MICROBIALITES: WHAT ON EARTH
Patricia M Valdespino2019, Frontiers for young minds
https://doi.org/10.3389/frym.2019.00112visibility
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Microbialites are rock-like underwater structures that look like reefs but are made entirely of millions of microbes. These structures are very ancient and can be found in dierent environments on every continent on Earth. Mexico has many microbialite reefs, in desert valleys, crater-lakes, and coastal lagoons. Science helps us to understand the microbes that build microbialites, to know whether the same kinds of microbes make up microbialites in dierent regions of the world, and to figure out how the microbes organize into microbialites. Many things are damaging microbialites in Mexico, including poorly planned development, pollution from lack of sewage treatment, too much water usage, and the fertilizers used for agriculture. Policies that regulate development are urgently needed to help save these diverse and ancient microbial reefs.
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The interactions between the geosphere and the biosphere are central questions in environmental and geological research. The relationship between bacteria and their environment is an important example of these interactions. By studying microbial communities in modern environments, it is possible to understand the underlying mechanisms that shape these environments and apply this knowledge to the rock record. Recently, new experimental and theoretical methods, ranging from nano-and biotechnology to mathematical and conceptual modelling, have come into play. Thus, new opportunities for interdisciplinary research in the field of geobiology have emerged. In this paper, we review aspects of state-of-the-art imaging and modelling techniques and propose a research concept linking the experimental and the theoretical approaches. Fig. 5 Sequence of model results showing the surface topography after an increasing number of atomic blocks are removed. The initial surface was flat. The bottom part of the figure shows the surface topography in 3D after 2000 atomic blocks are removed (compare Fig. 5D). REFERENCES Arvidson RS, Ertan IE, Amonette JE, Luttge A (2003) Variation in calcite dissolution rates: a fundamental problem? Geochimica et Cosmochimica Acta 67, 1623-1634. Beveridge TJ (1978) Response of cell-walls of Bacillus subtilis to metals and to electron-microscopic stains. Canadian Journal of Microbiology 24, 89-104. Beveridge TJ (1981) Ultrastructure, chemistry and function of the bacterial wall. International Review of Cytology 72, 229-317.
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BIODIVERSITY
Published: 13 September 2019
doi: 10.3389/frym.2019.00112
MICROBIALITES: WHAT ON EARTH?
Alfredo Yanez-Montalvo 1,2 , Bernardo Águila 1 , Elizabeth S. Gómez-Acata 1 , Yislem Beltrán 3 , Patricia
M. Valdespino-Castillo 4 , Carla M. Centeno 1 and Luisa I. Falcón 1*
1
Instituto de Ecología, Universidad Nacional Autónoma de México, Mérida, Mexico
2
El Colegio de la Frontera Sur, Chetumal, Mexico
3
Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
4
Lawrence Berkeley National Laboratory, Berkeley, CA, United States
YOUNG REVIEWERS:
DANA
AGE: 14
MARÍA
JOSE
AGE: 14
MARIANA
AGE: 15
Microbialites are rock-like underwater structures that look like reefs
but are made entirely of millions of microbes. These structures
are very ancient and can be found in different environments on
every continent on Earth. Mexico has many microbialite reefs,
in desert valleys, crater-lakes, and coastal lagoons. Science helps
us to understand the microbes that build microbialites, to know
whether the same kinds of microbes make up microbialites in
different regions of the world, and to figure out how the microbes
organize into microbialites. Many things are damaging microbialites
in Mexico, including poorly planned development, pollution from
lack of sewage treatment, too much water usage, and the fertilizers
used for agriculture. Policies that regulate development are urgently
needed to help save these diverse and ancient microbial reefs.
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What are Microbialites?
WHAT ARE MICROBIALITES?
MICROBIALITE
A rock-like structure
made by millions of
microbes that
precipitate carbonate.
MICROBE
An organism that is
seen under
the microscope.
STROMATOLITE
Fossilized microbialites,
and are the oldest
fossils dated so far.
CYANOBACTERIA
A phylum of bacteria
that can
make photosynthesis.
EXOPOLYMERIC
SUBSTANCES (EPS)
Mucous-like molecules
released by
microorganisms into
their environment,
which help the
microbes remain close
together and
communicate with
each other.
Do you know what a microbialite is? Not many people do. This is
because microbialites look like slimy underwater rocks, but they are
actually reefs made up of microbes (simple, one-celled organisms).
Microbialites are fascinating, because these rock-like structures are
made by the interaction of millions of microbes that live in certain
aquatic environments. The microbes facilitate the precipitation of
minerals from the water, to form the microbialite structure [1].
Since microbialites are like rocks, they have remained on earth
since extremely ancient times. Fossilized microbialites, known as
stromatolites (from the Greek strõma, meaning bed or layer, and
lithos, meaning rock), are the oldest evidence of life on Earth, dating
back to 3.7 billion years ago [2].
Cyanobacteria are one type of microbe found in microbialites, and
these bacteria do all kinds of important work. Cyanobacteria build
shelters that protect the microbial community from dangerous things
in the environment, including protecting them from drying out and
from damage by the sun’s UV rays. The shelters built by cyanobacteria
trap and bind sediments and minerals, which help to grow the
microbialites [3, 4]. Cyanobacteria are also involved in producing
slimy substances called exopolymeric substances (EPS), which are
like mucous. Exopolymeric substances help microbes to stay close
to each other and allow the cells to communicate with each other
[4]. Cyanobacteria also have pigments that interact with photons
from the Sun, allowing them to perform photosynthesis, which leads
to the incorporation of carbon from the atmosphere (in the form
of CO2 ) into their cells. Cyanobacteria take up water and produce
oxygen during photosynthesis. Since microbialites are so old, they
probably participated in oxygenating the early Earth. Gently and slowly,
bubble by bubble, microbialites produced oxygen, and by ∼2.4 billion
years ago, the chemistry of earth’s atmosphere had changed enough
to support the evolution of other life forms [5]. Cyanobacteria are
one of the food sources for other kinds of microbes, helping many
different kinds of microbes work together as a unit to form the
microbialite community.
WHERE DO MICROBIALITES LIVE?
There are living microbialites in different aquatic environments all
over the globe, including polar, temperate, and tropical locations.
In Mexico, there are microbialite communities in different locations,
including coastal lagoons, crater-lakes, and desert ponds (Figure 1).
ARE ALL MICROBIALITES IN MEXICO THE SAME?
In our study, we wanted to understand if microbialites from different
locations in Mexico are similar or different, in terms of the microbes
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What are Microbialites?
Figure 1
Microbialite reef locations
in Mexico that were
examined in our study:
Cuatro Ciénegas basin
in Northern México,
crater-lake Alchichica
in Central México, and
Bacalar lagoon in the
Yucatán Península.
Figure 1
POLYMERASE
CHAIN REACTION
(PCR)
A laboratory technique
for obtaining millions of
copies of pieces of
DNA, so that they can
be more
easily analyzed.
that make them up. To study this, we explored various sites using
catamarans, kayaks, and boats. Once we identified microbialite reefs,
we took small samples (∼2 g) of microbialites from the first few
millimeters of their surface, using clean, microbe-free tools and
containers. We stored these samples in coolers and then froze them
when we got back to the laboratory. Later, we extracted the DNA
from these microbialite samples, using different enzymes, soaps,
and organic molecules. To study this DNA, we first amplified it
using a technique known as polymerase chain reaction (PCR) and
analyzed how similar or different the microbial DNA sequences were
to each other.
By comparing certain regions of the microbial DNA, thousands of
microbes can be identified from a pea-sized rocky sample!
We found that all the microbialite communities we studied had
the same groups of microbes, just in slightly different proportions
(Figure 2) [6]. The main microbes in microbialites are Cyanobacteria
(which we already discussed), Proteobacteria and Bacteroidetes
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What are Microbialites?
Figure 2
Several different kinds
of bacteria make up the
microbialites found in
various regions of
Mexico. The types of
bacteria are listed on
the left, and the pie
charts under the
pictures of the
microbialites show that
microbialites from each
location are made up
of different proportions
of these same types
of bacteria.
Figure 2
(which are very diverse and can digest many types of substrates,
including carbon, nitrogen, and sulfur), Chloroflexi (which can do a
type of photosynthesis that does not produce oxygen, but instead
produces a substance called sulfide), and Archaea (which can produce
and eat methane) (Figure 3).
Proteobacteria are the most diverse bacteria in microbialites,
making up 30–40% of the total diversity in these structures,
followed by a group of bacteria that we know very little about
and are called unclassified bacteria, which make ∼20% of the
bacteria in microbialites. Other bacteria, including Bacteroidetes,
Plactomycetes, Verrucomicrobia, Chloroflexi, and Cyanobacteria
comprise the remaining diversity (Figure 2). The microbes in
microbialites have been interacting amongst themselves and with the
environment for many millions of years, and have helped transform the
Earth, making our life on this planet possible through the production
of oxygen and other important processes. Microbial communities
like the ones that form microbialites help the Earth to function
as a unit.
ARE MICROBIALITES IN MEXICO DOING WELL?
Since microbialites are self-sufficient, they only need clean water,
sunlight, and gases from the atmosphere to grow and develop. All
the microbialites we have studied in Mexico live in places with clean
and clear water, and we have found massive microbialite formations
that have been dated to be ∼10,000 years of age [7]. Some of
the beautiful aquatic environments where microbialites have thrived
for thousands of years have warm, clear, tropical waters. This is
the case for a coastal lagoon called Bacalar in southern Mexico,
which has attracted loads of tourists. But a problem arises when
there is no infrastructure to treat the sewage from the growing
population, leading to pollution of the lagoon. Microbialites in Bacalar
lagoon and in other areas of Mexico are being threatened by human
activities. In northern Mexico, the microbialites that thrive in the
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What are Microbialites?
Figure 3
Many microbes build
microbialites. They do
photosynthesis, and
capture CO2 ,
producing oxygen and
are active in the
nitrogen, sulfur and
methane cycles.
Figure 3
Cuatro Cienegas valley, which has many ponds in the middle of a
desert, are at risk because too much water is being removed from
the ponds for agriculture. In central Mexico, microbialites that live
in crater-lakes are also at risk, due to both pollution and too much
water usage.
Humans are the main problem for the world’s biodiversity, but we
are also the solution. Microbialites are part of Earth’s history and it
is wonderful that we can observe these ancient communities today!
We have the responsibility to be educated about our environment and
to make intelligent choices. Let us use efficient water treatment and
technology to save microbialites and other aquatic life! Before going
on a holiday, read about the places you will visit and learn about the
plants, animals, and bacteria that live there, so that you can enjoy their
company without harming them or their environment.
AUTHOR CONTRIBUTIONS
The authors contributed equally to writing this paper.
ORIGINAL SOURCE ARTICLE
Valdespino-Castillo, P. M., Hu, P., Merino-Ibarra, M., López-Gómez, L.
M., Cerqueda-García, D., González-De Zayas, R., et al. 2018. Exploring
biogeochemistry and microbial diversity of extant microbialites in
Mexico and Cuba. Front. Microbiol. 9:510. doi: 10.3389/fmicb.
2018.00510
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What are Microbialites?
REFERENCES
1. Reid, R. P., Visscher, P. T., Decho, A. W., Stolz, J. F., Bebout, B. M., Dupraz, C.,
et al. 2000. The role of microbes in accretion, lamination and early lithification of
modern marine stromatolites. Nature 406:989–92. doi: 10.1038/35023158
2. Nutman, A. P., Bennett, V. C., Friend, C. R., Van Kranendonk, M. J., and Chivas, A.
R. 2016. Rapid emergence of life shown by discovery of 3,700-million-year-old
microbial structures. Nature 537:535–8. doi: 10.1038/nature19355
3. Watnick, P., and Kolter, R. 2000. Biofilm, city of microbes. J. Bacteriol.
182:2675–9. doi: 10.1128/JB.182.10.2675-2679.2000
4. Flemming, H. C., and Wingender, J. 2010. The biofilm matrix. Nat. Rev. Microbiol.
8:623–33. doi: 10.1038/nrmicro2415
5. Johnston, D. T., Wolfe-Simon, F., Pearson, A., and Knoll, A. H. 2009. Anoxygenic
photosynthesis modulated proterozoic oxygen and sustained Earth’s middle
age. Proc. Natl. Acad. Sci. U.S.A. 106:16925–9. doi: 10.1073/pnas.0909248106
6. Valdespino-Castillo, P. M., Hu, P., Merino-Ibarra, M., López-Gómez, L. M.,
Cerqueda-García, D., González-De Zayas, R., et al. 2018. Exploring
biogeochemistry and microbial diversity of extant microbialites in Mexico and
Cuba. Front. Microbiol. 9:510. doi: 10.3389/fmicb.2018.00510
7. Gischler, E., GIbson, M. E., and Oschmann, W. 2008. Giant holocene freshwater
microbialites, laguna bacalar, quintana roo, Mexico. Sedimentology
55:1293–309. doi: 10.1111/j.1365-3091.2007.00946.x
SUBMITTED: 05 December 2018; ACCEPTED: 15 August 2019;
PUBLISHED ONLINE: 13 September 2019.
EDITED BY: Francisco Barona-Gomez, National Laboratory of Genomics for
Biodiversity, Center for Research and Advanced Studies of the National Polytechnic
Institute, Mexico
CITATION: Yanez-Montalvo A, Águila B, Gómez-Acata ES, Beltrán Y,
Valdespino-Castillo PM, Centeno CM and Falcón LI (2019) Microbialites: What on
Earth? Front. Young Minds 7:112. doi: 10.3389/frym.2019.00112
CONFLICT OF INTEREST STATEMENT: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
COPYRIGHT © 2019
Yanez-Montalvo, Águila, Gómez-Acata, Beltrán,
Valdespino-Castillo, Centeno and Falcón. This is an open-access article distributed
under the terms of the Creative Commons Attribution License (CC BY). The use,
distribution or reproduction in other forums is permitted, provided the original
author(s) and the copyright owner(s) are credited and that the original publication
in this journal is cited, in accordance with accepted academic practice. No use,
distribution or reproduction is permitted which does not comply with these terms.
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September 2019 | Volume 07 | Article 112 | 6
Yanez-Montalvo et al.
What are Microbialites?
YOUNG REVIEWERS
DANA, AGE: 14
My name is Dana. I am 14 years old and I live in Guanajuato, Mexico. I have been
dancing ballet and jazz since I was 2 years. I love science, specially astronomy.
I would like to study it in the future. I also would like to be an engineer or
a lawyer.
MARÍA JOSE, AGE: 14
My name is María Jose, my friends call me Majo. I am 14 years old, I live in Guanajuato,
Mexico. I like ballet, I have been practice it since I was 3 years old. I like science and
I want to be a doctor.
MARIANA, AGE: 15
My Name is Mariana, I am 15 years old and I live in Guanajuato, Mexico. My favorite
sport is squash, I have been playing it since I was 6 years old. My favorite subjects are
History and Chemistry. In the future I would like to become a Scientist.
AUTHORS
ALFREDO YANEZ-MONTALVO
I am Ph.D. student in Ecology and Sustainable Development. I am passionate about
the study of microbial ecology and the understanding of how this microbial diversity
is affected by natural and human activities. I love poetry, sports, and Bacalar lagoon.
Every day we can learn from people and nature.
BERNARDO ÁGUILA SALGADO
I am Ph.D. student, a curious and geeky person. I am in love with arts, technology
and popular science, specially natural science topics, such as biology, geology,
astronomy, and environmental sciences. I am very interested in microorganisms
that have an important role in the function of ecosystems. I am also aware of the
environmental problems we may face in a future and I would like to contribute in
some way to the solution.
ELIZABETH S. GÓMEZ-ACATA
I am a microbiologist working as a post-doctoral researcher at Universidad
Nacional Autonoma de Mexico. I am fascinated with microbial life. I love studying
microorganisms in any environment because they are very important for life on the
planet. I also like to investigate biotechnological applications of microorganisms
for taking care of the environment. I enjoy looking at them on the microscope
and studying them with molecular techniques. In my free time, I enjoy traveling,
photography, and cross-stitch embroidery. I love my family and enjoy life.
YISLEM BELTRÁN
I am a post-doctoral fellow at UNAM in Mexico. I am interested in microbial
diversity and to understand patterns that characterize the presence of bacterial
communities in different environments, as well as their response to environmental
changes. What I like about this research is that I have been able to travel and know
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Yanez-Montalvo et al.
What are Microbialites?
beautiful places, but also, I can combine field and molecular work and learn about
computer sciences.
PATRICIA M. VALDESPINO-CASTILLO
I am a Ph.D. in Marine Science and Limnology. I am fascinated by the microbes of
the environment, they are the most ancient and the most powerful mini-machines
of life. Science, music and outdoor activities are very important for me; therefore I
want to try any possible combination of these. I love being illuminated by curious
young minds.
CARLA M. CENTENO
Since I was a little girl I wanted to be a biologist, because I was interested in
understanding natural phenomena. When I learned about microorganisms I was
fascinated by their shape, their tricky simplicity, the time they spend on our planet
(millions of years) and their diversity. I love laboratory work and I really enjoy
teaching. I have two small children to whom I teach respect and love toward all
life forms.
LUISA I. FALCÓN
I am a microbial ecologist at UNAM in Mexico, fascinated with the diversity of bacteria
and archaea in the environment. I love how microbes interact with each other to
complement their metabolic capabilities, allowing for communities and ecosystems
to exist. *falcon@ecologia.unam.mx
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September 2019 | Volume 07 | Article 112 | 8
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