Microbiology Resource of the Month: Rock-Inhabiting Microbes

Oct. 8, 2021

Announcement: Amplicon Sequencing of Rock-Inhabiting Microbial Communities from Joshua Tree National Park, USA

Resource: Amplicon sequencing of microbial communities inhabiting 10 sandstone rocks collected in California


A cryptoendolithic lichen-dominated community colonizing sandstone.
A cryptoendolithic lichen-dominated community colonizing sandstone collected at Linnaeus Terrace by L. Selbmann during the XXXI (Dec. 2015–Jan. 2016) Italian Antarctic Campaign.
Source: Italian National Program for Antarctic Researches (PNRA)
Endoliths are organisms, including archaea, bacteria, fungi, lichens, algae and amoebas, that live inside rock, coral or animal shells. Many endoliths are extremophiles, capable of surviving in hot and cold drylands, where rocks provide thermal buffering, physical stability and UV protection for local inhabitants. Because endolithic organisms survive by feeding on traces of iron, potassium, sulfur or carbon, they play a key role in global biogeochemical processes. But understanding of endolithic microbial communities and worldwide rock diversity amongst different geographic locations and climates remains limited.

Recently, a team of scientists published the amplicon sequencing characteristics of microbial communities inhabiting 10 rocks collected from 3 different sites in the Joshua Tree National Park in California. We spoke with authors Claudia Coleine and Jason E. Stajich about their discovery and how this resource might be used to drive future research.

What are endoliths and where are they typically found?

Coleine: Endolithic communities are self-sustaining microbial ecosystems, spanning from very simple, composed of autotrophic prokaryotes only (Cyanobacteria), to the most complex organization of “lichen-dominated communities,” comprised of both prokaryotes and eukaryotes. Endoliths include both free-living and lichen-forming fungi, heterotrophic bacteria and autotrophs, such as algae and cyanobacteria.

These communities are amongst the most extreme-tolerant and extremophilic microorganisms on our planet. Endolithic microorganisms have been reported in all hot and cold deserts worldwide, where they represent the prevailing life-forms that ensure ecosystem functionality under even the harshest conditions.

What makes rocks a unique habitat for microbes?

Coleine: By inhabiting porous rock surfaces, endolithic microbes gain a number of key advantages that allow them to survive in extreme environmental conditions. For example, rocks provide thermal buffering, physical stability and protection against high ultraviolet (UV) and solar radiation. Rock habitats also ensure water retention, a factor that is especially important in very dry climates.

From where did you isolate these particular endolithic microbes?

Coleine: In this study, we performed amplicon sequencing to identify the diversity of endolithic fungi, bacteria and archaea found in sandstone rocks sampled from the Joshua Tree National Park.

But this work built upon research started more than 20 years ago, during which we conducted pioneering studies on endolithic communities of the McMurdo Dry Valleys in the Antarctic Desert, one of the harshest environments and the closest analogue to Mars that we have on Earth. At that time, we sampled a wide area in the Victoria Land (Continental Antarctica), as part of many Antarctic Expeditions funded by the Italian National Program for Antarctic Researches (PNRA), and isolated numerous microbes from endolithic samples. Some of these, including a genera of black fungi that had not been previously described, are now preserved in the culture collection of the Italian Antarctic National Museum (MNA-CCFEE).

What makes the Joshua Tree National Park a unique environment for microbial life?

Joshua Tree National Park sampling site.
Joshua Tree National Park sampling site.
Source: Coleine et al.
Coleine: JTNP is a unique confluence of two deserts (Mojave and Colorado), which have varied precipitation timing and regimes. The arid environment receives seasonal rain, either from summer monsoons in the southern part of the park or winter rains in the northern regions. These deserts also contain a variety of niches for microbial life, including a mixture of metamorphic and sedimentary rocks, soils, plant and animal life.

What type(s) of rocks were collected in this study?

Coleine: Endolithic microbes have been shown to colonize limestone, gypsum, granite and sandstone. We collected specifically sandstone samples in our study at JTNP.

Did you identify any unexpected microbes from this study?

Coleine: Although we have not yet isolated into pure culture the microorganisms that were collected from this study, we have found that, besides bacteria, archaea are particularly abundant in these rock samples, compared to other rock samples collected worldwide. And we believe this observation warrants future examination.

In addition to the fungal strains mentioned above, our team has described 21 new genera and 54 new species to date from various locations worldwide.

How will you use the data sets that you generated in your future research?

Coleine: We plan to conduct further analysis of the datasets we collected, and we will perform future sampling to help untangle biodiversity and functionality of the endolithic communities found in this area. We hope to further confirm that there is potential to uncover new microbial species in these environmental conditions. And we want to determine whether these environments represent new habitats for species that have already been described.

How will other scientists in the research community use this resource?

Coleine: Despite their importance, microbial endolithic communities remain largely understudied. Furthermore, comparative studies among different drylands remain limited. Considering that this resource reports new microbiome sequences for endolithic communities from hot deserts, this genetic and phylogenetic information may serve as a reference for incorporation into larger studies that address diversity and distribution of these neglected microorganisms.

In general, this resource will contribute to awareness of the immense scale of microbial diversity, and in particular it will improve understanding of the diversity found in ecological regions that are threatened by climate change.

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Author: Ashley Hagen, M.S.

Ashley Hagen, M.S.
Ashley Hagen, M.S. is the Senior Science Communications Specialist at the American Society for Microbiology and host of ASM's Microbial Minutes.