Seasons of the Microbiome Over the Amazon Rainforest | The Well

January 21st, 2021 @
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:

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...

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.


Zoe Cardon, MBL Ecosystems Center, elected to ESA's Governing Board

November 18th, 2019 @

Ecological Society of America Announces New Members Elected to Governing Board

The Ecological Society of America (ESA) is proud to announce the election results for its governing board members. Those selected by the membership to serve are Member-at-Large Zoe Cardon, Ecosystems Center at Marine Biological Laboratory; Vice President for Finance Jeannine Cavender-Bares, University of Minnesota; President-Elect for 2020 Dennis Ojima, Colorado State University; Vice President for Public Affairs Laura Petes, NOAA Office for Coastal Management; and Member-at-Large Sasha Reed, research ecologist.

"With the newest members elected to the ESA governing board, the Society will continue the tradition of strong leadership and dedication to the science of ecology,” says ESA President Osvaldo Sala. “I look forward to the new perspectives and experiences they will bring when their terms begin in August 2020, and I offer congratulations to each person joining the board.”

President-Elect for 2020 Dennis Ojima is a professor emeritus at Colorado State University in the Department of Ecosystem Science and Sustainability and a senior research scientist at the Natural Resource Ecology Laboratory. An ESA member since 1984, his research applies social-ecological approaches to climate and land use changes in dryland and grassland systems worldwide, including Mongolia, China, Central Asia, parts of Africa, and in the U.S. Ojima is instrumental in the development of many international science programs; he is named Champion of the Environment by the Mongolian government and is recognized for his contributions to the Millennium Ecosystem Assessment and the International Panel on Climate Change. He is also active in training young scholars and professionals in social-ecological system approaches to dealing with climate change impacts and responses in the United States and Asia.

“I am honored to be selected as President-Elect of the Ecology Society of America,” says Ojima. “Serving ESA over the coming years, and representing the members in their quest to pursue sound ecological research and to provide a platform to engage and communicate with civil society will be a role I will execute with integrity and with members’ guidance.”

Vice President for Public Affairs for the term of 2020-2023, Laura Petes is the manager of the Coastal Communities Program in the National Oceanic and Atmospheric Administration (NOAA) Office for Coastal Management. Petes has conducted research on coral disease and on the physiological ecology of rocky intertidal mussels, and she previously served as assistant director for climate adaptation and ecosystems at the White House Office of Science & Technology Policy (OSTP). There, she led the OSTP resilience portfolio under President Obama’s Climate Action Plan and launched a Climate Education and Literacy Initiative, which engaged federal agencies, companies, non-governmental organizations, and hundreds of students and educators. Petes is currently serving a second term on the ESA Public Affairs Committee.

Jeannine Cavender-Bares, a professor at the University of Minnesota, will serve as vice president for finance for the term of 2020-2023. She is interested in plant function, integrating ecology and evolution, and exploring ways to detect biodiversity and ecological processes. Over the last two decades, Cavender-Bares has led major research grants from multiple federal and state institutions and managed budgets for these projects, and she currently serves on NSF’s Biological Sciences Advisory Committee and its NEON subcommittee. As vice president for finance, she will aim to work with the Society to invest in activities that benefit ESA members while maintaining the Society’s solid financial path.

An elected member-at-large for the term 2020-2022, Zoe Cardon is a senior scientist at the Ecosystems Center, Marine Biological Laboratory (MBL), located in Woods Hole, Massachusetts. She is an ecosystems ecologist with roots in mechanistic plant physiology, and she considers ESA her “home” Society. Her diverse career path includes prior positions with UC Berkeley, Bowdoin College, and the University of Connecticut. Cardon works to build interdisciplinary communities supporting training and collaboration essential for understanding and sustaining Earth’s life support systems.

Sasha Reed, also elected a member-at-large for the term 2020-2022, works as an ecosystems ecologist and biogeochemist focusing on understanding how terrestrial ecosystems work and respond to change. She believes in linking relevant and accessible science with those who can use it; enjoys addressing complex problems with diverse groups; and thinks highly of the power of strong mentorship. Reed serves on a number of boards and committees, including ESA’s Publications Committee and on the Advisory Board for ESA’s Issues in Ecology.

“I continue to be impressed with the dedication of ESA’s volunteers that step up for board service,” says ESA Executive Director Catherine O’Riordan. “I want to extend a big thank you to the membership; this election process is important for providing the vision and voices needed to guide the Society’s efforts to positively affect and advance the community and science of ecology.”

The current ESA Governing Board Members are President Osvaldo Sala, professor, Arizona State University through August 2020; Immediate President-Elect Kathleen Weathers, senior scientist, Cary Institute of Ecosystem Studies; Immediate Past-President Laura Huenneke, emeritus professor, Northern Arizona University; Vice President for Science Diane Pataki, professor, University of Utah; Vice President for Finance Evan DeLucia, professor, University of Illinois Urbana-Champaign; Vice President for Public Affairs Frank Davis, professor, University of California, Santa Barbara; Vice President for Education and Human Resources, Pamela Templer, professor, Boston University; Secretary, Jessica Gurevitch, professor, Stony Brook University; Member-at-Large Manuel Morales, professor, Williams College; Member-at-Large Kathleen Treseder, professor, University of California, Irvine; and Member-at-Large Jacquelyn Gill, associate professor, University of Maine.


The Ecological Society of America (ESA), founded in 1915, is the world’s largest community of professional ecologists and a trusted source of ecological knowledge, committed to advancing the understanding of life on Earth. The 9,000 member Society publishes five journals and a membership bulletin and broadly shares ecological information through policy, media outreach, and education initiatives. The Society’s Annual Meeting attracts 4,000 attendees and features the most recent advances in the science of ecology. Visit the ESA website at

Original press release and photos online:

Contact: Alison Mize, 202-833-8773,

Team Studies how Viral Infections in Plants may Affect Carbon Storage in Soil

January 9th, 2019 @

Photo illustration by Zoe Cardon

MBL Senior Scientist Zoe Cardon has received a collaborative grant from the Department of Energy to study how viral infections in plants can affect the fate of the largest pool of organic carbon stored in soils: organic carbon bound to minerals.

As carbon dioxide (CO2) concentrations in the atmosphere continue to rise, driving further climate change, it becomes more and more urgent to understand how plant roots, soil microbes, and soil minerals interact to control whether soils store carbon or release CO2.

One way that plant roots strongly contribute to soil carbon storage is by producing sugars, organic acids, and even whole cells that are lost to soil. But there is a twist in the story. Certain types of compounds derived from roots may also destabilize the bonds between soil  minerals and existing soil organic matter (SOM), making that SOM more vulnerable to microbial attack and decomposition. Soil carbon loss, instead of storage, may result.

The question then becomes what types of compounds, and how much of them, are lost from plant roots to soils. Cardon and colleagues have found that, upon infection with particular plant viruses, plant roots can lose so many compounds to their surroundings that they become literally “sticky” to the touch. Understanding whether and how these “sticky roots” drive increased decomposition of existing mineral-stabilized soil carbon promises to transform our understanding of the importance of common virus infection for soil carbon dynamics and global change.

Co-principal investigators with Cardon, the lead principal investigator on this project, include Marco Keiluweit, University of Massachusetts, Amherst; Carolyn Malmstrom, Michigan State University; and William J Riley, Lawrence Berkeley National Laboratory.


Originally published in The Well

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