Hunting for Antibiotics in Caves

Featured Image courtesy Doronenko and Wikimedia Commons

Paper: High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits.

Authors: Marta Maciejewska , Magdalena Całusińska, Luc Cornet, Delphine Adam, Igor S. Pessi, Sandrine Malchair, Philippe Delfosse, Denis Baurain, Hazel A. Barton, Monique Carnol and Sébastien Rigali

Do you ever think about the microbes around you when you go caving? Me neither, but a team of scientists from Belgium did. 

Actinobacteria are found in many places around the world, including volcanic terrains and ice caves. They are of particular importance to cave ecosystems and structure since the formation of speleothems (cave formations) like moon milk is thought to be aided by Actinobacteria. These microbes are known for their ability to produce filaments and aid calcium carbonate deposition and precipitation, which could be important for the mineral deposition that forms speleothems. 

Moonmilk deposits from Bergmilchkammer cave (1862/20), courtesy Doronenko and Wikimedia Commons

Despite the importance of microbes in caves, our understanding of microbial communities and spatial distribution within a cave is still fairly limited, i.e. we still don’t know which microbes dominate cave formations and where they live. An international team of scientists set out to answer these questions using three speleothems in the Grotte des Collemboles (English: Springtails’ Cave) in Belgium. Using sterile scalpels, the team scraped soft moonmilk deposits from the walls of the cave into tubes to understand whether different speleothems in the same cave have different bacterial communities.

Using high-throughput DNA sequencing, they found that all the moonmilk deposits had over 700 species in common but distinct communities of bacteria. At least 10% of the species on a particular speleothem were unique to it, and they identified over 4,000 species in total. Actinobacteria was the second-most abundant group (after Proteobacteria) across deposits and many Actinobacterial groups like Nocardia, Pseudonocardia and Streptomyces were found at every speleothem.

Within Actinobacteria, the genus Streptomyces showed the highest diversity (19 species) across all sites even though they only comprised 3% of the actinobacterial community. Interestingly, the team could only grow 5 of these Streptomyces in the lab, which reinforces the significant obstacles to culturing microorganisms still faced by microbiologists.

Streptomyces coelicolor colonies, courtesy Norwich Research Park Image Library

Streptomyces are already a prodigious source of antibiotics and other biologically important compounds, but could these speleothem communities be a source of novel antibiotic compounds? The answer might be worth exploring, given the diversity of Streptomyces found in just this one cave but also the emerging roles of other Actinobacteria in antibiotic production.

The difficulty of growing in situ the bacteria we find in cave formations might complicate our ability to study the compounds they produce, but such adventures could still offer fascinating insights into the microbial inhabitants of caves and how they help bind mineral formations together. The next time you go caving, hopefully you’ll think about the Actinobacteria that surround you!

Creative Commons License

Hunting for Antibiotics in Caves by Janani Hariharan is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Deep Sea Bacteria have Thrived for Millions of Years

Image of the ocean floor

Featured Image courtesy Yannis Papanastasopoulos, Unsplash.

Paper: Atribacteria reproducing over millions of years in the Atlantic abyssal subseafloor

Authors: Aurèle Vuillemin, Sergio Vargas, Ömer K. Coskun, Robert Pockalny, Richard W. Murray, David C. Smith, Steven D’Hondt, William D. Orsi

If you, like me, imagine the seafloor to be inhabited by strange, mysterious creatures like vampire squids and goblin sharks, think again: bacteria continue to surprise us with their resilience in the oddest of environments. Scientists have detected microbes living in the mud and rocks on the seafloor, but we don’t know much about them. Are they alive? How do they get energy in such a nutrient-poor environment? Given the inhospitable conditions in the sub-seafloor, scientists have thought that most of these microbes were close to the energy limit for life, which is an estimate of the minimum amount of energy required to sustain life as we know it. For this reason, we’ve assumed that subseafloor microbes die faster than they grow because there simply isn’t enough energy in the deep sea to sustain life long-term. 

Continue reading “Deep Sea Bacteria have Thrived for Millions of Years”

Do Microbes Release Fluorine from Rocks?

Image of soil microcosm

Featured Image used with permission of photographer (Cassi Wattenburger)

Paper: Indigenous microbes induced fluoride release from aquifer sediments

Authors: Xubo Gao, Wenting Luo, Xuesong Luo, Chengcheng Li, Xin Zhang, Yanxin Wang

My science textbook taught me that fluorine (F) was really important for dental health, and I’ve since learned that both excessive and insufficient amounts of fluoride in groundwater can cause health issues. While the chemistry behind the release of fluoride ions from rocks or sediments into groundwater is well understood, the microbiology of this process is not. Specifically, scientists have been wondering whether microbes could speed up the release of F from sediments into groundwater. 

Continue reading “Do Microbes Release Fluorine from Rocks?”

Whose Faces do we See in Geology Textbooks?

Student standing on textbooks in library

Author’s Note: The last few weeks have left us grappling with the profound effects of systemic racism, as seen in the wake of the recent protests and violence all over the USA and the world, as well as the disproportionate effect of COVID-19 on Black communities. This week’s post is dedicated to exploring the impact of another effect of systemic racism: lack of representation in educational spaces, made apparent in geology textbooks. 

Continue reading “Whose Faces do we See in Geology Textbooks?”

Ancient microbes engineered sedimentary deposits

Cambrian Stromatolites from New York State

Featured image: Cambrian stromatolites from New York State. Image attribution: James St. John / CC BY 2.0; Wikimedia Commons

Paper: Evidence for microbes in early Neoproterozoic stromatolites

Authors: Zhongwu Lan, Shujing Zhang, Maurice Tucker, Zhensheng Li, Zhuoya Zhao

Stromatolites are ancient, layered deposits of sediments that are characterized by thin, alternating light and dark bands. While microbial fossils have been found in many stromatolites, the biological origin of these structures has been debated. Continue reading “Ancient microbes engineered sedimentary deposits”