations presented scientists with a unique chance to examine the effect of underwater tourism on marine fish. The findings of their study, published in the journal PLOS ONE, will aid resource managers in improving the management of Molokini and other vulnerable marine habitats.

    The study’s lead author, Dr. Kevin Weng of William & Mary’s Virginia Institute of Marine Science, says “The COVID-related tourism freeze provided a unique natural experiment to measure the effects of decreased tourism on fish behavior in a high-use, no-take marine protected area.” Joining Weng on the study were Dr. Alan Friedlander and Whitney Goodell of the National Geographic Society and Dr. Laura Gajdzik and Russell Sparks of the Hawaii Department of Land and Natural Resources. Friedlander and Goodell are also affiliated with the University of Hawaii at Mānoa.

    Molokini, which lies about 3 miles off the shore of Maui, was designated as a “no-take” marine protected area or MPA in 1977 based on tour operators’ concerns regarding the impacts of fishing and other “consumptive” uses. “Tour operators have always been interested in the conservation of Molokini, and have worked with the State on several measures,” says Sparks. As the volume of “non-consumptive” uses such as snorkeling and SCUBA diving increased, tour operators worked with the State to establish a limited-entry permit system for tour boats and to replace anchoring with permanent moorings to protect corals.

    The current study focused on the impacts of these non-consumptive uses. “Our research demonstrates that human presence alone can alter the community structure and possibly the functioning of an ecosystem,” says Weng. “This means we can improve how tourism is configured in Hawaii and around the world to reduce the impacts of human presence.”

    Community structure refers to the type and number of species present in an ecosystem. During Hawaii’s COVID lockdown—which began at full force in March of 2020 and was then slowly lifted until visitation returned to pre-pandemic levels in May of 2021—the researchers conducted SCUBA surveys on five separate occasions to record the species, abundance, size, and location of predatory and herbivorous fishes within Molokini’s submerged crater. They also tracked the movement of the predatory species using electronic tags. Comparing these observations with data from similar surveys conducted in the years before and after the lockdown allowed them to detect differences in fish community structure caused by human presence. The researchers gathered data on human presence using logbooks kept by the 40 charter boat companies permitted to bring tourists into Molokini’s waters.

    The results of this natural experiment were clear. “When tourism shut down due to COVID,” says Friedlander, “species that had been displaced from shallow habitats by high human presence moved back in on a timescale of months, increasing fish biomass as well as the proportion of larger predators.” The species that mainly drove the observed increase in lockdown biomass were fast-swimming predatory fishes known as jacks, which learn to fear humans as they are often targeted by anglers. When tourism resumed, the predators moved to deeper waters, reducing fish biomass and habitat use to pre-pandemic levels. Biomass is a combined measure of fish abundance and size.

    The observed changes in predator biomass were also reflected in the fish’s behavior. Before the COVID lockdown, jacks were known to leave the inside of the crater during the morning peak in tourist visits. However, during the lockdown, they remained in the shallow, sheltered interior. These predators were quickly displaced from this shallow-water habitat when tourism resumed. Their displacement is particularly concerning because their summertime spawning season overlaps with the annual peak in marine tourism.

    The human-induced displacement of predatory fishes from Molokini’s crater likely sends ripples throughout the local food web. Previous studies have shown that a drop in the abundance of predatory fishes affects not only the herbivorous fishes they count as prey, but the algae and other primary producers eaten by the herbivores. “Predators have diverse ecosystem roles,” says Friedlander, “and their loss can reduce the resistance and resilience of ecosystems to other stressors.”

    Overall, the team’s findings suggest that “Molokini is being over-used, and that management is needed to improve not only ecosystem health but the visitor experience,” says Sparks. “Our findings indicate that the business-as-usual conditions of high tourism alter community structure by displacing predatory fishes to deeper environments,” adds Weng. Moreover, a 2011 study found that more than two-thirds of visitors to Molokini felt crowded during their trip and supported actions that would reduce visitor numbers.

    “As Hawaii formulates marine management plans and undertakes the Sustainable Hawai`i Initiative,” says Gajdzik, “lessons from Molokini can help inform managers and help facilitate an effective response. As part of this process, we need to think strategically about the scale and configuration of tourism in Hawaii to optimize earnings and employment without damaging the environment.”

    “Our study indicates that the intensity of non-consumptive uses, especially in heavily visited MPAs, should be considered for the long-term health and resilience of these ecosystems,” says Weng. “Management of tourism should be guided by biological research, and include clear and well-enforced rules, adaptive management, and broad stakeholder involvement.”

    Reference: “Decreased tourism during the COVID-19 pandemic positively affects reef fish in a high use marine protected area” by Kevin C. Weng, Alan M. Friedlander, Laura Gajdzik, Whitney Goodell and Russell T. Sparks, 12 April 2023, PLOS ONE.
    DOI: 10.1371/journal.pone.0283683

    Virginia Institute of Marine Science

    Microbiology

    Surviving the Extreme: Scientists Discover Life in the Smoke of Underwater Volcanoes

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    In the depths of the ocean, along tectonic plate boundaries, hydrothermal vents emit hot fluids. These fluids lack oxygen and are rich in metals like iron, manganese, and copper, as well as potentially carrying sulfides, methane, and hydrogen. As the hot water interacts with the cold, oxygen-rich seawater nearby, it forms hydrothermal plumes composed of smoke-like metal sulfide particles.

    Rising hundreds of meters from the seafloor and dispersing thousands of kilometers away from their origin, hydrothermal plumes might appear to be inhospitable environments. Yet, a study recently published in Nature Microbiology reveals that specific bacteria manage to thrive in these seemingly precarious locations.

    “We took a detailed look at bacteria of the genus Sulfurimonas”, says first author Massimiliano Molari from the Max Planck Institute for Marine Microbiology in Bremen, Germany. These bacteria have so far only known to grow in low-oxygen environments, but gene sequences had occasionally also been detected in hydrothermal plumes. As their name suggests, they are known to use energy from sulfide.

    “It was assumed that they were flushed there from seafloor vent-associated environments. But we wondered whether the plumes might actually be a suitable environment for some members of the Sulfurimonas group.”

    Together with colleagues from the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research in Bremerhaven (AWI), and the MARUM Center for Marine Environmental Sciences of Bremen University, Molari thus took on a challenging sampling trip to hydrothermal plumes in the Central Arctic and South Atlantic Ocean.

    “We sampled plumes in extremely remote areas of ultraslow spreading ridges that were never studied before. Collecting hydrothermal plume samples is very complicated, as they are not easy to locate. Sampling becomes even more difficult when the plume is located at depths of more than 2500 meters and below Arctic sea ice, or within the stormy zones of the Southern Ocean”, explains Antje Boetius, group leader at the Max Planck Institute for Marine Microbiology and director of the AWI, who was the Chief scientist on the Arctic missions.

    Onboard of the research vessel Polarstern, the scientists managed to collect samples and within this water studied the composition and metabolism of bacteria.

    Molari and his colleagues identified a new Sulfurimonas species called USulfurimonas pluma (the superscript “U” stands for uncultivated) inhabiting the cold, oxygen-saturated hydrothermal plumes. Surprisingly, this microorganism used hydrogen from the plume as an energy source, rather than sulfide. The scientists also investigated the microbes’ genome and found it to be strongly reduced, missing genes typical for their relatives, but being well-equipped with others to allow them to grow in this dynamic environment.

    “We think that the hydrothermal plume does not only disperse microorganisms from hydrothermal vents, but it might also ecologically connect the open ocean with seafloor habitats. Our phylogenetic analysis suggests that USulfurimonas pluma could have derived from a hydrothermal vent-associated ancestor, which acquired higher oxygen tolerance and then spread across the oceans. However, that remains to be further investigated”, Molari says.

    A look at genome data from other plumes revealed that USulfurimonas pluma grows in these environments all over the world. “Obviously, they have found an ecological niche in cold, oxygen-saturated, and hydrogen-rich hydrothermal plumes”, says Molari. “That means we have to rethink our ideas on the ecological role of Sulfurimonas in the deep ocean – they might be much more important than we previously thought.”

    Reference: “A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes” by Massimiliano Molari, Christiane Hassenrueck, Rafael Laso-Pérez, Gunter Wegener, Pierre Offre, Stefano Scilipoti and Antje Boetius, 9 March 2023, Nature Microbiology.
    DOI: 10.1038/s41564-023-01342-w

    Max Planck Institute for Marine Microbiology

    Microbiology

    Researchers were able to take advantage of “an incredibly unique opportunity” to study the microbial life that rapidly …

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    Researchers were able to take advantage of “an incredibly unique opportunity” to study the microbial life that rapidly colonized a short-lived island that formed in the South Pacific after a volcanic eruption. This work, reported in mBio, revealed a variety of unique microbes that could metabolize sulfur and gases in their local atmosphere, like the extremophile microbes that are sometimes found near hydrothermal vents or in hot springs. The lead author of a report on the findings, CIRES graduate student Nick Dragone noted that, “These types of volcanic eruptions happen all over the world, but they don’t usually produce islands.”

    Hunga Tonga-Hunga Ha'apai in 2017 / Image credit: NASA/Damien Grouille/Cecile Sabau

    But in 2015, an eruption of a submarine volcano created the Hunga Tonga Hunga Ha’apai Island, which existed for seven years. The formation of the island is described in the NASA video below. During the island’s lifetime, the study authors collected soil samples from the site and sent them off to the laboratory so that DNA in those samples could be extracted. By analyzing the genetic sequences, the scientists determined that some unusual bacteria were living on the island.

    The investigators said they were surprised by the findings. Instead of revealing organisms that accompany the retreat of glaciers, or marine microbes like cyanobacteria, they found something else — an unusual bunch of microbes that metabolize sulfur and atmospheric gases.

    On January 15, 2022, the research team got another surprise; there was another eruption near the island, which destroyed the entire landmass in the 21st century’s largest volcanic explosion (so far). Now, the site can’t be monitored ever again.

    “We were all expecting the island to stay,” said Dragone. “In fact, the week before the island exploded we were starting to plan a return trip.”

    Luckily the team was able to make use of the island while it existed. “No one had ever comprehensively studied the microorganisms on this type of island system at such an early stage before,” added Dragone.

    The short life of the island, and its volcanic origins, fostered an unusual community of microbes, as well as an international group of researchers working together. Learning more about this unique type of microbial community can provide insights into how ecosystems might start to develop, even before organisms like plants or animals arrive on the scene, noted corresponding study author and CIRES fellow Noah Fierer, a professor of ecology and evolutionary biology at CU Boulder.

    Sources: University of Colorado Boulder (CU Boulder) and Cooperative Institute for Research in Environmental Sciences (CIRES), mBio


    Carmen Leitch

    Microbiology

    Experiment Proves Bacteria Really Eat Plastic – Broken Down Into Harmless Substances

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    The bacterium Rhodococcus ruber eats and actually digests plastic. This has been shown in laboratory experiments by PhD student Maaike Goudriaan at Royal Netherlands Institute for Sea Research (NIOZ). Based on a model study with plastic in artificial seawater in the lab, Goudriaan calculated that bacteria can break down about one percent of the fed plastic per year into CO2 and other harmless substances. “But,” Goudriaan emphasizes, “this is certainly not a solution to the problem of the plastic soup in our oceans. It is, however, another part of the answer to the question of where all the ‘missing plastic’ in the oceans has gone.”

    Goudriaan had a special plastic manufactured especially for these experiments with a distinct form of carbon (13C) in it. When she fed that plastic to bacteria after pretreatment with “sunlight” — a UV lamp — in a bottle of simulated seawater, she saw that special version of carbon appear as CO2 above the water. “The treatment with UV light was necessary because we already know that sunlight partially breaks down plastic into bite-sized chunks for bacteria,” the researcher explains.

    “This is the first time we have proven in this way that bacteria actually digest plastic into CO2 and other molecules,” Goudriaan states. It was already known that the bacterium Rhodococcus ruber can form a so-called biofilm on plastic in nature. It had also been measured that plastic disappears under that biofilm. “But now we have really demonstrated that the bacteria actually digest the plastic.”

    When Goudriaan calculates the total breakdown of plastic into CO2, she estimates that the bacteria can break down about one percent of the available plastic per year. “That’s probably an underestimate,” she adds. “We only measured the amount of carbon-13 in CO2, so not in the other breakdown products of the plastic. There will certainly be 13C in several other molecules, but it’s hard to say what part of that was broken down by the UV light and what part was digested by the bacteria.”

    Even though marine microbiologist Goudriaan is very excited about the plastic-eating bacteria, she stresses that microbial digestion is not a solution to the huge problem of all the plastic floating on and in our oceans. “These experiments are mainly a proof of principle. I see it as one piece of the jigsaw, in the issue of where all the plastic that disappears into the oceans stays. If you try to trace all our waste, a lot of plastic is lost. Digestion by bacteria could possibly provide part of the explanation.”

    To discover whether ‘wild’ bacteria also eat plastic ‘in the wild’, follow-up research needs to be done. Goudriaan already did some pilot experiments with real sea water and some sediment that she had collected from the Wadden Sea floor. “The first results of these experiments hints at plastic being degraded, even in nature,” she says. “A new PhD student will have to continue that work. Ultimately, of course, you hope to calculate how much plastic in the oceans really is degraded by bacteria. But much better than cleaning up, is prevention. And only we humans can do that,” Goudriaan says.

    Recently Goudriaan’s colleague Annalisa Delre published a paper about sunlight which breaks down plastics on the ocean’s surfaces. Floating microplastic is broken down into ever smaller, invisible nanoplastic particles that spread across the entire water column, but also to compounds that can then be completely broken down by bacteria. This is shown by experiments in the laboratory of NIOZ, on Texel.

    In the latest issue of the Marine Pollution Bulletin, PhD student Annalisa Delre and colleagues calculate that about two percent of visibly floating plastic may disappear from the ocean surface in this way each year. “This may seem small, but year after year, this adds up. Our data show that sunlight could thus have degraded a substantial amount of all the floating plastic that has been littered into the oceans since the 1950s,” says Delre.

    Reference: “A stable isotope assay with 13C-labeled polyethylene to investigate plastic mineralization mediated by Rhodococcus ruber” by Maaike Goudriaan, Victor Hernando Morales, Marcel T. J. van der Meer, Anchelique Mets, Rachel T. Ndhlovu, Johan van Heerwaarden, Sina Simon, Verena B. Heuer, Kai-Uwe Hinrichs and Helge Niemann, 30 November 2022, Marine Pollution Bulletin.
    DOI: 10.1016/j.marpolbul.2022.114369

    Royal Netherlands Institute for Sea Research (NIOZ)

    Microbiology

    There are many microbes that perform essential functions that we don’t even have to think about. For example, …

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    There are many microbes that perform essential functions that we don’t even have to think about. For example, the ocean is full of Prochlorococcus bacteria, which generate huge amounts of the oxygen in the seas, from the poles to the tropics. They are thought to be the most abundant photosynthetic organisms in the world. Now scientists have learned more about how these microbes are able to survive in so many places. Prochlorococcus bacterial cells can exchange genetic information with one another, which is no surprise; but they can do so in a way that has never been observed before. Huge segments of DNA with blocks of genes can be transmitted from one Prochlorococcus cell to another, enabling them to take on new abilities such as metabolic reactions or viral defense strategies even when few of the microbes are present in one location.

    A TEM image of Prochlorococcus marinus - a globally important marine cyanobacterium./ Public domain image courtesy of Luke Thompson from Chisholm Lab and Nikki Watson from Whitehead, MIT

    Scientists have now described this new process of horizontal gene transfer, in which one organism passes genetic material directly to another in a way that does not involve inheritance. The findings have been reported in Cell.

    Sequences of DNA that contain several genes and their surrounding sequences that get transferred through this method have been called tycheposons. They can separate from their original location spontaneously and then migrate to another organism, probably through cellular sacs known as vesicles, which bud from cell membranes.

    “We’re very excited about it because it’s a new horizontal gene transfer agent for bacteria, and it explains a lot of the patterns that we see in Prochlorococcus in the wild, the incredible diversity,” said Professor Sallie “Penny” Chisholm of MIT, who aided in the discovery of Prochlorococcus in 1988 and is featured in the video below.

    This work started with an analysis of genetic sequences from hundreds of different Prochlorococcus species. The researchers wanted to know how they quickly gained or lost functions, while they did not display any of the known mechanisms of horizontal gene transfer, or features of mobile genetic elements. The researchers found genetic regions or islands that were hotspots of variation, which often contained genes that conferred abilities to deal with certain nutrients.

    These islands often varied significantly between Prochlorococcus species, but they kept appearing in the same part of the Prochlorococcus genome, and sometimes they were almost the same, even in very different species; this was all evidence of that some kind of horizontal transfer was occurring.

    The scientists have discovered something that was like a genetic LEGO set, according to MIT postdoctoral researcher Thomas Hackl. The microbes could use this system to quickly adapt to their environment, such as by acquiring a gene that improved their ability to absorb an important nutrient that was scarce. The researchers were even able to collect some of these vesicles and capsids from the open ocean, and they were “actually quite enriched” with tycheposons.

    The team discovered that there are several mechanisms that Prochlorococcus uses to transport genes. They might use membrane vesicles as little sacs containing tycheposons, or they may hijack a viral infection that can then move the tycheposons along with the virus. These modes of transport are especially valuable in the open ocean, where cell to cell contact is very challenging, noted Hackl.

    This phenomenon may also occur in other marine bacteria, suggested Hackl. The researchers have already found genetic elements in other bacteria that are similar to those found in Prochlorococcus.

    Sources: Massachusetts Institute of Technology (MIT), Cell


    Carmen Leitch