We may find deep-sea microbes resting in tombs they built themselves

Featured Image: Alvin – a submersible Human Occupancy Vehicle (HOV) designed to allow data collection at depths up to 6,500 m below the ocean surface. Featured image courtesy of John Magyar, Caltech.

Paper: Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Authors: Daniela Osorio-Rodriguez, Kyle S. Metcalfe, Shawn E. McGlynn, Hang Yu, Anne E. Dekas, Mark Ellisman, Tom Deerinck, Ludmilla Aristilde, John P. Grotzinger, and Victoria J. Orphan

Maybe one weekend in your life, you found yourself piling into an SUV at 6 AM with seven other students, intermittently registering the drone of an overenthusiastic geology professor whose course you took to fulfill a degree requirement. If so, in that vehicle, the proclamation that “the present is the key to the past” was certainly uttered. A recent study conducted by Daniela Osorio-Rodriguez and collaborators epitomizes the power of those words.

You likely have heard a great deal about carbon dioxide (CO2) and its effect on the climate as a greenhouse gas in the past few years. The second most commonly discussed greenhouse gas is methane (CH4), largely because it has ~28x the warming potential of CO2 over a 100-year timescale. For this reason, scientists have been interested in microorganisms that convert CH4 to CO2 as their means of obtaining energy to live – a process referred to as methane oxidation. These organisms play an important role in preventing the accumulation of methane in the atmosphere. In most soils, including the grass outside your home, methane oxidation occurs with the help of oxygen (aerobically). However, in sediments at the bottom of the ocean, oxygen is exhausted and methane-oxidizing bacteria must carry out this process anaerobically.

For over two decades, microbial ecologists have been studying the anaerobic oxidation of methane (AOM) by a syntrophic consortium of methanotrophic archaea and sulfate-reducing bacteria (ANME-SRB) living as aggregates around ocean floor methane seeps. The AOM leaves a chemical signature in the limestone rocks that the microbes live in. This signature has been used to identify ancient methane seeps throughout the geologic past. At these sites, geologists have searched for fossilized evidence of ANME-SRB aggregates in rocks. You can imagine this search being like looking for dinosaur bones, except the fossils you are looking for are microscopic.

For decades, geologists have collected rocks from ancient methane seeps all over the world and searched for ANME-SRB under the microscope. Despite significant effort, geologists have yet to observe fossilized aggregates of ANME-SRB. This is the mystery that Osorio-Rodriguez and collaborators are helping resolve in their recent paper. While they did not find fossils of ancient aggregates, they have found what we should be looking for! They observed microbially enhanced precipitation of silica (chemically similar to everyday glass) on the exterior of aggregates in lab cultures, carbonate rocks, and methane-rich sediments. By changing the water chemistry around them, the microbes cause silica to precipitate from the solution in the same way mineral coatings precipitate around a faucet if the water is ‘hard’. To determine the co-occurrence of ANME-SRB aggregates and silica, the authors interrogated laboratory cultures of ANME-SRB with a number of techniques.

  1. Fluorescence in situ hybridization (FISH) – This technique attaches a fluorescent molecule to a target DNA sequence, so that cells expressing this target DNA glow. Using target DNA for both ANME and SRB, the researchers can identify ANME-SRB aggregates as clusters of pink (ANME) and blue SRB) cells.
  2. Scanning Electron Microscopy (SEM) – This technique produces highly magnified images, allowing the researchers to identify ∼230 nanometer-sized amorphous silica spheres (small glass beads nearly 500x smaller than the thickness of a piece of paper) adjacent to the cell aggregates.
  3. Energy dispersive X-ray spectroscopy (EDS) – This technique allows scientists to make maps of elements (ex. silicon, carbon, etc.) around an aggregate while it is being photographed on the SEM.

Not only did the researchers observe the repeated precipitation of silica around the aggregates, by studying the chemistry of the artificial seawater, they could confirm that the silica could not be precipitating abiotically (without the presence of microbes) in their experiments. This allowed them to confirm that the cellular activity must play a role in the silica precipitation they observed. Also, they found that the silica precipitated near the aggregates is chemically different (containing less Mg, Al, and Fe) from other silicate minerals found at methane seeps.

Like all groundbreaking research, this study has raised new questions that have yet to be answered. While the authors are confident that the microbial activity is inducing the silica precipitation, how the microbes are doing this is still unknown. The eventual explanation will involve homing in on biochemical processes occurring in either ANME clusters, SRB clusters, or at the interface between the two that locally changed the water chemistry such that silica preservation is favorable. All that means is there is more exciting science be carried out.

Importantly, this research on modern aggregates has armed geologists with a new target in the search to identify fossilized consortia in the geologic past.

We may find deep-sea microbes resting in tombs they built themselves © 2024 by Joshua Anadu is licensed under CC BY-SA 4.0 

A New Role for Nitrogen Fixers in Oceanic Carbon Sequestration

Paper: Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean

Authors: Sophie Bonnet, Mar Benavides, Frédéric A. C. Le Moigne, Mercedes Camps, Antoine Torremocha, Olivier Grosso, Céline Dimier, Dina Spungin, Ilana Berman-Frank, Laurence Garczarek, and Francisco M. Cornejo-Castillo

You swell up and down with each salty wave, until suddenly, the thought of lunch triggers a pang of hunger. A ray of sunshine stifles the starvation, and you take a satiating bite of carbon dioxide with a side of nitrogen. As a nitrogen-fixing, photosynthetic bacterium you use energy from sunlight to convert nitrogen gas to necessary nutrients for yourself and your neighbors.

Photosynthesizers in the ocean play a crucial role in regulating the earth’s climate in the face of climate change. Through a process called the biological carbon pump, the carbon dioxide that these microbes incorporate into their cells can sink to the bottom of the ocean, keeping that carbon out of the atmosphere for decades to millions of years. However, more than carbon dioxide and sunlight are necessary to prime this pump. These cells need nitrogen, and a category of microbe called a diazotroph converts nitrogen gas in the atmosphere to the nitrogen currency that most cells can use: ammonia.

For a long time, these nitrogen-converting microbes – diazotrophs –  were thought to only play an indirect role in carbon sequestration by marinemicrobes. Scientists thought that diazotrophs supplied the oceanic food web with nitrogen but wouldn’t themselves be the ones to sink down and store carbon in the deep ocean. A new open access paper, first authored by Sophie Bonnet at Université de Toulon in France, calls this paradigm, and its implications for climate change, into question.

On a ship in the Pacific Ocean, Bonnet and the team collected samples of water in an enormous 1.5-meter-tall sampler. After retrieving the water, they let it sit on board the ship for 2 hours. This allowed the microbes that were sinking toward the deep ocean to separate. They then collected water at the very bottom of the sampler to represent the quickly sinking cells, the water just above the bottom of the sampler to represent the slower-sinking cells, and the water from the top to represent cells that didn’t sink. Sinking can be a result of cells being eaten by zooplankton and excreted in fecal pellets, of cells sticking together into larger agglomerates, or of metabolic processes decreasing buoyancy. By repeating this process at different locations and different depths, Bonnet was able to determine which diazotrophs were present and which ones were actively sinking.

To identify the various diazotrophs present, the team amplified and sequenced a gene called nifH, which codes for a part of the nitrogenase enzyme. This enzyme catalyzes the conversion of di-nitrogen gas to ammonia – a defining characteristic of diazotrophs. This single gene amplification and sequencing can be done qualitatively as a survey to determine which genes are present in that environment, or can be performed quantitatively, to understand the relative number of copies of the gene in that environment. This paper employed both techniques.

Using the nifH sequences, the authors identified two main groups of diazotrophs in their samples – photosynthetic (cells that can photosynthesize and fix nitrogen) and non-photosynthetic. The photosynthetic diazotrophs primarily consisted of Trichodesmium, a large filamentous cyanobacteria, and a diverse group of unicellular cyanobacteria abbreviated UCYN. Both of these groups are common marine diazotrophs. Surprisingly, in the qualitative surveys, the majority of the non-photosynthetic diazotrophs were novel and unidentified. The paper disclaims that their quantitative analyses would not pick up these unidentified nifH sequences, and therefore no claims about their abundance could be made.

The team found that the same diazotrophs present in the surface water (identified by their nifH sequences) were also present at depths of 1000m, indicating that these nitrogen-fixing cells do sink to the deep ocean. While Trichodesmium and UCYN were both abundant in shallow water, samples of the settled material from the 1.5m water sampler indicated that the smaller UCYN cells were sinking more efficiently. This seemingly contradicts a previously-held idea that large cells sink faster than small ones, and therefore contribute more to carbon sequestration. To unravel this apparent paradox, the team looked at material that was settling toward the deep ocean under the microscope. They saw UCYN cells clumped into large aggregates of hundreds of cells, this large particle size likely explaining their efficient sinking. Aggregation of organic material is crucial in facilitating the transport of carbon to the deep ocean. The fact that ubiquitous diazotrophs, such as UCYN cells, are clumping together and sinking was unexpected and indicates that these organisms contribute more than anticipated to the biological carbon pump

Bonnet and the team’s findings lay the groundwork to redefine the role that marine diazotrophs play, both in the marine food web and in sequestering carbon. UCYN cells are some of the most abundant diazotrophs in the ocean and this research indicates that they are efficiently exported from the upper ocean to depth. While Trichodesmium sinks less efficiently, they were also found sinking and at depths that indicate that this ubiquitous diazotroph is also directly involved in the biological carbon pump. Additionally, the discovery of unidentified nifH sequences implies that there may be other major diazotrophs at play. Once thought to only ‘prime’ the biological carbon pump by providing nutrients to other photosynthesizers, diazotrophs themselves may be sinking, bringing carbon to the deep ocean, and helping to counteract climate change!

A New Role for Nitrogen Fixers in Oceanic Carbon Sequestration © 2024 by  William Christian is licensed under CC BY-SA 4.0 

Unlocking Magma’s Mysteries

Understanding magma’s behavior may predict eruptions and reveal historic landscapes

By: Ellen Beshuk

Sometimes magma calmly flows; other times, it explodes. Ph.D. candidate Ivana Torres-Ewert is figuring out why with her magma-making machine at the University of Missouri-Kansas City (UMKC). Her discoveries could help people know where to go when a volcano explodes and provide a foundation for further volcanic research.

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Impacts of global warming on soil carbon storage, biodiversity, and crop yields

Image credit: Public Domain (Pexels)

Paper: Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism.

Authors: Ye Li, Zengming Chen, Cameron Wagg, Michael J. Castellano, Nan Zhang, Weixin Ding.

Few issues are as pressing and relevant for the future of our own species as climate change. We may think first about glaciers and polar bears when we consider its devastating impacts. However, new research brings our attention to much smaller organisms, microbes, as major players in stabilizing soils and preventing agriculture from collapsing under global warming.

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Nuevo soporte para el origen de la vida en fumarolas hidrotermales alcalinas

Imagen de la portada: Tapetes blancos floculantes dentro y alrededor de fumarolas blancas extremadamente gaseosas de alta temperatura (>100°C, 212°F) en la Fumarola Champagne. Copyright: CC BY-SA 4.0 a través de wikimedia commons.

Artículo: Chimeneas de óxidos blancos y verdes acumulan ARN en un jardín químico ferruginoso.

Autores: Vanessa Helmbrecht, Maximilian Weingart, Frieder Klein, Dieter Braun, William D. Orsi

Cuando pensamos en mundos extraterrestres, posiblemente evocamos una imágen de vastos oceános con estructuras altas verticales dispersas, como columnas o torres. Al observar imágenes de fumarolas hidrotermales alcalinas, te darás cuenta de que esos mundos extraterrestres no existen solamente en las películas de ciencia ficción. Las fumarolas hidrotermales alcalinas son ambientes marinos profundos abundantes en la Tierra hace más de 4000 millones de años, caracterizados por chimeneas blancas globulares y puntiagudas que se elevan desde el fondo del mar.  Ofrecen una combinación de condiciones químicas en las que pueden haber surgido las primeras formas de vida en la Tierra. Sin embargo, las fumarolas hidrotermales alcalinas se han considerado inhóspitas para la formación de ácidos nucleicos, las moléculas que almacenan información en todas las células vivas. Un artículo nuevo de investigadores de LMU Munich reta esta suposición al proporcionar evidencia clave para la estabilización de ácidos nucleicos en fumarolas hidrotermales alcalinas, un descubrimiento que podría hacer estos ambientes los candidatos más adecuados para el origen de la vida en la Tierra.

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New support for the origin of life in alkaline hydrothermal vents

Featured image: White flocculent mats in and around the extremely gassy, high-temperature (>100°C, 212°F) white smokers at Champagne Vent. Copyright: CC BY-SA 4.0 via. wikimedia commons.

Paper: White and green rust chimneys accumulate RNA in a ferruginous chemical garden

Authors: Vanessa Helmbrecht, Maximilian Weingart, Frieder Klein, Dieter Braun, William D. Orsi

When we think of alien worlds, we may evoke an image of vast oceans with tall scattered vertical structures, like columns or towers. By looking at pictures of alkaline hydrothermal vents, you will realize that such alien worlds do not just exist in science fiction movies. Alkaline hydrothermal vents are deep ocean environments widespread on Earth more than 4 billion years ago, in which light globular and spiky chimneys rise from the dark ocean floor. They offer a combination of chemical conditions that may have supported the first forms of life on Earth. However, alkaline hydrothermal vents have been considered inhospitable for the formation of nucleic acids, the information-storage molecules present in all living cells. A new paper from researchers at LMU Munich challenges this assumption by providing critical evidence for the stabilization of nucleic acids in alkaline hydrothermal vents, a discovery that would make these environments the most suitable candidates for the origin of life on Earth.

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Making Mountains Out of Molehills? Long-Term Geomorphic Surface Impacts of Mountaintop Removal Mining

Featured Image:  Mountaintop removal mining site in Appalachia. Copyright: CC BY-SA 4.0 via. wikimedia commons.

Report: Peripheral gully and landslide erosion on an extreme anthropogenic landscape produced by mountaintop removal coal mining (2020)

Authors: Miles Reed & Dr. Steve Kite

There’s a general consensus that coal mining is ‘bad’ for the environment, but beyond carbon emissions, what is its visible, physical impact on our surroundings? What lasting damage does mining create on the Earth’s surface? The answer is that it has a tremendous impact; specifically, mining in Appalachia is linked to distorting the natural flow of water on the landscape, which creates ripple (no pun intended) effects on the greater environment. A recent study by Reed and Kite details those effects on Appalachian landscapes, directly linking mountaintop mining to erosion and landslides. Now, as worries about access to safe, clean water being jeopardized by fossil fuel production abound nationwide, exploring the impacts of mountaintop mining on Appalachian freshwater becomes incredibly important with immediate and personal impacts.

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How Much is War Fuelling the Climate Crisis?

Featured Image: Global militaries are a major contributor to climate change, however, we face many challenges when assessing their environmental footprint. Copyright: CC BY-SA 4.0 via. wikimedia commons.

Report: Estimating the Military’s Global Greenhouse Gas Emissions (2022)

Authors: Dr. Stuart Parkinson & Linsey Cottrell

Organisations: Scientists for Global Responsibility & Conflict and Environment Observatory

War is likely to worsen in the near-future as climate change forces more disasters, political instability, and poverty onto the planet and strains resource supplies. Yet war is not just a product of climate change: it is also a major cause. In addition to the societal devastation it creates, militarism is a major emitter of greenhouse gases and contributor to environmental degradation. Politicking from the worst emitters has ensured that military emissions are shielded from the same type of accountability seen across other sectors such as agriculture, transport, land use, technology, and waste. For example, the latest installment of the IPCC report barely mentioned military emissions despite its immensely detailed analysis of other sectors. A recent report from Stuart Parkinson (Scientists for Global Responsibility) and Linsey Cottrell (Conflict and Environment Observatory) helps correct this oversight and unpacks the impact of war on climate change.

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How sediments can save drowning river deltas

Featured image: A satellite image of the Ganges – Brahmaputra delta along the Bangladesh coastline.captured by the Envisat satellite of the European Space Agency (ESA). The image also shows sediment plumes in the coastal area. (Image credit: ESA CC BY-SA 3.0 IGO)

Paper: Sediment delivery to sustain the Ganges- Brahmaputra delta under climate change and anthropogenic impacts

Authors: Jessica L. Raff, Steven L. Goodbred Jr., Jennifer L. Pickering, Ryan S. Sincavage, John C. Ayers, Md. Saddam Hossain, Carol A. Wilson, Chris Paola, Michael S. Steckler, Dhiman R. Mondal, Jean-Louis Grimaud, Celine Jo Grall, Kimberly G. Rogers, Kazi Matin Ahmed, Syed Humayun Akhter, Brandee N. Carlson, Elizabeth L. Chamberlain, Meagan Dejter, Jonathan M. Gilligan, Richard P. Hale, Mahfuzur R. Khan, Md. Golam Muktadir, Md. Munsur Rahman, Lauren A. Williams

The Ganges – Brahmaputra delta is the largest river delta in the world, covering an area of 1,00,000 sq. km. About two-thirds of the delta lies in Bangladesh, and the rest in the Indian state of West Bengal. Today, sea level rise due to climate change poses a massive challenge to the delta region which more than 200 million people call home!

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Biomolecules on icy worlds

Featuring image: Artists impression of Hayabusa2 approaching Ryugu. Image credit: NASA/JPL, Public Domain (CC0)

Paper: Uracil in the carbonaceous asteroid (162173) Ryugu

Authors: Y. Oba, T. Koga, Y. Takano, N. O. Ogawa, N. Ohkouchi, K. Sasaki, H. Sato, D. P. Glavin, J. P. Dworkin, H. Naraoka, S. Tachibana, H. Yurimoto, T. Nakamura, T. Noguchi, R. Okazaki, H. Yabuta, K. Sakamoto, T. Yada, M. Nishimura, A. Nakato, A. Miyazaki, K. Yogata, M. Abe, T. Okada, T. Usui, M. Yoshikawa, T. Saiki, S. Tanaka, F. Terui, S. Nakazawa, S. Watanabe, Y. Tsuda and Hayabusa2-initial-analysis SOM team

Bringing a space probe to an asteroid is hard. Bringing back a piece of that asteroid to Earth is even harder. Nevertheless, Hayabusa2 successfully brought back samples from the asteroid Ryugu and gives us valuable insight on the abundance of biomolecules in our solar system.

What the Japanese space agency JAXA accomplished is extraordinary. After the successful sample return mission of Hayabusa from asteroid 25143 Itokawa in 2010, the successor mission again was able to bring us back precious, pristine asteroid material, including gas samples. In contrast to Itokawa, the new target Ryugu represents a much more pristine asteroid, chemically connected to a class of meteorites called carbonaceous chondrites. Researchers already detected the very building blocks of life, like amino acids and nucleobases, in these meteorites. The careful analysis of the Hayabusa2 samples revealed that one of the nucleobases, uracil, is also present in Ryugu.

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