“Soil is mostly microorganisms, both alive and dead,” says Jennifer Bhatnagar, soil microbiologist and Boston University College of Arts & Sciences assistant professor of biology. It’s typical to see several hundred different types of fungi and bacteria in a single pinch of soil off the ground, she says, making it one of the most diverse ecosystems that exist.

Because there’s still so much unknown about soil organisms, until now scientists have not attempted to predict where certain species or groups of soil microbes live around the world. But having that knowledge about these organisms — too small to see with the naked eye — is key to better understanding the soil microbiome, which is made up of the communities of different microbes that live together.

A team of BU biologists, including Bhatnagar, took on that challenge — and their research reveals, for the first time, that it is possible to accurately predict the abundance of different species of soil microbes in different parts of the world. The team recently published their findings in a new paper in Nature Ecology & Evolution.

“If we know where organisms are on earth, and we know how they change through space and time due to different environmental forces, and something about what different species are doing, then we can much better predict how the function of these communities will change in terms of carbon and nutrient cycling,” Bhatnagar says. That kind of knowledge would have huge implications for agriculture, climate change, and public health.

“The health of the soils is so tied to the soil microbes,” says Michael Dietze, senior author on the study and a BU College of Arts & Sciences professor of earth and environment. Dietze, Bhatnagar, and researchers from their labs joined forces to work on this project, which involved analyzing hundreds of soil samples collected by National Ecological Observatory Network (NEON) research sites. Bhatnagar and her lab members brought to the team their soil expertise, while Dietze and his lab offered their unique ability to develop precise ecological forecasts and near-term environmental predictions.

The team learned that microbe predictability increases as spatial area increases, so the bigger the piece of land their model makes forecasts about, the more likely the predictions about what types of microbes live there will be accurate.

Dietze says the ability to accurately predict which microbes would likely be found in a given soil sample also increased as the researchers looked at organism groupings higher up on the phylogenetic scale, a system that classifies organisms based on evolutionary relatedness. On the smallest end of the scale, a “species” represents the finest level of classification; on the other end, a “phylum” makes up the largest and most diverse groupings of organisms. They were surprised to find that they were better able to predict the presence of a whole phylum, as opposed to individual species.

After receiving the genomic data of the soil samples from NEON, the research team’s forecasting models take into account environmental factors specific to the place where the soil came from — what plants live there, the soil acidity (pH), temperature, climate, and many others. They found their model was best able to predict the presence of microorganisms based on their symbiotic relationship with local plant species. Mycorrhizal fungi, for example, is a very common soil microbe that about 90 percent of plant families associate with, including pines and oak trees in New England.

In contrast, the team found it was more difficult to predict large groups of organisms based on their relationship with soil acidity. Despite knowing soil acidity levels, and what types of bacteria would typically like to live in that environment, their model couldn’t accurately predict the amount of bacteria that were actually present in the soil sample, Bhatnagar says. “That means there is something else beyond the relationship with [acidity], beyond the relationship with any other environmental factor that we typically measure in our ecosystems,” she says.

Now, Dietze and Bhatnagar’s team are expanding their forecasts beyond predicting microbes based on only their location, to also include specific times of the year.

“Building a framework for forecasting the soil microbiome at sites across the US will improve our understanding of seasonal and interannual change,” says Zoey Werbin, a PhD student working in Bhatnagar’s lab and an author on the paper. “This could help us anticipate how climate change could affect microbial processes like decomposition or nitrogen cycling.”

With her dissertation project, Werbin hopes to answer fundamental questions about how and why the soil microbiome varies over time and space.

“The more we learn, the more we realize how important soil microbes are for agriculture, public health, and climate change. It’s really exciting to investigate how microscopic organisms can have such large-scale effects,” Werbin says. “We know certain factors, like temperature and moisture, affect microbial communities. But we don’t know how important those factors are compared to natural variability, or interactions between microbes. My PhD project will help identify the driving forces of the soil microbiome, as well as the biggest sources of uncertainty.”

Segrè, director of the Boston University Microbiome Initiative, says he and other scientists in his field of synthetic and systems biology are studying microbiomes — microscopic communities of bacteria, fungi, or a combination of those that exert influence over each other and the surrounding environment. They want to know how microbiomes might be directed to carry out important tasks like absorbing more atmospheric carbon, protecting coral reefs from ocean acidification, improving the fertility and yield of agricultural lands, and supporting the growth of forests and other plants despite changing environmental conditions.

“Microbes affect us as humans through their own metabolic processes, they affect our planet through what they consume and secrete, they help create the oxygen we breathe,” says Segrè, a BU College of Arts & Sciences professor of biology and bioinformatics, and a College of Engineering professor of biomedical engineering. “A long time ago microbes are what made multicellular life possible.”

But, unlike many other synthetic biologists who are working to enhance or genetically engineer microbes directly, Segrè is more interested in how to direct the behavior of a microbiome by tweaking the environmental conditions it lives within — an approach he says could be better described as “synthetic ecology.”

“The more traditional synthetic biology approach would be to manipulate the genomes of the microbes,” Segrè says. “But we’re trying to manipulate microbial ecosystems using environmental molecules.”

“We know that microbial interactions with the environment are important,” says Alan Pacheco, who earned his PhD in bioinformatics working in Segrè’s lab. Some of those interactions benefit several microbial species, some only benefit one species in a community, and some can be harmful to certain species, he says. “But there’s still so much we don’t know about why these interactions happen the way that they do.”

In a new study recently published in Nature Communications, Segrè, Pacheco, and their collaborator Melisa Osborne, a research scientist in Segrè’s lab, explored how the presence of 32 different environmental molecules or nutrients, alone or in combination with others, would influence the growth rate of microbial communities and the mix of diverse species making up a given microbiome.

“In the back of our minds we had this idea of diet, framed by studies that have looked at differences in the gut microbiome based on Western vs hunter-gatherer diets,” says Pacheco, who is now a postdoctoral fellow at ETH Zürich. Hunter-gatherer diets, opportunistic and comprising a wide range of plant-based food sources, are considered much more diverse than the Western diet, which is why the hunter-gatherer diet is thought to cultivate a healthier gut.

But the experimental results surprised the team. They expected they would see growth and diversity of microbiomes increase as the “bugs” had more access to a variety of foods — a range of carbons, including sugars, amino acids, and complex polymers — but that’s not what their carefully controlled experiments revealed. Instead, they observed that competition for food between different species of microbes hampered diversification within the microbial community.

“Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems,” the authors write.

So, what are the mechanisms that control a microbiome’s diversity? “It’s going to take some time to figure out the cause of all these interactions,” Segrè says.

Although increasing the variety of food sources didn’t increase the variety of microbial species within their experiments, more food did fuel more microbial growth. “We found yield depends on the total number of carbon sources, but not on the variety of those sources,” Segrè says. “It’s like people at a picnic — if enough people come to a picnic, no matter what the spread of different foods, eventually everything will be eaten up. In many of our experiments, the microbial communities used up every last bit of carbon source to the fullest extent.”

Pacheco adds that if somebody can consume something, somebody else can outcompete them for it. “Our experiments showed that the crucial modulator in microbial diversity is how much these different organisms compete with one another for resources,” he says. “The more organisms compete, the less diverse that community is going to be.”

The team plans to do more research into additional environmental factors, investigating how nutrient access and variety changes microbial communities over time, and how the medium that the microbial community lives in affects their consumption and secretion of molecules. They are also exploring how metabolic processes amongst different microbial species could interact and interplay with each other, and how the ability of some organisms to sequentially or simultaneously consume multiple resources affects the microbiome overall.

Further unlocking and eventually harnessing all these environmental “dials and knobs” could open doors to using microbiomes to influence human metabolisms and health or disease states in people and in natural ecosystems.

The researchers, including UW-Madison geography Professor Lisa Naughton, investigated mining-related deforestation in a biodiverse and ecologically sensitive area of the Peruvian Amazon to see whether formalizing and legalizing these mining operations might curb some of their negative effects.

Their study, published June 2 in the journal Environmental Research Letters, was co-authored by a group including UW-Madison alumnae Nora Álvarez-Berríos, now studying land-use and climate impacts at the International Institute of Tropical Forestry, and Jessica L’Roe, now a geography professor at Middlebury College.

The team focused on an area around the Tambopata National Reserve in Peru from 2001 to 2014. During this time period, Naughton says, demand for gold rose, roads penetrated the region and mining surged. In turn, mining-related deforestation rose by almost 100,000 acres over their study period.

“Because the gold is in the sediment scattered under the forest floor, to extract the gold, you have to remove the forest and dig,” Álvarez-Berríos says. “You have to cut a lot of the forest and excavate sensitive waterways.”

While these mining operations are often called “artisanal” or “small-scale,” in aggregate they are very destructive. In many countries they operate outside the law, and millions of people are involved across the tropics. Álvarez-Berríos says the typical first step to reducing the environmental impact of artisanal mining is bringing it under governmental oversight, formalizing the activity. That way, local agencies can manage the impacts and protect both ecologically sensitive areas and the economic well-being of poor mine workers.

“Peruvian authorities, like authorities in other gold-rush sites, have given up on trying to stop gold mining. They’re trying to confine it and contain it,” L’Roe says. “Most of the studies about formalization are mainly about trying to help the poor, or make it more fair for the poor. Seldom, almost never, as far as we can tell, have these formalization projects been assessed for their environmental impact. So that’s what we were looking at.”

During their study period, local agencies issued provisional titles to miners to conduct their operations safely. After receiving a provisional title, miners would, in theory, undergo a series of environmental impact and compliance assessments before they started work.

But, as L’Roe says they found, the regulation process took a long time. Many miners simply took their provisional title as a green light to start mining, and never went through with the environmental impact assessments. Over their study period, no mining operations made it through the full compliance process, and as such they found little evidence for improved environmental outcomes in formalized mining areas.

To assess environmental outcomes, the team used satellite imagery analysis to see how much of the forest had been cut down, as compared to areas without formalized mining regulations.

Naughton says while formalizing mining has the potential to decrease environmental damage, it needs enforcement and regulations that match the local context. Formalization without environmental impact assessment or enforcement could just encourage more damaging and dangerous mining, or the expansion of these operations under the pretense that what they’re doing is legal.

But gold rushes are exactly what they sound like, Naughton says: rushed. They’re fast, and slow formalization processes with many steps and provisions and impact assessments often cannot keep up with the pace of extraction.

“To sort out in a fair way who owns what land, with what rights, that is a slow process,” Naughton says. “This gold rush is explosive. By the time you have well-regulated and transparent public land and property rights, the forest will be gone.”

The team plans to go back to Tambopata to present its results to local stakeholders. Many members of the community are already aware of the problems with mining formalization but have not had a chance to systematically study the environmental consequences. The three co-authors hope their study will set a precedent for monitoring formalization interventions in Tambopata and other tropical sites losing forest to mining. They are already sharing results and methods with colleagues concerned about gold mining impacts in Colombia, Brazil and Bolivia.

“We’ll go back to our study site and share the results — but in a humble way because folks there know that it hasn’t worked well, and they know the problems,” says Álvarez-Berríos. “So, yes, it’s important to share it with that group of stakeholders and experts, but maybe even more important is to share the results and our methods and design for studying this problem with folks working in the many, many other areas where there’s uncontrolled small-scale gold mining and where formalization efforts are being launched with best intentions.”

New research shows a crucial piece has been missing from the conventional explanation for what happens between this first “fixing” of CO₂ into phytoplankton and its eventual release to the atmosphere or descent to depths where it no longer contributes to global warming. The missing piece? Fungus.

“Basically, carbon moves up the food chain in aquatic environments differently than we commonly think it does,” said Anne Dekas, an assistant professor of Earth system science at Stanford University. Dekas is the senior author of a paper published June 1 in Proceedings of the National Academy of Sciences that quantifies how much carbon goes into parasitic fungi that attack microalgae.

Underwater merry-go-round

Researchers until now have predicted that most carbon fixed into colonies of hard-shelled, single-celled algae known as diatoms then funnels directly into bacteria — or dissolves like tea in the surrounding water, where it’s largely taken up by other bacteria. Conventional thinking assumes carbon escapes from this microbial loop mainly through larger organisms that graze on the bacteria or diatoms, or through the CO₂ that returns to the atmosphere as the microbes breathe.

This journey is important in the context of climate change. “For carbon sequestration to occur, carbon from CO₂ needs to go up the food chain into big enough pieces of biomass that it can sink down into the bottom of the ocean,” Dekas said. “That’s how it’s really removed from the atmosphere. If it just cycles for long periods in the surface of the ocean, it can be released back to the air as CO₂.”

It turns out fungus creates an underappreciated express lane for carbon, “shunting” as much as 20 percent of the carbon fixed by diatoms out of the microbial loop and into the fungal parasite. “Instead of going through this merry-go-round, where the carbon could eventually go back to the atmosphere, you have a more direct route to the higher levels in the food web,” Dekas said.

The findings also have implications for industrial and recreational settings that deal with harmful algal blooms. “In aquaculture, in order to keep the primary crop, like fish, healthy, fungicides might be added to the water,” Dekas said. That will prevent fungal infection of the fish, but it may also eliminate a natural check on algal blooms that cost the industry some $8 billion per year. “Until we understand the dynamics between these organisms, we need to be pretty careful about the management policies we’re using.”

Microbial interactions

The authors based their estimates on experiments with populations of chytrid fungi called Rhizophydiales and their host, a type of freshwater algae or diatom named Asterionella formosa. Coauthors in Germany worked to isolate these microbes, as well as bacteria found in and around their cells, from water collected from Lake Stechlin, about 60 miles north of Berlin.

“Isolating one microorganism from nature and growing it in the laboratory is difficult, but isolating and maintaining two microorganisms as a pathosystem, in which one kills the other, is a true challenge,” said lead author Isabell Klawonn, who worked on the research as a postdoctoral scholar in Dekas’ lab at Stanford. “Only a few model systems are therefore available to research such parasitic interactions.”

Scientists surmised as early as the 1940s that parasites played an important role in controlling the abundance of phytoplankton, and they observed epidemics of chytrid fungus infecting Asterionella blooms in lake water. Technological advances have made it possible to pick apart these invisible worlds in fine and measurable detail — and begin to see their influence in a much bigger picture.

“We’re realizing as a community that it’s not just the capabilities of an individual microorganism that’s important for understanding what happens in the environment. It’s how these microorganisms interact,” Dekas said.

The authors measured and analyzed interactions within the Lake Stechlin pathosystem using genomic sequencing; a fluorescence microscopy technique that involves attaching fluorescent dye to RNA within microbial cells; and a highly specialized instrument at Stanford — one of only a few dozen in the world — called NanoSIMS, which creates nanoscale maps of the isotopes of elements that are present in materials in vanishingly small amounts. Dekas said, “To get these single-cell measurements to show how photosynthetic carbon is flowing between specific cells, from the diatom to the fungus to the associated bacteria, it’s the only way to do it.”

The exact amount of carbon diverted to fungus from the microbial merry-go-round may differ in other environments. But the discovery that it can be as high as 20 percent in even one setting is significant, Dekas said. “If you’re changing this system by more than a few percent in any direction, it can have dramatic implications for biogeochemical cycling. It makes a big difference for our climate.”

Why do some babies react to perceived danger more than others? According to new research from Michigan State University and the University of North Carolina, Chapel Hill, part of the answer may be found in a surprising place: an infant’s digestive system.

The human digestive system is home to a vast community of microorganisms known as the gut microbiome. The MSU-UNC research team discovered that the gut microbiome was different in infants with strong fear responses and infants with milder reactions.

These fear responses — how someone reacts to a scary situation — in early life can be indicators of future mental health. And there is growing evidence tying neurological well-being to the microbiome in the gut.

The new findings suggest that the gut microbiome could one day provide researchers and physicians with a new tool to monitor and support healthy neurological development.

“This early developmental period is a time of tremendous opportunity for promoting healthy brain development,” said MSU’s Rebecca Knickmeyer, leader of the new study published June 2 in the journal Nature Communications. “The microbiome is an exciting new target that can be potentially used for that.”

Studies of this connection and its role in fear response in animals led Knickmeyer, an associate professor in the College of Human Medicine’s Department of Pediatrics and Human Development, and her team to look for something similar in humans. And studying how humans, especially young children, handle fear is important because it can help forecast mental health in some cases.

“Fear reactions are a normal part of child development. Children should be aware of threats in their environment and be ready to respond to them” said Knickmeyer, who also works in MSU’s Institute for Quantitative Health Science and Engineering, or IQ. “But if they can’t dampen that response when they’re safe, they may be at heightened risk to develop anxiety and depression later on in life.”

On the other end of the response spectrum, children with exceptionally muted fear responses may go on to develop callous, unemotional traits associated with antisocial behavior, Knickmeyer said.

To determine whether the gut microbiome was connected to fear response in humans, Knickmeyer and her co-workers designed a pilot study with about 30 infants. The researchers selected the cohort carefully to keep as many factors impacting the gut microbiome as consistent as possible. For example, all of the children were breastfed and none was on antibiotics.

The researchers then characterized the children’s microbiome by analyzing stool samples and assessed a child’s fear response using a simple test: observing how a child reacted to someone entering the room while wearing a Halloween mask.

“We really wanted the experience to be enjoyable for both the kids and their parents. The parents were there the whole time and they could jump in whenever they wanted,” Knickmeyer said. “These are really the kinds of experiences infants would have in their everyday lives.”

Compiling all the data, the researchers saw significant associations between specific features of the gut microbiome and the strength of infant fear responses.

For example, children with uneven microbiomes at 1 month of age were more fearful at 1 year of age. Uneven microbiomes are dominated by a small set of bacteria, whereas even microbiomes are more balanced.

The researchers also discovered that the content of the microbial community at 1 year of age related to fear responses. Compared with less fearful children, infants with heightened responses had more of some types of bacteria and less of others.

The team, however, did not observe a connection between the children’s gut microbiome and how the children reacted to strangers who weren’t wearing masks. Knickmeyer said this is likely due to the different parts of the brain involved with processing potentially frightening situations.

“With strangers, there is a social element. So children may have a social wariness, but they don’t see strangers as immediate threats,” Knickmeyer said. “When children see a mask, they don’t see it as social. It goes into that quick-and-dirty assessment part of the brain.”

As part of the study, the team also imaged the children’s brains using MRI technology. They found that the content of the microbial community at 1 year was associated with the size of the amygdala, which is part of the brain involved in making quick decisions about potential threats.

Connecting the dots suggests that the microbiome may influence how the amygdala develops and operates. That’s one of many interesting possibilities uncovered by this new study, which the team is currently working to replicate. Knickmeyer is also preparing to start up new lines of inquiry with new collaborations at IQ, asking new questions that she’s excited to answer.

“We have a great opportunity to support neurological health early on,” she said. “Our long-term goal is that we’ll learn what we can do to foster healthy growth and development.”

Salt marshes are the link between the land and open ocean ecosystems, and — in a way — between urban environments and the wild ocean. Microplastics (plastic particles smaller than 5 millimeters) tend to float on the water surface, but salt marshes fill and empty with the tides, so particles that would normally float get trapped within branches and roots and settle into the marsh soil.

Sediments accumulate in the salt marsh layer after layer, like tree rings, keeping an historical record of sedimentation within the ecosystem. “By accumulating sediments, they are keeping a record in time,” says Javier Lloret, MBL research scientist and co-first author on the paper.

Globally, scientists estimate that about 8 million tons of plastic enter the ocean each year. But until now, there’s been no estimation of the amount of that plastic that gets trapped in salt marsh ecosystems.

By taking core samples of the marsh sediment at six different estuaries in the Waquoit Bay system on Cape Cod, as well as New Bedford, Mass., harbor, the researchers were able to trace the abundance of microplastics dating back decades in areas with very contrasted degrees of land use.

“As you go into the past, the amount of microplastics you find decreases clearly,” says Lloret. “The amount of microplastics you find in sediments is related to the population numbers… but also the amount of plastic that people use.”

“Waquoit Bay is the perfect salt marsh system to study plastic pollution because we can contrast one area that is almost pristine… with another area that is highly impacted by human activity,” says Rut Pedrosa-Pàmies, also an MBL research scientist and co-first author on the paper. “We found a broad range of plastic pollution.”

The researchers focused on two types of microplastic pollution: fragments (from the breakdown of larger plastic pieces) and fibers (thread-like plastics which tend to shed from clothing and fishing gear). They found that fragment pollution increased both through time and with urbanization. The more populated the area surrounding the collection site, the more plastic fragments the researchers observed.

One surprise in the data was that microplastic concentration in the sediments wasn’t linear as urbanization grew. Up to 50% development, the concentration of microplastic fragments was relatively unchanged, but once the land was occupied at 50%, the number of microplastics grew exponentially.

“Just a few people in the surrounding area is not going to change much, but when urban uses occupy more than 50% of the land, the number of microplastics goes crazy,” says Lloret.

The microplastic fibers didn’t have the same relationship with urbanization. “Even in the more pristine areas that don’t have urbanization, we find fiber plastic pollution” says Pedrosa-Pàmies.

The researchers believe the fragments have a local origin (people using and disposing of plastics where they live) whereas fibers can be transported long distances by air or by water from large-scale urban areas.

“When we started, we didn’t know if microplastics were an issue here on Cape Cod, or not. No one had analyzed the marsh sediments on Cape Cod for microplastics before,” says Lloret.

Now that the scientists have shown there is microplastic pollution in New England salt marshes, the next step is to gain further insight. How are those particles arriving in the ecosystem? What are the sources? How are they impacting the ecosystem and the food web of the organisms that live there?

“There are still a lot of unanswered questions,” says Pedrosa-Pàmies. “This is the first step for management, too.”

Story Source:

Materials provided by Marine Biological Laboratory. Original written by Emily Greenhalgh. Note: Content may be edited for style and length.

Perchlorate, a negative ion consisting of one chlorine atom bonded to four oxygen atoms, occurs naturally in some soils on Earth, and is especially abundant in Martian soil. As a powerful oxidizer, perchlorate is also manufactured and used in solid rocket fuel, fireworks, munitions, airbag initiators for vehicles, matches and signal flares. It is a byproduct in some disinfectants and herbicides.

Because of its ubiquity in both soil and industrial goods, perchlorate is a common water contaminant that causes certain thyroid disorders. Perchlorate bioaccumulates in plant tissues and a large amount of perchlorate found in Martian soil could make food grown there unsafe to eat, limiting the potential for human settlements on Mars. Perchlorate in Martian dust could also be hazardous to explorers. Current methods of removing perchlorate from water require either harsh conditions or a multistep enzymatic process to lower the oxidation state of the chlorine element into the harmless chloride ion.

Doctoral student Changxu Ren and Jinyong Liu, an assistant professor of chemical and environmental engineering at UC Riverside’s Marlan and Rosemary Bourns College of Engineering, took inspiration from nature to reduce perchlorate in water at ambient pressure and temperature in one simple step.

Ren and Liu noted anaerobic microbes use molybdenum in their enzymes to reduce perchlorate and harvest energy in oxygen-starved environments.

“Previous efforts in constructing a chemical molybdenum catalyst for perchlorate reduction have not been successful,” Liu said. “Many other metal catalysts either require harsh conditions or are not compatible with water.”

The researchers tried to emulate the complicated microbial perchlorate reduction process with a simplified approach. They found by simply mixing a common fertilizer called sodium molybdate, a common organic ligand called bipyridine to bind the molybdenum, and a common hydrogen-activating catalyst called palladium on carbon, they produced a powerful catalyst that quickly and efficiently broke down the perchlorate in water using hydrogen gas at room temperature with no combustion involved.

“This catalyst is much more active than any other chemical catalyst reported to date and reduces more than 99.99% of the perchlorate into chloride regardless of the initial perchlorate concentration,” Ren said.

The new catalyst reduces perchlorate in a wide concentration range, from less than 1 milligram per liter to 10 grams per liter. This makes it suitable for use in various scenarios, including remediating contaminated groundwater, treating heavily contaminated wastewater from explosives manufacturing, and making Mars habitable.

“A convenient catalytic reduction system may help harvest oxygen gas from perchlorate washed from the Martian soil when the catalyst is coupled with other processes,” Liu said.

Story Source:

Materials provided by University of California – Riverside. Original written by Holly Ober. Note: Content may be edited for style and length.