It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Friday, October 04, 2024
Permanent and unique IDs for individual (digital) specimens from natural history museums streamline and future-proof science
First-of-its-kind scientific article demonstrates how scientists create machine-actionable persistent records for specimens packaged with all related valuable information
Pensoft Publishers
image:
The jumping spider Chrysilla lauta, one of the species studied in the first scientific publication to use digital specimen DOIs.
The wealth of data hosted in natural history collections can contribute to finding a response to global challenges ranging from climate change to biodiversity loss to pandemics. However, today’s practices of working with collected bio- and geodiversity specimens lack some efficiency, which limits what scientists can achieve. In particular, there is a serious lack of linkages between data centred around specimens and coming from various databases (e.g. ecological and genomic data), which poses significant obstacles when researchers attempt to work with specimens from multiple collections.
Now, a publication in the scientific open-access Biodiversity Data Journal becomes the first to demonstrate novel workflows to further digitise and future-proof biodiversity data. The paper updates the knowledge about two genera of jumping spiders from across two collections and describes a newly discovered species by utilising novel workflows and formats: digital specimen DOIs and nanopublications.
Persistent identifiers: the DOIs
Several initiatives have been launched in recent years to establish a globally accepted system of persistent identifiers (PIDs) that guarantee the “uniqueness” of collection specimens—physical or digital—over time.
You can think of a PID as a marker, an identifier that points at a single individual object and only one, differentiating it from any other in the world. You must have heard of acronyms such as ISBN or ORCID. Those are PIDs for books and individual scholars, respectively. For digital research content, the most widely used PID is the DOI (Digital Object Identifier), proposed by the DOI Foundation.
A DOI is an alphanumeric code that looks like this: 10.prefix/sufix
For example, if you type https://doi.org/10.15468/w6ubjx in your browser, you will reach the Royal Belgian Institute of Natural Sciences’s mollusk collection database, accessed through GBIF. This specific DOI will never point at anything else, and the identifier will remain the same in the future, even if changes occur in the content of this particular database.
DiSSCo and the DOIs
The Distributed System of Scientific Collections (DiSSCo) aims to provide a DOI for all individual digital specimens in European natural history collections. The point is not only to accurately identify specimens. That is, of course, crucial, but the DOI of a digital specimen provides a number of other advantages that are extremely interesting for DiSSCo and natural history collections in general. Among them, two are simply revolutionary.
Firstly, using DOIs allows linking the digital specimen to all other relevant information about the same specimen that might be hosted in other repositories (e.g. ecological data, genomic data, etc.). In creating this extended digital specimen that links different data types, digital specimen DOIs make a huge contribution to inter-institutional scientific work, filling the gap that is described at the beginning of this piece. Now scientists will be in a much better position to really exchange and link data across institutions.
Second, in contrast to most other persistent identifiers, the DOI of a digital specimen stores additional metadata (e.g. name, catalogue number) beyond the URL to which it redirects. This allows access to some information about the specimen without having to retrieve the full data object, i.e. without having to be redirected to the specimen HTML page. This metadata facilitates AI systems to quickly navigate billions of digital specimens and perform different automated work on them, saving us (humans) precious time.
Use of DOIs in publications
With all this in mind, it is easier to understand why being able to cite digital specimens in scholarly publications using DOIs is an important step. So far, the only DOIs that we could use in publications were those at the dataset level, not at the individual specimen level. In the example above, if a scientist were to publish an article about a specific type of bivalve in the Belgian collection, the only DOI that she or he would have available for citation in the article would be that of the entire mollusk database -containing hundreds or thousands of specimens- not the one of the specific oyster or scallop that might be the focus of the publication.
The publication in Biodiversity Data Journal about the Chrysilla and Phintelloides genera is the first of its kind and opens the door to citing not only dataset-level objects but also individual specimens in publications using DOIs. You can try it yourself: Hover over the DOIs that are cited in the publication and you will get some basic information that might save you the time of visiting the page of the institution where the specimen is. Click on it and you will be taken to DiSSCo’s sandbox -the future DiSSCover service- where you will find all the information about the digital specimen. There you will also be able to comment, annotate the specimen, and more, thus making science in a more dynamic and efficient way than until now.
*
A note about Christa Deeleman-Reinhold
At 94 years old, the Dutch arachnologist Christa Deeleman-Reinhold is not only one of the authors of the Chrysilla and Phintelloides article but also one of the most important arachnologists in the world. Born in 1930 on the island of Java -then part of the Dutch East Indies- Christa gained her PhD from Leiden University in 1978. Since then, she has developed a one-of-a-kind scientific career, mainly focused on spider species from South Asia. In her Forest Spiders of South East Asia (2001), Dr. Deeleman-Reinhold revised six spider families, describing 18 new genera and 115 new species. The Naturalis Biodiversity Center hosts the Christa Laetitia Deeleman-Reinhold collection, with more than 20,000 specimens.
***
Research article:
Deeleman-Reinhold CL, Addink W, Miller JA (2024) The genera Chrysilla and Phintelloides revisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications. Biodiversity Data Journal 12: e129438. https://doi.org/10.3897/BDJ.12.e129438
The genera Chrysilla and Phintelloides revisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications
Neuroscience breakthrough: A Princeton-led research team has mapped the entire brain of an adult fruit fly for the first time
Princeton-led FlyWire Consortium built a complete connectome of every neuron in a Drosophila brain
Princeton University
image:
For many heartbreaking diseases of the brain — dementia, Parkinson’s, Alzheimer’s and others — doctors can only treat the symptoms. Medical science does not have a cure.
Why? Because it’s confounding to cure what we don’t understand, and the human brain, with its millions of neurons connected by a hundred trillion synapses, is almost hopelessly complex.
A Princeton-led team of neuroscientists has now made a massive step toward understanding the human brain, by building a neuron-by-neuron and synapse-by-synapse roadmap — scientifically speaking, a “connectome” — through the brain of an adult fruit fly (Drosophila melanogaster).
This image is a video still showing the brain inside an adult fruit fly. The full video is available by request to flywire@princeton.edu.
Credit: Amy Sterling / FlyWire / Princeton University
A Princeton-led team of scientists has built the first neuron-by-neuron and synapse-by-synapse roadmap through the brain of an adult fruit fly (Drosophila melanogaster), marking a major milestone in the study of brains. This research is the flagship article in the Oct. 2 special issue of Nature, which is devoted to the new fruit fly “connectome.”
Previous researchers mapped the brain of a C. elegans worm, with its 302 neurons, and the brain of a larval fruit fly, which had 3,000 neurons, but the adult fruit fly is several orders of magnitude more complex, with almost 140,000 neurons and roughly 50 million synapses connecting them.
Fruit flies share 60% of human DNA, and three in four human genetic diseases have a parallel in fruit flies. Understanding the brains of fruit flies is a steppingstone to understanding brains of larger more complex species, like humans.
“This is a major achievement,” said Mala Murthy, director of the Princeton Neuroscience Institute and, with Sebastian Seung, co-leader of the research team. “There is no other full brain connectome for an adult animal of this complexity.” Murthy is also Princeton’s Karol and Marnie Marcin ‘96 Professor of Neuroscience.
Princeton’s Seung and Murthy are co-senior authors on the flagship paper of the Nature issue, which includes a suite of nine related papers with overlapping sets of authors, led by researchers from Princeton University, the University of Vermont, the University of Cambridge, the University of California-Berkeley, UC-Santa Barbara, Freie Universität-Berlin, and the Max Planck Florida Institute for Neuroscience. The work was funded in part by the NIH’s BRAIN Initiative, the Princeton Neuroscience Institute’s Bezos Center for Neural Circuit Dynamics and McDonnell Center for Systems Neuroscience, and other public and private neuroscience institutes and funds, listed at the end of this document.
The map was developed by the FlyWire Consortium, which is based at Princeton University and made up of teams in more than 76 laboratories with 287 researchers around the world as well as volunteer gamers.
Sven Dorkenwald, the lead author on the flagship Nature paper, spearheaded the FlyWire Consortium.
“What we built is, in many ways, an atlas,” said Dorkenwald, a 2023 Ph.D. graduate of Princeton now at the University of Washington and the Allen Institute for Brain Science. “Just like you wouldn’t want to drive to a new place without Google Maps, you don’t want to explore the brain without a map. What we have done is build an atlas of the brain, and added annotations for all the businesses, the buildings, the street names. With this, researchers are now equipped to thoughtfully navigate the brain as we try to understand it.”
And just like a map that traces out every tiny alley as well as every superhighway, the fly connectome shows connections within the fruit fly brain at every scale.
The map was built from 21 million images taken of a female fruit fly brain by a team of scientists led by Davi Bock, then at the Howard Hughes Medical Institute’s Janelia Research Campus and now at the University of Vermont. Using an AI model built by researchers and software engineers working with Princeton’s Sebastian Seung, the lumps and blobs in those images were turned into a labeled, three-dimensional map. Instead of keeping their data confidential, the researchers opened their in-progress neural map to the scientific community from the beginning.
“Mapping the whole brain has been made possible by advances in AI computing. It would have not been possible to reconstruct the entire wiring diagram manually. This is a display of how AI can move neuroscience forward,’ said Prof. Sebastian Seung, one of the co-leaders of the research and Princeton’s Evnin Professor in Neuroscience and a professor of computer science.
“Now that we have this brain map, we can close the loop on which neurons relate to which behaviors,” said Dorkenwald.
The development could lead to tailored treatments to brain diseases.
“In many respects, it (the brain) is more powerful than any human-made computer, yet for the most part we still do not understand its underlying logic,” said John Ngai, director of the U.S. National Institutes of Health’s BRAIN Initiative, which provided partial funding for the FlyWire project. “Without a detailed understanding of how neurons connect with one another, we won’t have a basic understanding of what goes right in a healthy brain or what goes wrong in disease.”
-------
This research was supported by the National Institutes of Health (NIH) BRAIN Initiative (RF1 MH117815, RF1 MH129268, 1RF1MH120679-01 and U24 NS126935) and National Institute Of Neurological Disorders And Stroke (NINDS) (RF1NS121911); the Princeton Neuroscience Institute’s Bezos Center for Neural Circuit Dynamics and McDonnell Center for Systems Neuroscience; Google; the Allen Institute for Brain Science; the National Science Foundation (NSF Neuronex2 2014862, Neuronex2 MRC MC_EX_MR/T046279/1, MRC MC-U105188491, PHY-1734030); Wellcome Trust Collaborative Award (203261/Z/16/Z and 220343/Z/20/Z); a Marie Skłodowska-Curie postdoctoral fellowship (H2020-WF-01-2018-867459); the Portuguese Research Council (Grant PTDC/MED-NEU/4001/2021); and the Intelligence Advanced Research Projects Activity (IARPA) via the Department of Interior (DOI) (D16PC0005).
For brain video, high resolution images and copies of the papers, please view our press kit.
Author contacts:
Princeton University, USA: To arrange an interview the study authors Mala Murthy or Sebastian Seung, please contact Molly Seltzer at ms80@princeton.edu and Dan Vahaba at
MRC LMB in Cambridge, UK: To arrange an interview with study author Greg Jefferis, please contact Hilary Jones in the UKRI media team: +44 7892 770105, hilary.jones@ukri.org; out of hours press@ukri.org, 01793 298902.
University of Vermont, USA: To arrange an interview with study author Davi Bock, please contact Angela Ferrante, Public Relations Manager at the Larner College of Medicine at the University of Vermont by calling +1 516-458-0721 or emailing: Angela.Ferrante@med.uvm.edu
About FlyWire
The FlyWire Consortium includes researchers from at least 76 laboratories and 287 individuals around the world as well as a network of gamers and other volunteers — see: https://flywire.ai/consortium. The senior authors for the two papers describing and annotating the complete connectome are Mala Murthy and Sebastian Seung (Princeton University), Gregory Jefferis (MRC LMB and University of Cambridge), and Davi Bock (University of Vermont).
About Princeton University
Princeton University is a vibrant community of scholarship, research, and teaching that stands in the nation's service and the service of humanity. As a global research university with world-class excellence across the arts and humanities, the social sciences, the natural sciences, and engineering, the University is home to more than 1,250 faculty members who share a commitment to innovation, free inquiry, and the discovery and transmission of knowledge and new ideas. Princeton combines its strengths in research with a distinctive emphasis on undergraduate and doctoral education, preparing its 5,500 undergraduates and 3,200 graduate students for positions of leadership and lives of service.
About the National Institute of Mental Health (NIMH)
The mission of the NIMH is to transform the understanding and treatment of mental illnesses through basic and clinical research, paving the way for prevention, recovery and cure. For more information, visit the NIMH website. NIH’s The BRAIN Initiative, a multidisciplinary collaboration across 10 NIH Institutes and Centers, is uniquely positioned for cross-cutting discoveries in neuroscience to revolutionize our understanding of the human brain. By accelerating the development and application of innovative neurotechnologies, The BRAIN Initiative® is enabling researchers to understand the brain at unprecedented levels of detail in both health and disease, improving how we treat, prevent, and cure brain disorders. The BRAIN Initiative involves a multidisciplinary network of federal and non-federal partners whose missions and current research portfolios complement the goals of The BRAIN Initiative.
About the MRC Laboratory of Molecular Biology
The Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) is one of the world's leading research institutes. Discoveries and inventions developed at the LMB, for example DNA sequencing and methods to determine the structure of proteins, have revolutionised all areas of biology. Its scientists work to advance understanding of biological processes at the molecular level. This information will help us to understand the workings of complex systems, such as the immune system and the brain, and solve key problems in human health. http://www2.mrc-lmb.cam.ac.uk/
About the University of Cambridge
The University of Cambridge is one of the world’s leading universities, with a rich history of radical thinking dating back to 1209. Its mission is to contribute to society through the pursuit of education, learning and research at the highest international levels of excellence. Cambridge was second in the influential 2024 QS World University Rankings, the highest rated institution in the UK. The University comprises 31 autonomous Colleges and over 100 departments, faculties and institutions. Its 24,000 students include around 9,000 international students from 147 countries. In 2023, 73% of its new undergraduate students were from state schools and more than 25% from economically disadvantaged backgrounds. Cambridge research spans almost every discipline, from science, technology, engineering and medicine through to the arts, humanities and social sciences, with multi-disciplinary teams working to address major global challenges. In the Times Higher Education’s rankings based on the UK Research Excellence Framework, the University was rated as the highest scoring institution covering all the major disciplines. A 2023 report found that the University contributes nearly £30 billion to the UK economy annually and supports more than 86,000 jobs across the UK, including 52,000 in the East of England. For every £1 the University spends, it creates £11.70 of economic impact, and for every £1 million of publicly-funded research income it receives, it generates £12.65 million in economic impact across the UK. The University sits at the heart of the ‘Cambridge cluster’, in which more than 5,000 knowledge-intensive firms employ more than 71,000 people and generate £21 billion in turnover. Cambridge has the highest number of patent applications per 100,000 residents in the UK.
About the Larner College of Medicine at the University of Vermont
Founded in 1822, the Robert Larner, M.D., College of Medicine at the University of Vermont is dedicated to developing exceptional physicians and scientists by offering innovative curriculum designs, state-of-the-art research facilities, and clinical partnerships with leading health care institutions. The college’s commitment to excellence has earned national recognition, attracting talented students, trainees, physicians, and researchers from across the country. With a focus on diversity, equity, and inclusion, the Larner College of Medicine prides itself on cultivating an environment that uplifts and supports its faculty and student populations while advancing medical education, research, and patient care in Vermont and beyond.
Fruit fly connectome: All 139,255 neurons in an adult fruit fly brain (IMAGE)
Princeton University
This image shows the complete fruit fly connectome: all 139,255 brain cells in the brain of an adult fruit fly. Activity within these neurons drives an entire organism, from sensory perception to decision-making to flying. These neurons are connected by more than 50 million connections (synapses). A Princeton-led team of gamers, neuroscientists and professional tracers painstakingly mapped out the locations and connections of every brain cell, using 21 million images.
Credit
Tyler Sloan / FlyWire / Princeton University
The 50 largest neurons of the fly brain connectome
This map shows the precise location and arrangement of the 50 largest neurons of the fly brain connectome. These 50, along with another 139,205 brain cells in the brain of an adult fruit fly, were painstakingly mapped by a Princeton University-led team of neuroscientists, gamers and professional tracers. Activity within these neurons (brain cells) drives everything the organism does, from sensory perception to decision-making to controlling flight. The brain cells are connected by more than 50 million connections (synapses). Find more here: https://doi.org/10.1038/s41586-024-07558-y
Credit
Tyler Sloan and Amy Sterling / FlyWire / Princeton University
Seattle, WA – October 1, 2024 – The BRAIN Initiative® Cell Atlas Network (BICAN) has launched its first major data release, marking a significant milestone in the ambitious effort to map the whole human brain.
The data, accessible through the BICAN Rapid Release Inventory, includes single-cell and single-nucleus transcriptomic and epigenomic profiles from humans, mice, and 10 other mammalian species. Sourced from multiple grants and labs within the consortium, including the Allen Institute, these data are from projects that aim to identify and define brain cell types based on molecular profiles.
“The tap is open, the data is flowing, and more is on the way,” said Carol Thompson, Ph.D., associate director of data management at the Allen Institute. “The hope is that if we can encourage data reuse and sharing by multiple labs, we can maximize the value of these datasets and really amplify the public investment into research.”
This effort is funded by the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies® Initiative, or The BRAIN Initiative®. BICAN unites neuroscientists, computational biologists, and software engineers to create a comprehensive atlas of the human brain. This effort builds on earlier NIH BRAIN Initiative-funded projects at the Allen Institute and elsewhere, which mapped the cells of the entire mouse brain and parts of the human brain by studying the genes active in individual cells.
“This release represents a major step forward to this next frontier of neuroscience, where we finally will start to understand what sets the human brain apart,” said Fenna Krienen, Ph.D., an assistant professor at the Princeton Neuroscience Institute whose lab contributed data to today’s release.
“By bringing together experts across multiple specialties, the BICAN project is a model of open science,” said John Ngai, Ph.D., director of the NIH BRAIN Initiative. “The availability of this rapidly growing treasure trove of data will enable researchers around the world to propel the field toward a deeper understanding of the human brain in both health and disease, ultimately paving the way to more precise treatments and cures for devastating brain disorders.”
The open data release is designed to accelerate discoveries in neuroscience by providing unprecedented access to raw data from brain cells across species and developmental stages. Traditionally, it can take years between a scientist generating data and that information becoming available through a published paper.
This initiative marks a departure from that conventional approach, prioritizing early data sharing to foster collaboration and speed up research. “I hope this model becomes the norm, where we release data before it’s published and work together to create resources for the entire community,” Krienen said.
Researchers can now use this open dataset to map and define brain cell types, offering new insights into brain cellular diversity and function. “Neuroscience is a challenging field," Thompson said. "The more we can do to ensure the data we generate fuels more studies and helps the community, the better off we'll be.”
About the Allen Institute The Allen Institute is an independent, 501(c)(3) nonprofit research organization founded by philanthropist and visionary, the late Paul G. Allen. The Allen Institute is dedicated to answering some of the biggest questions in bioscience and accelerating research worldwide. The Institute is a recognized leader in large-scale research with a commitment to an open science model. Its research institutes and programs include the Allen Institute for Brain Science, launched in 2003; the Allen Institute for Cell Science, launched in 2014; the Allen Institute for Immunology, launched in 2018; and the Allen Institute for Neural Dynamics, launched in 2021. In 2016, the Allen Institute expanded its reach with the launch of The Paul G. Allen Frontiers Group, which identifies pioneers with new ideas to expand the boundaries of knowledge and make the world better. For more information, visit alleninstitute.org.
# # #
How Soviet legacy has influenced foreign policy in Georgia and Ukraine
Uppsala University
image:
Per Ekman, Doctor in Political Science, Uppsala University
The legacy of the Soviet Union’s collapse plays a greater role in the foreign policies of Georgia and Ukraine than previous studies have suggested. Conducting foreign policy in former Soviet countries can be a major challenge as the Russian state does not accept the new order. These are the findings outlined in the thesis of political scientist Per Ekman from Uppsala University.
“To understand Russia’s war in Ukraine, for example, it is important to see the war as part of a longer historical event. Since their first day of independence, Georgia and Ukraine have had to deal with Russian ambitions to control the region. For many in the West, it took a long time after the end of the Cold War to realise that a significant part of the Russian political leadership had not let go of the idea of controlling the countries that Moscow ruled during the Soviet era,” explains Per Ekman, doctor of political science at Uppsala University.
The end of the Cold War has often been described as peaceful because it did not lead to a world war. For Georgia and several other Soviet republics, however, the period was far from peaceful, with conflicts in several border regions, including with Russian involvement. In his thesis, Ekman shows how these experiences came to characterise the foreign policy that was subsequently pursued.
In the late 1990s, there was a strong desire in Georgia to create distance from Russia, something which was reinforced after the Rose Revolution in 2003. Russia’s interference in the country’s independence process was perceived by policymakers as highly negative and a main reason behind Georgia losing the conflicts with the breakaway regions of South Ossetia and Abkhazia in the 1990s.
“These early experiences pushed Georgia away from Russia and towards closer cooperation with the US, NATO and the EU, despite Russian protests and the fact that Georgia received no security guarantees from the West,” notes Ekman.
He also posits that Ukraine experienced a completely different situation. Russia certainly put political pressure on Ukraine in negotiations in the 1990s, particularly over the Black Sea Fleet and the Crimean peninsula. Moreover, it took time for the Kremlin to recognise Ukraine’s borders. But the result was seemingly peaceful agreements, which contributed to a significant proportion of Ukraine's decision-makers and population favouring a continued pragmatic relationship with Russia, although they also wanted to cooperate with the EU, the US and to some extent NATO. “There was a minority of Ukrainian politicians who wanted to cut ties with Russia, but the country’s largest party led by the influential Donetsk Network, rejected future Ukrainian membership of NATO and extended the Russian military presence in Crimea in 2010.
“Ukraine’s foreign policy changed monumentally when then-president Viktor Yanukovych rejected the association agreement with the EU, triggering the major Euromaidan protests in 2013. The protests were followed by Russia’s annexation of the Crimean peninsula in 2014. As I show in my thesis, these events resulted in a growing consensus in Ukraine to distance itself from Russia. Paradoxically, the Russian leadership’s behaviour contributed greatly to Ukraine’s increasingly clear move towards the EU and NATO and away from Russia, something Vladimir Putin said he wanted to avoid at all costs,” notes Ekman.
Article Title
Foreign Policy After Empire: Explaining Georgia’s and Ukraine’s International Orientation from Independence until 2021
2-billion-year-old rock home to living microbes
New research could help us understand very early life on Earth and the hunt for evidence of life on Mars
University of Tokyo
image:
This picture shows a very famous outcrop where nearly horizontal black and white layers are observed. The BIC made of layers of igneous rock in a basin shape, formed over a period of about 1 million years, after which it seems to have barely changed.
Pockets of microbes have been found living within a sealed fracture in 2-billion-year-old rock. The rock was excavated from the Bushveld Igneous Complex in South Africa, an area known for its rich ore deposits. This is the oldest example of living microbes being found within ancient rock so far discovered. The team involved in the study built on its previous work to perfect a technique involving three types of imaging – infrared spectroscopy, electron microscopy and fluorescent microscopy – to confirm that the microbes were indigenous to the ancient core sample and not caused by contamination during the retrieval and study process. Research on these microbes could help us better understand the very early evolution of life, as well as the search for extraterrestrial life in similarly aged rock samples brought back from Mars.
Deep in the earth lies something ancient and alive. Colonies of microbes live in rocks far beneath the surface, somehow managing to survive for thousands, even millions of years. These tiny, resilient organisms appear to live life at a slower pace, scarcely evolving over geological time spans and so offering us a chance to peek back in time. Now, researchers have found living microbes in a rock sample dated to be 2 billion years old.
“We didn’t know if 2-billion-year-old rocks were habitable. Until now, the oldest geological layer in which living microorganisms had been found was a 100-million-year-old deposit beneath the ocean floor, so this is a very exciting discovery. By studying the DNA and genomes of microbes like these, we may be able to understand the evolution of very early life on Earth,”said Yohey Suzuki, lead author and associate professor from the Graduate School of Science at the University of Tokyo.
The rock sample was taken from the Bushveld Igneous Complex (BIC), a rocky intrusion in northeastern South Africa which formed when magma slowly cooled below the Earth’s surface. The BIC covers an area of approximately 66,000 square kilometers (roughly the size of Ireland), varies in thickness by up to 9 km, and contains some of the richest ore deposits on Earth including about 70% of the world’s mined platinum.
Due to the way it was formed and minimal deformation or change occurring to it since then, the BIC is believed to have provided a stable habitat for ancient microbial life to continue until today.
With the aid of the International Continental Scientific Drilling Program, a nonprofit organization that funds exploration at geological sites, the team obtained a 30-centimeter-long rock core sample from about 15 meters belowground. The rock was cut into thin slices and analyzed, which is when the team discovered living microbial cells densely packed into cracks in the rock. Any gaps near these cracks were clogged with clay, making it impossible for the organisms to leave or for other things to enter.
The team built on a technique they had previously developed to confirm that the microbes were native to the rock sample, and not due to contamination during the drilling or examination process. By staining the DNA of the microbial cells and using infrared spectroscopy to look at the proteins in the microbes and surrounding clay, the researchers could confirm that the microorganisms were both alive and not contaminated.
“I am very interested in the existence of subsurface microbes not only on Earth, but also the potential to find them on other planets,” said Suzuki. “While Martian rocks are generally much older (20 billion to 30 billion years old), NASA’s Mars rover Perseverance is currently due to bring back rocks that are a similar age to those we used in this study. Finding microbial life in samples from Earth from 2 billion years ago and being able to accurately confirm their authenticity makes me excited for what we might be able to now find in samples from Mars.”
-----
Paper
Yohey Suzuki, Susan J. Webb, Mariko Kouduka, Hanae Kobayashi, Julio Castillo, Jens Kallmeyer, Kgabo Moganedi, Amy J. Allwright, Reiner Klemd, Frederick Roelofse, Mabatho Mapiloko, Stuart J. Hill, Lewis D. Ashwal, Robert B. Trumbull. Subsurface Microbial Colonization at Mineral‐Filled Veins in 2‐Billion‐Year‐Old Mafic Rock from the Bushveld Igneous Complex, South Africa. Microbial Ecology. 2nd October 2024. doi: 10.1007/s00248-024-02434-8
This study was supported by the Japan Society for the Promotion of Science (JSPS)/National Research Foundation (NRF) Bilateral Joint Research Project and the Astrobiology Center Program of National Institutes of Natural Sciences (NINS; AB0502).
Competing interests
None
About the University of Tokyo
The University of Tokyo is Japan’s leading university and one of the world’s top research universities. The vast research output of some 6,000 researchers is published in the world’s top journals across the arts and sciences. Our vibrant student body of around 15,000 undergraduate and 15,000 graduate students includes over 4,000 international students. Find out more at www.u-tokyo.ac.jp/en/ or follow us on X at @UTokyo_News_en.
This picture was taken on site when the drill core sample was washed, flamed and then cracked. The 30-centimeter-long, 85-millimeter-diameter core was taken back to Japan for further study.
Credit
Y. Suzuki
This picture shows many tiny cells in which DNA is abundantly included inside the cells. First, the microbial cells were detected in fractures in the rock sample using an infrared imaging technique called O-PTIR spectroscopy. After that, they were stained with a green solution and analyzed using both a scanning electron microscope and then fluorescent microscopy. The combination of readings from these three imaging techniques enabled the researchers to confirm the indigenous and living microbial cells in the 2-billion-year-old rock fissure.
Credit
Y. Suzuki, S. J. Webb, M. Kouduka et al. 2024/ Microbial Ecology
