Seasons of the Microbiome Over the Amazon Rainforest | The Well

Posted 6 days, 11 hours ago @
Seasons of the Microbiome Over the Amazon Rainforest

Isabella Hrabe de Angelis on top of the Amazon Tall Tower Observatory north of Manaus, Brazil. Credit: Oliver Lauer

One may not think of the Earth’s atmosphere as “inhabited,” but it holds a multitude of suspended, biological particles (bioaerosols) that originate from bacteria, fungi, algae, plants and animals. Bioaerosols play an important role for ecosystems and the climate because they disperse microbes, influence radiation absorption, scatter sunlight, or nucleate cloud condensation. The diverse microbes living in bioaerosols are collectively called the aerosol microbiome.

The Amazon Basin, which harbors the world’s largest tropical forest, may contribute significantly to emissions of bioaerosols on a global scale. But little is known about how environmental variables affect bioaerosol composition in the Amazon. A new study led by scientists from the Universidade Federal do Paraná in Brazil (with MBL’s Emil Ruff collaborating) suggests that microbes in Amazon Basin bioaerosols originate mostly from leaf surfaces, not from the soil. Further, seasonal changes in temperature, relative humidity and precipitation are the primary drivers of compositional changes in this aerosol microbiome.

Isabella Hrabe de Angelis, a PhD student at the Max Planck Institute for Chemistry in Germany, supported the study with bioinformatic analyses of the Amazon microbiome data. (MBL scientist Zoe Cardon is on her doctoral committee.) As part of her work, Hrabe de Angelis participated in six field expeditions to the Amazon Tall Tower Observatory, a remote and pristine sampling site in the rainforest north of Manaus, Brazil.

The Amazon Tall Tower Observatory is 325 meters high and was built to study and monitor interactions between the rainforest and the atmosphere. Credit: Isabella Hrabe de Angelis


Felipe F.C. Souza et al (2021) Influence of seasonality on the aerosol microbiome of the Amazon rainforest. Science of the Total Environment, DOI: 10.1016/j.scitotenv.2020.144092

Further info:

Not All Nitrogen is Created Equal: A Long-Term Study from a New England Salt Marsh | The Well

December 11th, 2020 @

In a study published this week, scientists including MBL Ecosystems Center Director Anne Giblin reveal that different forms of nitrogen have different impacts on a salt marsh ecosystem. The study, conducted at the Plum Island Ecosystem LTER, argues that both the form and quantity of nitrogen influx to the coasts, and how these different forms of nitrogen mediate the balance between marsh carbon storage and loss, will be crucial for managing coastal wetlands as sea levels continue to rise. This article is provided by Northeastern University’s Marine Science Center.

On the cover of this month’s issue of BioScience, the tranquil scene of an evening in the tidal marsh belies the complex biological interplay of nutrients and organisms found within. The impacts and mechanisms of nutrient enrichment in this coastal zone, particularly of nitrogen introduced by human activity, are well documented in literature — but a new study in December’s BioScience suggests that understanding the forms of nitrogen in the system is a missing piece of the coastal management puzzle.

The study, led by Dr. Jennifer Bowen, Associate Professor and Associate Chair of the Northeastern’s Marine and Environmental Sciences Department, synthesizes a decade of research from her team and collaborators, focused on understanding human impacts on the structure and function of salt marsh systems. Dr. Bowen has long used the living labs of the Boston area coasts to examine how urban ecosystems and microbial communities influence biogeochemical cycling. Her latest work examines nitrogen forms and flows in the TIDE project, a long-term nutrient enrichment experiment led by co-author Linda Deegan of the Woodwell Climate Research Center that is based at the NSF supported Plum Island Long-Term Ecological Research site in northern Massachusetts. Co-author Anne Giblin of the Marine Biological Laboratory, Woods Hole, is lead principal investigator of the Plum Island research site. Read more …

Photo: Cordgrass in a salt marsh at the Plum Island research site. Credit: David Johnson @DavidSamJohnson

Cover photo: Jennifer Bowen of Northeastern University.

Source: Understanding Nitrogen’s Impact on Coastal Zones – Northeastern University College of Science

Originally posted on The Well

Moore Foundation Funds MBL Teams for Symbiosis Research | The Well

July 28th, 2020 @

The Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative is investing $19 million over the next three years to support 42 teams of scientists, including four teams with MBL researchers, to collaboratively develop tools and methods to advance model systems in aquatic symbiosis. The Initiative’s funding aims to equip the scientific community with Moore Foundation Funds MBL Teams for Symbiosis Researchinfrastructure such as new genetic tools, cultivation methods, and nanoscale microscopy to improve experimental capabilities in aquatic symbiosis research over the coming decade. Read more about the initiative …

The MBL scientists funded in this grant include:

Project title: Underground Allies: Dynamic Interactions Among Cordgrass (Spartina alterniflora) and Sulfur-Cycling Microbes in the Rhizosphere
Principal Investigator: Zoe Cardon, MBL
Co-Investigators: Anne Giblin, Elena L. Peredo, Blair Paul, and Emil Ruff, MBL

Summary: Spartina alterniflora  is a native cordgrass dominating intertidal salt marsh platforms along thousands of miles of the U.S. East and Gulf coasts. The interaction among Spartina roots, sulfate reducing bacteria, and sulfur oxidizing bacteria is at the core of salt marsh health. We aim to establish a model system for understanding mechanisms underlying this symbiosis using plants and microbes isolated from the Plum Island Ecosystem Long Term Ecological Research site north of Boston. The Spartina root system and its associated sulfur-cycling microbes control an ecosystem-scale production, recycling and detoxification system, maintaining vast expanses of clonal Spartina that are crucibles for marine coastal life, and creating peat platforms critical for salt marsh persistence in the face of rising sea levels.

Read the complete story on The Well...

UMass Amherst Microbiologists Clarify Relationship Between Microbial Diversity and Soil Carbon Storage | UMass Amherst News

July 27th, 2020 @

More diverse soils did perform better, but drought stress found to be a limiting factor

In what they believe is the first study of its kind, researchers led by postdoctoral researcher Luiz A. Domeignoz-Horta and senior author Kristen DeAngelis at the University of Massachusetts Amherst report that shifts in the diversity of soil microbial communities can change the soil’s ability to sequester carbon, where it usually helps to regulate climate.

They also found that the positive effect of diversity on carbon use efficiency – which plays a central role in that storage – is neutralized in dry conditions. Carbon use efficiency refers to the carbon assimilated into microbial products vs carbon lost to the atmosphere as CO2 and contributing to climate warming, DeAngelis explains. Among other benefits, soil carbon makes soil healthy by holding water and helping plants grow.

She and colleagues addressed these questions because they point out, “empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce.” To explore further, they experimentally manipulated microbial communities while varying factors such as microbe community species composition, temperature and soil moisture. Details are in Nature Communications.

In addition to first author Domeignoz-Horta and others at UMass Amherst, the team includes Serita Frey at the University of New Hampshire and Jerry Melillo at the Ecosystems Center, Woods Hole, Mass.

Read the complete story from the News Office at UMass, Amherst.

Desert Algae Shed Light on Desiccation Tolerance in Green Plants | The Well

July 10th, 2020 @


WOODS HOLE, Mass. — Deserts of the U.S. Southwest are extreme habitats for most plants, but, remarkably, microscopic green algae live there that are extraordinarily tolerant of dehydration. These tiny green algae (many just a few microns in size) live embedded in microbiotic soil crusts, which are characteristic of arid areas and are formed by communities of bacteria, lichens, microalgae, fungi, and even small mosses. After completely drying out, the algae can become active and start photosynthesizing again within seconds of receiving a drop of water.

Acutodesmus deserticola, a desert-derived green algae, grows in liquid culture at MBL. This alga’s cells are tiny but extremely resilient, capable of surviving multiple cycles of desiccation and rehydration in a single day. Credit: E.L. Peredo.

Acutodesmus deserticola, a desert-derived green algae, grows in liquid culture at MBL. This alga’s cells are tiny but extremely resilient, capable of surviving multiple cycles of desiccation and rehydration in a single day. Credit: E.L. Peredo.

How are they so resilient? That question is at the core of research by Elena Lopez Peredo and Zoe Cardon of the Marine Biological Laboratory (MBL), published this week in Proceedings of the National Academy of Sciences. Given the intensified droughts and altered precipitation patterns predicted as the global climate warms, understanding the adaptations that facilitate green plant survival in arid environments is pressing.

Working with two particularly resilient species of green microalgae (Acutodesmus deserticola and Flechtneria rotunda), Peredo and Cardon studied up- and down-regulation of gene expression during desiccation, and added a twist. They also analyzed gene expression in a close aquatic relative (Enallax costatus) as it dried out and ultimately died. Surprisingly, all three algae – desiccation tolerant or not – upregulated the expression of groups of genes known to protect even seed plants during drought. But the desiccation-tolerant algae also ramped down expression of genes coding for many other basic cellular processes, seemingly putting the brakes on their metabolism. The aquatic relative did not.

Peredo’s and Cardon’s research suggests this new perspective on desiccation tolerance warrants investigation in green plants more broadly. Upregulation of gene expression coding for protective proteins may be necessary but not sufficient; downregulation of diverse metabolic genes may also be key to survival.

Citation: Elena L. Peredo and Zoe G. Cardon (2020) Shared upregulation and contrasting downregulation of gene expression distinguish desiccation tolerant from intolerant green algae. PNAS, doi: 10.1073/pnas.1906904117

Homepage photo: Desiccation-tolerant green microalgae are frequently found in the microbiotic crusts covering soil in arid areas, such as the deserts of the Southwestern U.S.A. (Credit: Z.G. Cardon).


The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.

Originally posted on The Well.

New DOE Award | Sticky Roots and the Fate of Soil Carbon in Natural Ecosystems

June 30th, 2020 @

MBL Ecosystems Center Senior Scientist Zoe Cardon has received a collaborative grant from the U.S. Department of Energy (DOE) to study "sticky roots" and the fate of soil carbon in natural ecosystems. This grant was one of nine funded under the DOE Environmental Systems Science Program aimed at improving the understanding of watersheds, wetlands, and other terrestrial environments.  The official press release may be found on the Office of Science website.

Grass roots grown in soil, ready for imaging. (Zoe Cardon)

Grass roots grown in soil, ready for imaging. [Photo credit: Zoe Cardon]

Human activities are driving increasing concentrations of CO2 in the atmosphere, and the resulting climate change is becoming more and more obvious. But there are natural mechanisms operating in ecosystems that can transform atmospheric CO2 into organic forms and store it in soil long-term. In particular, that organic matter can become bound to soil minerals, where it can remain protected for millennia. Such long-term protection has great value to humans as climate change looms. However, the growth of living plants and soil microbes may depend on accessing nutrients trapped in the mineral-associated organic matter. In this DOE-funded work, Cardon (MBL), Keiluweit (UMass Amherst), Malmstrom (MSU), and Riley (LBNL) are using experiments and modeling to examine mechanisms by which plant roots and their associated microbes can dislodge organic matter from soil minerals, making nutrients available for recycling supporting new growth, but also making carbon vulnerable to re-release to the atmosphere as CO2.

Switchgrass growing at the MBL Research Greenhouse in root imaging boxes. [Photo credit: Zoe Cardon]

Switchgrass growing at the MBL Research Greenhouse in root imaging boxes. (Zoe Cardon)

A novel twist of the planned work lies in the aboveground treatment through which the researchers will test belowground ecosystem function: controlled viral infection of plants. Viral infection strongly affects the types and amounts of compounds released by plant roots, and Cardon and colleagues hypothesize that some of those compounds can dislodge stored organic matter from minerals. Since viral infection of plants is widespread in terrestrial ecosystems (with 25-70% of plants commonly infected), this new work promises to build knowledge about a prevalent, natural phenomenon with large potential to affect the productivity of ecosystems and the fate of large reserves of carbon stored in soil.


Lauren Johnson earns MBL Associates Prize for Excellence | The Well

February 26th, 2020 @

Lauren JohnsonLauren Johnson—student of Trinity University in San Antonio, Texas—was awarded the MBL Associates Prize for Excellence in Independent Research in the Semester in Environmental Science (SES). The prize, sponsored by Friends of the MBL, was awarded based on her presentation at the 23rd annual SES student research symposium, which was held at the MBL in December 2019.  Johnson’s research explored the effects of nutrients and agitation on carbon update and isotopic composition in the macroalga Ulva lactuca.

According to her advisor, MBL Research Scientist Javier Lloret, Johnson’s work provided “fresh insights” into claims in the literature that Ulva can switch between 3-carbon and 4-carbon photosynthetic pathways during nutrient limitation. Evidence for this “switch” has been based on changes in the isotopic composition of the algae thought to occur when high nutrient supply stimulates rapid algae growth. Johnson demonstrated that similar isotopic changes could also be induced by diffusion limitation of carbon uptake.

“Lauren did a superb job of fielding questions after her presentation,” said Lloret.

Originally published on The Well

Marine Microorganisms, Ocean Chemistry, and Thermodynamics | Future Health Tech

January 31st, 2020 @

MBL Senior Scientist Joseph Vallino chats marine microorganisms, ocean chemistry, and thermodynamics with the Future Tech Health Podcast team. 

By: Future Tech Health PodcastJoseph Vallino on Future Tech Health Podcast

At the Marine Biological Laboratory, Senior Scientist Joseph Vallino is researching how microbes impact the chemistry of the ocean.

He joins the podcast to discuss his work in the field of biogeochemistry, which includes questions like the following:

What dictates the distribution of microbes and what types of metabolic activities they carry out in ocean water. How the dissipation of energy gradients in nonliving systems works, and how this idea can be applied to biological systems to better understand how living organisms organize. How the theory of maximum entropy production relates to marine biology and microbial function. There are thousands of different species of bacteria and phytoplankton in just one liter of ocean water, and billions of individual microbes. Since they all carry out different metabolic processes at different times and in different locations, it can be difficult to develop a holistic understanding of the complex chemistry that’s occurring in the ocean. Learn more…

Source: Marine Microorganisms, Ocean Chemistry, and Thermodynamics—Joseph Vallino—Marine Biological Laboratory

Making "Lemonade": Chance Observation Leads to Insight on Microbial Bloom Formation

January 30th, 2020 @

A scientific discovery often starts with a chance observation made by open minds who realize its potential. This happens over and over again in the MBL’s Advanced Research Training courses.

Sampling at the Trunk River Lagoon. The sulfur bloom is the yellow patch at left. Credit: Emil Ruff

A Microbial Diversity course student sampling at Trunk River Lagoon, Falmouth. The yellow patch at left is a natural bloom of sulfide-oxidizing phototrophs. Credit: Elise Cowley

In 2014, students and faculty in the MBL’s Microbial Diversity course made such a serendipitous observation. A team followed up on it in the coming years and last week, published their insights in the journal Environmental Microbiome.

The story started at Trunk River lagoon, near the Shining Sea Bike Path in Falmouth, Mass., which for decades has been a “natural laboratory” for the Microbial Diversity course along with other local field sites, such as Sippewissett Marsh. (The course, established at MBL in 1971 by Holger Jannasch, will celebrate its 50th anniversary this year).

“A few days after we had waded through the shallow section of Trunk River lagoon, our footprints turned yellow,” says senior author Emil Ruff, a course teaching assistant in 2014-15 and now a scientist at the MBL.

Ruff hypothesized that the yellow suspension (which the course participants called microbial “lemonade”) was a sulfur bloom generated by microorganisms that couple photosynthesis to the oxidation of sulfur. The students’ footsteps likely stirred up decaying sea grass and other organic material, releasing sulfide into the water and creating a habitat suitable for rare microbes to bloom.

Lead authors (l-r) Srijak Bhatnager, Elise S. Cowley and Emil Ruff at Trunk River Lagoon. Bhatnager and Cowley were Microbial Diversity course students and Ruff was a teaching assistant when this research began. Credit: Emil Ruff

Lead authors (l-r) Srijak Bhatnagar, Elise S. Cowley and Emil Ruff after sampling at Trunk River Lagoon. All three were Microbial Diversity teaching assistants and led the research team (self-dubbed “Lemonheads”) that completed the study. Credit: Emil Ruff

Blooms of microorganisms are not uncommon in water bodies. Some are so huge that they are visible from satellites. Some are harmful, because they can be toxic for animals, or lead to oxygen depletion in certain areas of the ocean. Blooms generated by high sulfide concentrations are generally a concern, as they can become toxic for fish, mussels and birds. There are many open questions about what triggers bloom formation and collapse.

The next year, Ruff and a team from the Microbial Diversity course returned to Trunk River with the goal of intentionally creating and tracking blooms to study how microbial communities form and change over time. They dug holes in the lagoon and added poles that allowed them to sample daily from several depths without disturbing the water column.

“Often in microbial ecology, we try to understand an ecosystem in its steady state. But it remains unclear how long it takes for an ecosystem to recover after a disturbance and what it takes to establish a diverse [microbial] community,” says Ruff. The experimental design allowed the research team to follow the microbial community as it began to assemble, matured and stratified over time, and collapsed at the end of the bloom.

Understanding these dynamics is particularly important in estuarine ecosystems, such as Trunk River lagoon, that are exposed to natural and human disturbances. Estuaries not only provide important protection from coastal erosion, they also capture carbon from the atmosphere and sequester it. They also serve as a food source and breeding ground for much of the coastal biodiversity.

“The ecology and biogeochemistry causing the sulfur-driven blooms showed us how quickly things can turn, and how ecosystems and microbiomes can rapidly change upon disturbances,” says Ruff.

The Microbial Diversity course team sampling at Trunk River. Credit: Drone photo by Rhys Probyn

The Microbial Diversity course team sampling at Trunk River. Credit: Drone photo by Rhys Probyn

One surprising finding was where the bloom’s microbes — called anoxygenic phototrophs — found optimal living conditions. Prior to the study, it was generally thought that many of the bloom microbes could not grow in the presence of oxygen. Finding them in mildly oxic waters led the researchers to examine their genomes. They found that certain species of Chlorobiales – the bacterial lineage responsible for most of the bloom biomass and the yellow color — encode enzymes that combat oxygen stress, which could explain the microbes’ oxygen tolerance. This and other insights have already initiated new course research projects.

Like the different functions of the microbes in the Trunk River estuarine community, the Microbial Diversity course brings together teaching fellows, faculty and students with diverse backgrounds and research foci.

“What I found remarkable is the range of expertise in the course,” says Ruff. “You can assemble a group of researchers that can look at all aspects of an ecosystem, including microbiology, physics, chemistry and everything in between. This holistic approach is what the course stands for and passes on to its students each year, for the past 49 years.”

Citation: Srijak Bhatnagar et al (2019) Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome, DOI: 10.1186/s40793-019-0348-0

By Jennifer Tsang

This work was carried out at the Microbial Diversity course at the Marine Biological Laboratory in Woods Hole, Mass. The course was supported by grants from National Aeronautics and Space Administration, the US Department of Energy, the Simons Foundation, the Beckman Foundation, and the Agouron Institute.


The Marine Biological Laboratory (MBL) is dedicated to scientific discovery – exploring fundamental biology, understanding marine biodiversity and the environment, and informing the human condition through research and education. Founded in Woods Hole, Massachusetts in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.

Synthetic Biology: A New Tool to Tackle Climate Change? | MIT Global Change

December 12th, 2019 @

On December 3 and 4, Boston University convened a workshop exploring how synthetic biology—the engineering of genetic “circuits” in living cells and organisms to enable them to perform specified tasks—can help address climate change.Synthetic Biology: A New Tool to Tackle Climate Change? | MIT Global Change

Participants, who included thought leaders in science, economics, policy and ethics, considered a wide range of complex challenges and potential benefits of proposed synthetic biology approaches to reducing greenhouse gas emissions.

Among the presenters and moderators were four researchers affiliated with the MIT Joint Program on the Science and Policy of Global Change who explored some of the scientific and policy implications of tackling climate change with a synthetic biology toolset.

In a session on land, atmosphere and ocean systems, Jerry Melillo, a senior scientist at the Marine Biological Laboratory, highlighted the strong interactions among carbon, nitrogen and phosphate cycles that present opportunities and limits to any biological solution to mitigating greenhouse gases (GHGs). He observed that it will likely take decades of monitoring to fully understand how ecosystems and soils respond to human-initiated changes in the climate system. Read more …

Photo: MIT biological engineers have devised a programming language that can be used to give new functions to E. coli bacteria. Image: Janet Iwasa

By Mark Dwortzan

Source: Synthetic biology: A new tool to tackle climate change? | MIT Global Change

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