How can extremophiles form caves

Unrooted approximate maximum likelihood tree showing the relationship and occurrences of Actinobacteria OTUs across all four sample locations. Bootstrap values are indicated. The number of shared OTUs in the three locations was relatively low; three out of five belonged to Pseudonocardiaceae and two were Euzebyales Supplemental Figure 1A.

Chao 1 estimator suggests that even though a more comprehensive sampling is required to provide a more complete assessment of these microbial communities, our sampling effort was probably enough to describe the cosmopolitan OTUs Supplemental Figure 1B. None of the sequences recovered were classified as Streptomyces , which was odd, given that Streptomyces are present in almost every other environment studied i. We believe this anomaly is due to primer bias.

While this does not conclusively establish that our sequencing missed Streptomyces that are present, it is cause for concern. Future sequencing efforts will utilize Actinobacteria-specific primers to test our hypothesis that Streptomyces are being missed and to better characterize the diversity of the Actinobacteria in caves.

Euzebyales was recently described and has two known genera Kurahashi et al. The Acidimicrobiales order was described by Stackebrandt et al. It has already been described in caves Macalady et al. Figure 6. Due to some variation in sampling effort in each case, a re-sampling analysis was performed, randomly selecting the smallest number of sequences across the different groups , times per each sample, to standardize the values.

Diversity indices and estimators are summarized in Table 1A. Non-parametric Shannon and Shannon suggested more diverse communities within New Mexico caves compared to Hawai'i and Azores. Simpson diversity indices suggest the highest diversity values for Hawai'i. All indices agree with the less diverse communities being in Azores. The Shannon index gives more weight to the rare species and Simpson to the dominant ones.

Considering the Simpson indexes of the three locations, the community composition in Azores caves would include more cosmopolitan species with high abundance and Hawai'i caves would be composed of phylotypes with narrower distribution.

In islands, population size and genetic diversity tend to be limited due to the smaller extension of the habitats. Comparable taxa—area relationships Bell et al. However, we found differences between the diversity indices for Azores and Hawai'i, which could be related to differences in island size, isolation and age of lava flows.

We should be aware that the amount of data available is still small and that further studies may still reveal different trends. Table 1A. They were found in all four locations, however, more of the OTUs were found in the Azorean islands 13 out of than in Hawai'i 2 out of 30 or New Mexico 3 out of Physical isolation is an important driver of microbial evolution Papke and Ward, ; thus, island isolation would promote unique evolutionary forces that result in the development of a novel genetic reservoir.

However, in our results we did not observe significant differences between continental and island territories according to genetic novelty. An approximate maximum likelihood tree shows the relationship between the sequences and occurrence of OTUs Figure 5. For this analysis Pico and Terceira were considered separate locations.

Gaiellaceae -like sequences were found in New Mexico and the Azores, but not Hawai'i. All but one of the sequences were singletons.

Gaiellaceae , another recently described family, was originally found in a water borehole, and sequences from this family have subsequently been found in soil, volcanic soil, thermal springs and marine ascidians Albuquerque et al.

Rubrobacterales occurred in the New Mexico and Hawai'i samples. The order Actinomycetales has many polytomies with most of them occurring in the samples from Hawai'i, Pico, and Terceira. These samples are either unresolved parts of the tree due to missing data or represent rapid speciation in the Actinomycetales.

Representatives of Euzebyales were found in all four locations Figure 5. The different clades suggest there is significant diversity within the sequences found. While we acknowledge the limitation of our study to capture the full range of diversity in these sites, the high number of singletons found in this study suggests that there are Actinobacteria belonging to the rare biosphere in caves.

The rare biosphere has been shown to influence both alpha and beta diversity, exhibiting unique geographic patterns Lynch and Neufeld, With over two thirds of our OTUs being singletons and most of the doubletons from one location, there is evidence to suggest endemism in cave Actinobacteria.

Endemism in caves has been documented for obligate cave fauna in the United States and the Azores Culver et al. Furthermore, studies of Actinobacteria in other environments have been shown to display endemism Wawrik et al. The combination of rare and endemic Actinobacteria, together with their abundance in caves, support the idea that caves are a good location to further test hypotheses regarding bacterial biogeography as well as to look for novel actinobacterial metabolites.

Rigorous testing will require that future studies be conducted with next generation sequencing to comprehensively sample the diversity present in these habitats.

The observed structure of the microbial communities in volcanic caves in the three locations is consistent with bacterial communities composed of consortia of few cosmopolitan members and a high number of low abundant phylotypes.

To test whether this structure could be biased by the fact of having a limited number of sequences, a pyrosequencing approach was performed with the same sample points considered for clone libraries in Azores.

Actinobacterial sequences amplified using the universal primers were identified and after quality control and filtering of the crude pyrotags, 19, sequences with good quality were retained, consisting of unique sequences. The average sequence length was After clustering, a total of OTUs were obtained. Nine orders were found in Azorean caves with pyrosequencing, the seven previously found, i. While Rubrobacterales was found in the clone libraries, it was only found in New Mexico and Hawai'i Figure 5.

Amplicon sequencing revealed this order to be present in the Azores as well, highlighting the importance of pyrosequencing to capture the full range of diversity in these samples. Actinomycetales and Gaiellales orders showed an increase in the percentage of sequences and OTUs recovered; Bifidobacteriales had a higher percentage of OTUs.

All other orders displayed lower percentages both for sequences and OTUs. Unclassified sequences represented 0. Figure 8. The amplicon libraries approach showed a more complete picture of the subterranean diversity in Azorean volcanic caves. Rubrobacterales was first described in cave environments in Niu Cave Zhou et al. This order includes members with heat, cold, dryness and high radiation resistance, found in high number in biodeteriorated monuments Gurtner et al. Solirubrobacterales have also been described in caves Paterson, ; De Mandal et al.

Coriobacteriales Stackebrandt et al. This order was previously described in cave habitats in speleothem formations in Kartchner Caverns Ortiz et al. Diversity indices revealed a higher diversity at Pico Island compared to Terceira Island as well as chao richness estimator Table 1B. The dominance of the Pseudonocardiaceae family compared to any other member of the microbial community is remarkable, in accordance with results from both clone and amplicon libraries.

Pseudonocardiaceae encompases a wide array of rare Actinomycetes , many of which can produce secondary metabolites Tiwari and Gupta, While we acknowledge that this finding may be in part the result of primer bias, the prevalence of this family is not uncommon in caves Barton et al.

Little is known of role these bacteria play in most ecosystems, however the family encompases a wide variety of metabolic pathways and physiologies Huang and Goodfellow, Most of our sequences were unable to be classified at the genus level, leaving some doubt as to the true role of this group of bacteria in volcanic caves.

However, the ubiquity of this family in cave studies emphasizes the need for further molecular studies with improved primers to capture Actinobacteria diversity and cultivation of members of this family found in subterranean bacterial biofilms. An examination of the communities in situ combined with metatranscriptome analysis would shed light on the question of this group's role in volcanic cave ecosystems. Our collective attempt to better understand actinobacterial diversity and functions in volcanic caves led us to observe patterns of diversity and novelness through a range of data obtained from pyrosequencing to cloning.

To date, within the realm of actinobacterial community study, our work is one of the largest sampling efforts in volcanic caves from different parts of the world including Spain, Portugal, USA and Canada.

The sequencing effort, both in clone and amplicon libraries, represents one of the most comprehensive studies of Actinobacteria in volcanic caves around the world. The clone libraries illustrate the novelness and phylogenetic relationship of Actinobacteria in volcanic caves from three geographically distant locations. The amplicon libraries of the Azorean sequences gave a more in-depth view of the Actinobacteria communities and revealed more diversity than has previously been described.

Both methods showed large numbers of newly described orders, and a dominance of Actinomycetales. Together they provide an outline of the community structure of Actinobacteria in caves, and highlight the importance of caves as a source of rare and novel Actinobacteria. Through scanning electron microscopy examinations, we learned about bacterial morphology, their relationships and possible contribution of the Actinobacteria to cave environment.

The identification of Ca-rich elements coated within some of the filamentous networks in the colored microbial mats suggests a possible role of Actinobacteria in calcium deposition. Both constructive and destructive mineral features, such as biominerals, cell imprints, microboring and mineralized filaments were some of the biosignatures found associated with samples studied herein. We can thus consider that volcanic caves on Earth are plausible repositories of terrestrial biosignatures where we can look for evidence of early life.

Beyond contributing to understanding cave microbial ecology, community and microbial roles and related function in such extreme subsurface habitats, our study hopes to initiate more study in such an interesting and understudied frontier of the Earth, where unique compounds could be isolated and used as important sources of industrial processes.

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. The authors would like to thank Dr. Albuquerque, L. Gaiella occulta gen. Altschul, S. Nucleic Acids Res. Banfield, J. Mineralogical biosignatures and the search for life on Mars. Astrobiology 1, — Barton, H. Geomicrobiology in cave environments: past, current and future perspectives.

Cave Karst Stud. Google Scholar. The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments. CrossRef Full Text. Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi Class Ktedonobacterales and Thaumarchaeota Group I.

Benzerara, K. Significance, mechanisms and environmental implications of microbial biomineralization. Bell, T. Larger islands house more bacterial taxa. Science , — Boston, P. Cave biosignature suites: microbes, minerals, and Mars. Furthermore, these microbes may alter our ideas about the origin of life on Earth, because they have the ability to live within rock thereby escaping damaging UV rays. Endoliths may also play a role in environmental issues. For instance, microbes living beneath the ocean floor have been suggested to play a role in the carbon cycle and global warming.

Endoliths may also have environmental benefits including bioremediation of contaminated sites and mines and improvement of groundwater quality by converting harmful compounds into non-toxic waste products. In addition, these organisms may be responsible for biomineralization of economically important ores. Deep subsurface microbes are important in our understanding the possibilities for life and have the potential for a wide range of applications that can improve the quality of life.

Therefore, continued geomicrobiological research in these deep, dark environments is crucial to understanding the possibilities for life in extreme environments and for remediating environmental problems. General Collection : Resources such as news articles, web sites, and reference pages provide a comprehensive array of information about endoliths for students and non-scientists.

Advanced Collection : Compiled for professionals and advanced learners, this endolith collection includes online resources such as journal articles, academic reviews, and surveys.

They can live where we can't live. They can do things we can't do. NOVA: Are these cave extremophiles completely outside of the carbon-based system found on the surface? Northup: The ones in Lechuguilla are mainly but not totally outside the surface world. There's obviously no sunlight, and some of these organisms are 1, feet or more below the surface. But they get some indirect products from sunshine. Water seeps down through that 1, feet of rock and brings a little organic carbon from the surface.

Cueva de Villa Luz has some skylights and a stream running through it, so the surface contributes to the food base in that way. Yet some of the organisms that we study, like the sulfur bacteria in Cueva de Villa Luz, derive their energy from inorganic substances such as hydrogen sulfide, the gas that smells like rotten eggs.

So in that respect they are independent of the sun. NOVA: Many field biologists become quite attached to their research subjects. Do you feel similarly about extremophile microbes?

Northup: Yeah, I get pretty attached to them, because I think they're pretty cool-looking. Some of the ones I see have long stalks; they look like sperm on testosterone. Some of them look like braided ropes. They're really cool. And the stuff they produce is just incredible. I can go on and on about blue goo and slime balls and "snottites," the slimy bacterial stalactites found in Cueva de Villa Luz.

My husband teases me about whether he should start enticing me with manganese slime. Northup: Well, take snottites. When you're in Cueva de Villa Luz, you see these things that look just like a two-year-old's runny nose, and when you look at them with the scanning electron microscope, they're nothing but bacteria and mucilaginous products and a little bit of minerals that get produced from these microbes. They're so tiny that we can't see them, yet they can build up these snottite structures that can then, if you use your imagination a bit, turn to rock and represent some of the formations we see in caves such as Lechuguilla.

Northup: They do, and we're just starting to look into that. This is not restricted to extremophiles. I have a colleague, Larry Mallory, who works in Lechuguilla Cave and elsewhere. His thought was that because these bacteria live in an environment where there's not a lot of organic carbon—that is, there's not a lot to eat—it may be to their benefit to produce compounds that would keep their neighbors at bay.

I call them "microbial assault weapons. Larry thought if they produce these secondary metabolites, as he calls them, those are the ones that are often useful in treating human disease.

So he has cultured hundreds of different strains, maybe even thousands, and he and his colleagues have tested those for their ability to kill cancer cells and malaria and stuff like that. And they've gotten really positive results.

The microbes' environment helps to select for organisms that produce some of these compounds. It's a great thing for telling people why they should be careful about contaminating caves. How life began? NOVA: Are you finding new species all the time, and are they very different from known bacteria? Northup: We do, and they are. I produce what are called phylogenetic trees.

Each is like a family tree, and it tells me how the genetic sequences that I pull out of microbial material from the caves fit in with known life. Why would astrobiologists be interested in tiny cave-dwellers on Earth? Astrobiologists study environmental conditions and adaptations that may make life possible in outer space. Astrobiologists are extremely interested in extremophiles. They have studied ocean vents , Antarctic valleys , and even the toxic environment of Chernobyl to study how organisms can adapt to seemly harmful conditions.

Like this: Like Loading Leave a Reply Cancel reply. Explore ideas, activities, and resources to spark creativity and curiosity from anywhere! Loading Comments Email Required Name Required Website. Sorry, your blog cannot share posts by email.