Madeline Guman

TWiM#51
Major topics covered: Diversity in cave microbiomes and microbes’ role in the
formation of caves
It has been theorized that microorganisms living in caves play a vital role in
their formation. This concept, known as biospeleogenesis, is relatively new, but it is
quickly gaining merit in the scientific community for a number of reasons. The
foremost of these is that, in terms of geology and chemistry alone, caves must form
over millions of years through complicated and unlikely chemical reactions that
require exceedingly specific conditions. When the metabolic processes of microbes
are introduced, cave formation becomes a much shorter, simpler, and more likely
occurrence. However, proving this theory completely may not be possible with
current technologies due to the difficulties that arise when attempting to culture
cave microorganisms in the lab. One possible explanation for this difficulty is that
most of the organisms are archaea and require irreproducible cave conditions in
order to grow. (Barton)
The idea of biospeleogenesis was first proposed by Hazel Barton, who has
since taken samples from over twenty caves around the world. Dr. Barton began her
studies in South Dakota within Wind Cave, one of the largest caves in the USA. At
first, it was believed that cave microbiomes would be sparse and free of diversity
due to the nutrient-limited conditions. The first sample, the filtrate of one liter of
water from a lake within the cave, reinforced this idea, containing only 3,000 cells
per milliliter of water. The only other samples ever found to have a cell density
lower than this were the ice cores retrieved from polar ice caps in Antarctica.
However, after filtering 200 liters of water in an attempt to collect a sample large
enough to extract and sequence DNA, the lake was found to contain over 12,000
different species of microbes. This number is thought to be low because of the
difficulty of collecting large samples and the wide dispersion of the microbes.
The diversity found in the cave microbiome has been attributed to water
trickling down through the soil and carrying microbes with it. It contains both
autotrophs and heterotrophs that may be predatory or mutualistic. The high
numbers of mutualistic relationships has been cited as another likely contributor to
the difficulty of culturing these organisms in the lab. It may also account for the lack
of competitive exclusion. If one organism were to begin multiplying rapidly, it would
run out of resources produced by the others very quickly. Predatory microbes thrive
in low numbers as well; since the cell density is so low, they cannot multiply too
rapidly or they will run out of food. Like most ecosystems, each microbe in the cave
relies on the others and the environment to persist and continue the circle of life.
The theory of biospeleogenesis quickly followed the discovery of the
previously unknown diversity of cave microbiomes. It was and continues to be a
much better and more likely explanation of cave formation than the complex
chemical reactions proposed by geologists and chemists. Microbes have very diverse
metabolic processes that use and produce countless compounds that are implicated
in the degradation or dissolution of rocks and minerals and the subsequent
formation of caves (Barton). One example is the formation of dolomite deposits in
some caves. Dolomite is a magnesium-carbonate compound formed from calcium
carbonate. In order to form this compound without microbial assistance, a
magnesium-rich solution must come into contact with calcium carbonate at very
high temperatures during which both compounds go into solution and then
precipitate as dolomite (Matthews). In order to form the dolomite deposits
discussed in the podcast, this process would take approximately ten million years.
However, sulfate-reducing microbes can produce dolomite relatively quickly and
under more normal conditions, such as lower temperatures (Van Lith). Other
processes that lead to cave formation that are a result of microbial metabolism
include the formation of weak carbonic acids as water percolates down through the
soil and the formation of hydrogen sulfide gas. Both of these dissolve rock and
create caves after years of ongoing exposure.
There were many other notable findings regarding cave microbes included in
this podcast as well. The most prominent of these was the experiment done on
antibiotic resistance. The microbes used in this study, which contained
representatives from about one hundred species, were extracted from a special cave
in a nature reserve in an area of the cave in which no human had ever been.
However, despite the complete isolation from antibiotic exposure, these microbes
showed resistance to every antibiotic tested aside from Vancomycin. Upon closer
inspection, they were also found to have different methods of circumventing the
antibiotic actions than microbes found in normal settings. (Bhullar)
Aside from the description of Dr. Hazel Barton’s research and theories, this
podcast contained little. There were no concerns raised about the subject matter at
hand aside from the difficulties in culturing cave microbes in the lab. There were no
additional topics mentioned, although the hosts did ask Dr. Barton about her pre-
cave microbiology years working as a graduate student and a post-doc. There were
no email questions discussed at the end of the podcast.
This topic was extremely interesting to me because it is absolutely awe-
evoking that organisms so small and seemingly insignificant can create something
as vast and imposing as a cave. I was delighted to learn that each cave has an equally
important yet completely different microbiome composed of organisms that are
essential for that specific cave ecosystem. I would have loved to hear more examples
of microbial activity from different caves. Those presented were so intriguing, and
although I’m sure they covered the most exciting examples in the podcast, the others
must be fascinating as well. I would also like to have heard more about the practical
uses that these microbes may have. For example, one cave microbe found in iron
mines in Brazil actually purified stores of iron ore, making it much more valuable
when mined because it did not have to be processed as much to create the same end
product. Microbes such as these definitely have a place in modern technology. They
are efficient and environmentally friendly, and they are available to us.
I would like to cover biogeochemical cycling and the products of microbial
metabolism more in depth in a general microbiology class. I feel that it would have
given me a better foundation to understand this topic, which relied heavily on the
understanding that microbial metabolism can utilize and produce many different
compounds and elements that may make up or carve out a cave. Biogeochemical
cycling and the products of microbial metabolism are also potentially useful to us as
a population and knowing more could inspire innovative ideas in areas such as clean
energy, agriculture, and even the isolation of useful minerals like iron ore.

Sources:
1. Barton, Hazel A. “Biospeleogenesis.” Karst Geomorphology 6 (2013): 38-56.
Web.
2. Bhullar, Kirandeep, Nicholas Waglechner, and Hazel Barton. “Antibiotic
Resistance Is Prevalent in an Isolated Cave Microbiome.” PLOS One (2012):
Web.
3. Matthews, Alan and Amitai Katz. “Oxygen Isotope Fractionation During the
Dolomitization of Calcuim Carbonate.” Geochimica et Cosmochimica Acta
41.10 (1977): 1431-8. Web.
4. Van Lith, Yvonne, Rolf Warthmann, and Crisogono Vasconcelos. “Sulphate-
Reducing Bacteria Induce Low Temperature Ca-Dolomite and High Mg-
Calcite Formation.” Geobiology 1.1 (2003): 71-9. Web.