Abstract and Figures

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.
Content may be subject to copyright.
EARTH, ATMOSPHERIC,
AND PLANETARY SCIENCES
ECOLOGY
Transitory microbial habitat in the hyperarid
Atacama Desert
Dirk Schulze-Makucha,b,1, Dirk Wagnerc,d, Samuel P. Kounavese,f, Kai Mangelsdorfg, Kevin G. Devineh,
Jean-Pierre de Verai, Philippe Schmitt-Kopplinj,k, Hans-Peter Grossartl,m, Victor Parron, Martin Kaupenjohanno,
Albert Galyp, Beate Schneidera,c, Alessandro Airoa, Jan Fr ¨
oslerq, Alfonso F. Davilar, Felix L. Arenss, Luis C´
acerest,
Francisco Sol´
ıs Cornejot, Daniel Carrizon, Lewis Dartnellu, Jocelyne DiRuggierov, Markus Fluryw, Lars Ganzertl,
Mark O. Gessnerl,x, Peter Grathwohly, Lisa Guanz, Jacob Heinza, Matthias Hessaa , Frank Kepplerbb, Deborah Mausa,
Christopher P. McKayr, Rainer U. Meckenstockq, Wren Montgomeryf, Elizabeth A. Oberline, Alexander J. Probstq,
Johan S. S ´
aenzz, Tobias Sattlerbb, Janosch Schirmacka, Mark A. Sephtonf, Michael Schloterz,cc , Jenny Uhlk,
Bernardita Valenzuelat, Gisle Vestergaardz, Lars W ¨
ormerdd, and Pedro Zamoranot
aCenter of Astronomy & Astrophysics, Technical University Berlin, 10623 Berlin, Germany; bSchool of the Environment, Washington State University,
Pullman, WA 99164; cSection Geomicrobiology, GFZ German Research Centre for Geosciences, 14473 Potsdam, Germany; dInstitute of Earth and
Environmental Science, University of Potsdam, 14476 Potsdam, Germany; eDepartment of Chemistry, Tufts University, Medford, MA 02153; fDepartment of
Earth Science & Engineering, Imperial College London, London SW72AZ, United Kingdom; gSection Organic Geochemistry, GFZ German Research Centre for
Geosciences, 14473 Potsdam, Germany; hSchool of Human Sciences, London Metropolitan University, London N7 8BD, United Kingdom; iAstrobiological
Laboratories, Management and Infrastructure, Institute for Planetary Research, German Aerospace Center, 12489 Berlin, Germany; jAnalytical Food
Chemistry, Technical University M ¨
unchen, 85354 Freising-Weihenstephan, Germany; kAnalytical BioGeoChemistry, Helmholtz Zentrum M¨
unchen, 85764
Oberschleissheim, Germany; lDepartment of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin,
Germany; mInstitute of Biochemistry & Biology, University of Potsdam, 14476 Potsdam, Germany; nMolecular Evolution Department, Centro de
Astrobiolog´
ıa, Instituto Nacional de T ´
ecnica Aeroespacial-Consejo Superior de Investigaciones Cient´
ıficas (INTA-CSIC), 28850 Madrid, Spain; oFachgebiet
Bodenkunde, Technical University Berlin, 10623 Berlin, Germany; pCentre de Recherches P´
etrographiques et G ´
eochimiques, CNRS, Universit ´
e de Lorraine,
54500 Vandoeuvre les Nancy, France; qBiofilm Centre, University of Duisburg-Essen, 45141 Essen, Germany; rPlanetary Systems Branch (Code SST), NASA
Ames Research Center, Moffett Field, CA 94035; sInstitute for Geological Sciences, Freie University Berlin, 12249 Berlin, Germany; tLaboratorio de
Microorganismos Extrem ´
ofilos, University of Antofagasta, Antofagasta 02800, Chile; uDepartment of Life Sciences, University of Westminster, London W1W
6UW, United Kingdom; vDepartment of Biology, The John Hopkins University, Baltimore, MD 21218; wDepartment of Crop & Soil Sciences, Washington
State University, Pullman, WA 99164; xDepartment of Ecology, Technical University Berlin, 10587 Berlin, Germany; yCenter for Applied Geosciences,
University of T ¨
ubingen, 72074 T ¨
ubingen, Germany; zComparative Microbiome Analysis, Helmholtz Zentrum M ¨
unchen, 85764 Oberschleissheim, Germany;
aaSystems Microbiology & Natural Products Laboratory, University of California, Davis, CA 95616; bbInstitute of Earth Sciences, Heidelberg University, 69120
Heidelberg, Germany; ccSoil Science, Technical University M ¨
unchen, 85354 Freising-Weihenstephan, Germany; and ddCenter for Marine Environmental
Sciences (MARUM), University of Bremen, 28359 Bremen, Germany
Edited by Mary K. Firestone, University of California, Berkeley, CA, and approved January 25, 2018 (received for review August 17, 2017)
Traces of life are nearly ubiquitous on Earth. However, a cen-
tral unresolved question is whether these traces always indicate
an active microbial community or whether, in extreme environ-
ments, such as hyperarid deserts, they instead reflect just dormant
or dead cells. Although microbial biomass and diversity decrease
with increasing aridity in the Atacama Desert, we provide multi-
ple lines of evidence for the presence of an at times metabolically
active, microbial community in one of the driest places on Earth.
We base this observation on four major lines of evidence: (i) a
physico-chemical characterization of the soil habitability after an
exceptional rain event, (ii) identified biomolecules indicative of
potentially active cells [e.g., presence of ATP, phospholipid fatty
acids (PLFAs), metabolites, and enzymatic activity], (iii) measure-
ments of in situ replication rates of genomes of uncultivated
bacteria reconstructed from selected samples, and (iv) microbial
community patterns specific to soil parameters and depths. We
infer that the microbial populations have undergone selection and
adaptation in response to their specific soil microenvironment and
in particular to the degree of aridity. Collectively, our results high-
light that even the hyperarid Atacama Desert can provide a habit-
able environment for microorganisms that allows them to become
metabolically active following an episodic increase in moisture
and that once it decreases, so does the activity of the microbiota.
These results have implications for the prospect of life on other
planets such as Mars, which has transitioned from an earlier wet-
ter environment to today’s extreme hyperaridity.
habitat |aridity |microbial activity |biomarker |Mars
The core region of the Atacama Desert is the most arid mid-
latitude desert on Earth and in the past has been devoid of
precipitation for decades. A mean annual precipitation of <20
mm reduces weathering rates and leaching losses to levels below
the accumulation rates of atmospheric salts and dust (1). Hence,
Significance
It has remained an unresolved question whether microorgan-
isms recovered from the most arid environments on Earth are
thriving under such extreme conditions or are just dead or
dying vestiges of viable cells fortuitously deposited by atmo-
spheric processes. Based on multiple lines of evidence, we
show that indigenous microbial communities are present and
temporally active even in the hyperarid soils of the Atacama
Desert (Chile). Following extremely rare precipitation events
in the driest parts of this desert, where rainfall often occurs
only once per decade, we were able to detect episodic inci-
dences of biological activity. Our findings expand the range
of hyperarid environments temporarily habitable for terres-
trial life, which by extension also applies to other planetary
bodies like Mars.
Author contributions: D.S.-M. designed research; D.S.-M., D.W., S.P.K., K.M., K.G.D.,
J.-P.d.V., P.S.-K., H.-P.G., V.P., A.G., B.S., A.A., J.F., A.F.D., F.L.A., L.C., F.S.C., D.C., L.D., J.D.,
M.F., L. Ganzert, M.O.G., P.G., L. Guan, J.H., M.H., F.K., D.M., R.U.M., W.M., E.A.O., A.J.P.,
J.S.S., T.S., J.S., M.A.S., M.S., J.U., B.V., G.V., L.W., and P.Z. performed research; D.W., S.P.K.,
K.M., K.G.D., P.S.-K., H.-P.G., V.P., M.K., A.G., M.O.G., P.G., F.K., R.U.M., A.J.P., M.S., G.V.,
and L.W. contributed new reagents/analytic tools; D.S.-M., D.W., S.P.K., K.M., K.G.D.,
J.-P.d.V., P.S.-K., H.-P.G., V.P., M.K., A.G., B.S., A.A., J.F., A.F.D., F.L.A., L.D., J.D., M.F.,
L. Ganzert, M.O.G., P.G., M.H., F.K., C.P.M., R.U.M., A.J.P., J.S., M.S., J.U., B.V., G.V., and
L.W. analyzed data; and D.S.-M., D.W., S.P.K., H.-P.G., and M.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This open access article is distributed under Creative Commons Attribution-
NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Data deposition: The metagenome sequences reported in this paper have been deposited
in the EMBL-EBI database (accession no. PRJEB20402 with the sample IDs ERS1666624–
ERS1666714) and in the GenBank/EMBL database (BioProject ID PRJNA395196).
1To whom correspondence should be addressed. Email: schulze-makuch@tu-berlin.de.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.
1073/pnas.1714341115/-/DCSupplemental.
www.pnas.org/cgi/doi/10.1073/pnas.1714341115 PNAS Latest Articles |1 of 6
atmospheric deposition over millions of years has resulted in high
salt concentrations in the soils of the hyperarid area (2). The only
documented microhabitats in the core region of the Atacama
Desert are colonized by microbial communities thriving in sur-
ficial salt crusts, where microbial activity is enabled through del-
iquescence (3, 4). Even though there are traces of microbial life
in the subsurface of the Atacama Desert (5), it remains unclear
whether these environments support active microbial growth or
whether the observed cells are sporadically introduced by atmo-
spheric transport and continuously inactivated and degraded. To
answer this question, in April of 2015 we sampled soils from
the surface and near subsurface at six locations along a decreas-
ing moisture gradient [coastal soil (CS), alluvial fan (AL), red
sands (RS), Maria Elena (ME), Yungay (YU), and Lomas Bayas
(LB)] (SI Appendix, Fig. S1) and characterized them and their
microbial communities by using a broad suite of complemen-
tary methods. Since this sampling occurred shortly after an unex-
pected rain event, we repeated sampling in February 2016 and
January 2017 to determine whether the detected microbial activ-
ity in 2015 was ongoing or episodic and related to the temporary
increased availability of moisture.
Results
Environmental Setting. The selected CS site has been occasion-
ally subject to fog and rain, while sites further inland (ME, YU,
and LB) are located in hyperarid areas (6, 7), where water con-
tent of surface soils is generally <1% by weight (SI Appendix,
Fig. S2). Water activity is often below the threshold of 0.6
required to sustain metabolic activity (8). Relative humidity lev-
els are generally below 30% and daily UV irradiation doses
were ca. 30 J·m2. Except for LB, where total organic carbon
(TOC) reached 0.25% (wt/wt), TOC at all other sites was less
than 0.1%. A prerequisite of our study was that the sampled
sites are relatively pristine and little affected by human contam-
ination, which was the case based on measured polycyclic aro-
matic hydrocarbon concentrations which are extremely low and
generally in the microgram per kilogram range or lower. Soil
minerals at all sites are dominated by alkali feldspar and pla-
gioclase with minor amounts of quartz, chlorite, and amphibole,
with some sites displaying a significant amount of anhydrite, bas-
sanite, gypsum, and carbonates. Sites subject to higher levels
of moisture (CS, AL, RS) contain large amounts of chlorides
(e.g., halite), while soils obtained from the hyperarid areas (YU,
ME, LB) mostly contain sulfates (e.g., gypsum or anhydrite),
perchlorates (ClO
4), and chlorates (ClO
3) (SI Appendix, Fig.
S3). The first set of field samples was taken in April 2015 1 mo
after a major El Ni˜
no triggered one of the rare rainfall events in
the Atacama Desert (9). Eight millimeters of precipitation was
recorded at Baquedana and 33 mm at Antofagasta, which was
the highest amount of precipitation since the beginning of the
official recording in 1978 (SI Appendix, Fig. S2C) and affected
all study sites. The second and third sampling campaigns were
conducted in February 2016 and January 2017, respectively, with
only two minor rain events in between (each 6.7 mm, recorded at
Antofagasta).
Microbial Diversity. Metagenomic analyses of the DNA pool from
topsoils revealed a high bacterial diversity at CS (nonpareil diver-
sity index of 21.2 ±0.5), similar to sandy soils, but considerably
higher compared with the drier areas of YU and ME (nonpareil
indexes of 19.5 ±0.6 and 18.9 ±0.1, respectively; SI Appendix,
Fig. S4A). Phylogenetic profiles (SI Appendix, Fig. S4B) indi-
cate that soils at YU were associated with microbiomes typical
for sandy environments and desert soils, mainly consisting of
Actinobacteria (5) with Corynebacteriales,Streptomycetales, and
Micrococcales being the dominant suborders and a proportional
decline of Rubrobacterales from the surface to the subsurface. In
contrast, ME was dominated by Geodermatophilaceae, known to
colonize hyperarid habitats (10) and tolerate high levels of oxida-
tive stress, desiccation, salts, and metals (11). The same general
trend of decreased biomass and diversity with increasing aridity
was found for Archaea and Fungi, even though their proportion
was lower than that of Bacteria. In all soil samples 200 fun-
gal marker genes were detected, almost exclusively belonging to
Ascomycota and Basidiomycota (SI Appendix, Fig. S5 Aand B).
At CS, Archaea (mainly halobacteria) reached a maximum and
dominated the microbial community at a depth of 20–30 cm,
while everywhere else they accounted for <4% of sequence
reads (SI Appendix, Fig. S5C). Our DNA-based data were cor-
roborated by phospholipid fatty acid profiles (Fig. 1 Band D),
serving as biomarkers for living bacteria (12), and cultivation-
based approaches both identifying Actinobacteria (e.g., Acti-
nobacterium lienomycini,Kocuria sp.,Pseudonocardina sp.,Strep-
tomyces sp.), Proteobacteria (e.g., Pseudomonas sp.,Paracoccus
marinus), and Firmicutes (e.g., Bacillus litoralis,Bacillus simplex,
Halobacillus sp.).
Abundance and Identification of Dead and Living Microorganisms.
A unique cell-separation technique (13) was used to differen-
tiate between intracellular DNA (iDNA) indicating physically
intact and potentially viable cells and extracellular DNA (eDNA)
mainly representing preserved DNA from dead cells.
Quantitative PCR (qPCR) using universal bacterial primers
was performed for both DNA pools, for all soil samples taken
along the moisture gradients in 2015 and 2017, and at YU in
2016. After the rain event in 2015, the abundance of 16S rRNA
genes in the iDNA pool (proxy of living bacterial biomass) was
generally higher than in 2016/2017 (between 103and 106
gene copies per gram soil; SI Appendix, Table S1), increasing with
moisture (SI Appendix, Fig. S6). The copy numbers in the eDNA
pool showed larger variations of between 101and 107gene
copies per gram soil, and only at LB was no eDNA detectable
with the primers applied in the qPCR. In contrast to the rel-
atively high gene copy numbers in 2015, soil samples from the
same sites, but taken 2 y after the rain event, revealed a drastic
decrease in living cells (iDNA; equal to or less than 102gene
Fig. 1. (Aand B) Concentrations of intracellular ATP (iATP) and extracel-
lular ATP (eATP) (both n= 3) (A) and PLFAs (B) in Atacama Desert soils. A
decrease in the number of identified PLFAs indicates a decrease in diver-
sity, which is related to increasing aridity. (Cand D) Average cell-based ATP
concentrations were obtained by relating iATP concentrations (C) to total
biomass levels (D) measured at specific locations, which were obtained from
PLFA analysis.
2 of 6 |www.pnas.org/cgi/doi/10.1073/pnas.1714341115 Schulze-Makuch et al.
EARTH, ATMOSPHERIC,
AND PLANETARY SCIENCES
ECOLOGY
copies per gram soil). The same trend was also visible in the
eDNA pool although gene copy numbers were somewhat higher
than in the iDNA pool (SI Appendix, Table S1).
To provide a detailed characterization of living and dead
microorganisms, high-throughput sequencing of 16S rRNA gene
amplicons of both DNA pools was performed. In environments
supporting an active microbial community, the eDNA pool is
continuously replenished through biomass turnover of living cells
(14). As indicated by the large number of shared operational tax-
onomic units (OTUs), this was likely the case at CS where rel-
ative humidity (RH) and nutrients were highest, constantly sup-
plied by coastal fog. In contrast, OTUs identified at the hyperarid
locations showed less overlap between eDNA and iDNA com-
pared with CS, suggesting the dominance of autochthonous
microbial taxa rather than of inactive transitory microorgan-
isms periodically introduced by wind (Fig. 2A). Key organisms
of these communities consisted of unclassified Acidimicrobiales,
Actinobacteria,Alicyclobacillus,Burkholderia,Comamonadaceae,
and Xanthomonadaceae. Although abundances differed among
sites and soil depths, these characteristic taxa identified from
iDNA were found in all samples from all sites and depths, sug-
gesting a native and metabolically active desert core community.
Fig. 2. Microbial community structure and relationship between iDNA and
eDNA pools at six soil sampling sites in the Atacama Desert: CS, AL, RS, ME,
YU, and LB. (A) Venn diagrams of iDNA and eDNA OTU intersections for
samples collected at 0–5 cm and 20–30 cm depth. Numbers indicate the
numbers of different OTUs, and percentages refer to relative abundances
of reads unique to iDNA or eDNA. Bars to the left of the Venn diagrams
show relative abundances of bacterial orders in the subsets unique to the
iDNA and eDNA pools of the indicated sampling depth. (B) Classification of
iDNA pools from soil surface samples (0–5 cm) collected at the six sampling
sites in comparison with the iDNA and eDNA pools in subsurface soil layers.
(C) Classification of the subsurface iDNA pools (20–30 cm, 50 cm, 100 cm) in
comparison with the iDNA and eDNA pools in the surface soils (0–5 cm). The
bars show the percentages of OTU reads in the corresponding subsets, and
numbers indicate the numbers of different OTUs.
In general, as dryness increased, microbial diversity decreased,
analogous to previous observations (15, 16).
Abundance of Endospores. The dormant component of the bac-
terial communities was specifically assessed for the 2015 sam-
pling period by quantifying endospores, which are characteris-
tic of the phylum Firmicutes and stand out by their exceptional
resistance to environmental stresses. Dipicolinic acid (DPA),
a specific biomarker of intact endospores, was detected at all
sites. Endospore concentrations in surface layers, however, de-
creased with increasing aridity by almost two orders of magni-
tude (7.7 ×105to 1.5 ×104spores per gram soil; SI Appendix,
Table S2). The large size of this community suggests that an
extensive and persistent Firmicutes seed bank remains available
in the Atacama Desert, which is in agreement with the domi-
nance of isolates from this phylum in our cultivation experiments.
Importantly, the contribution of endospores to the iDNA pool
was likely minor, because the conventional extraction methods
that were used to extract iDNA from intact cells do not usu-
ally extract DNA from spores (17). Therefore, it is not surprising
that the phylogenetic composition derived from iDNA sequenc-
ing does not reflect the abundance of endospores from the phy-
lum Firmicutes (SI Appendix, Fig. S7).
Metabolic Activity. As many of the cultivated bacteria were
spore formers, we used independent complementary analytical
approaches to obtain conclusive evidence for living microorgan-
isms and their potential activity in hyperarid habitats.
First, evidence for microbial activity was obtained by a fluores-
cein diacetate hydrolysis assay to determine enzymatic activity
(SI Appendix, Table S3). Enzymatic activity was highest at the
surface of CS, ME, and LB sites, but still detectable at all other
sites and shallow depths (0–5 cm and 20–30 cm, respectively),
except for LB 20–30 cm, where it was below the detection limit
of 103nmol·g1·h1.
Second, our hypothesis of active, native microbial communi-
ties was supported by ATP analyses. These analyses allow the
separation of intracellular ATP (iATP), indicative of viable cells,
and extracellular ATP (eATP), indicative of ATP remaining in
the soil after cell lysis. iATP levels were up to three orders of
magnitude higher (3 ×1012 mol·g1) at CS compared with
the sampling sites located in the driest desert core (e.g., 2 ×
1015 mol·g1at YU 100 cm depth; Fig. 1). Overall, ATP anal-
yses supported the general trend of decreasing microbial activity
with increasing aridity, both along the studied moisture transect
(2015) and in YU surface soils from 2015 to 2017 (SI Appendix,
Table S1). The ATP analyses provide evidence that even in the
most arid sites of the Atacama core region native microorgan-
isms can be at times metabolically active.
Third, the presence of metabolically active microorganisms
was supported by the analyses of water-extractable metabolites
via direct injection electrospray ionization Fourier-transform ion
cyclotron resonance mass spectrometry [ESI(-) FT-ICR-MS],
which allowed the accurate calculation of elemental formulas.
On average, a rich signature of 1,600 elemental compositions
(CHNOS) was detected in all samples, indicating a geochemi-
cal footprint (18) typical of natural organic matter superimposed
by a biological footprint of fresh organic material (19) involving
amino acids, small peptides, and fatty acids (SI Appendix, Fig. S8).
Results suggest that water-soluble organic compounds consisted
mainly of aliphatic carbohydrates and fatty acids (CHO), while
nitrogen- and sulfur-containing compounds (CHNO and CHOS)
were less abundant. The relative abundance of compounds, pre-
dominantly reflecting metabolic activity, decreased significantly
along the aridity gradient from the coast to inland with con-
stant low amounts of organic compounds at the hyperarid loca-
tions of ME, YU, and LB. This trend again suggests a marked
decline in metabolic activity from moist to hyperarid soil habitats
Schulze-Makuch et al. PNAS Latest Articles |3 of 6
(SI Appendix, Fig. S9). Nevertheless, there was clear conserva-
tion of biosignatures even in the hyperarid locations, showing evi-
dence of past and, most likely, recent metabolic activity, especially
at a depth of 20–30 cm in YU (2015), where different types of
metabolites were distinguishable (SI Appendix, Fig. S9F).
Fourth, the metagenomic analysis from the soil samples ob-
tained in April 2015 indicated that microorganisms were active
even in the driest soil samples. Sequence abundance of mycobac-
teriophages, gordoniaphages, and streptomycophages correlated
positively with that of their respective hosts found in the differ-
ent samples [Spearman coefficient correlations of ρ= 0.69 at CS,
ρ= 0.88 at ME, and ρ= 0.67 at YU (SI Appendix, Fig. S4 C–E)].
The detected virus–host relationships seem to be consistent with
the observations that microbial blooms are followed by a bloom
of phages specific for the microbes that dominated the micro-
bial bloom (20, 21). However, while most identified viruses are
phages persistent in the environment that have also been iden-
tified by other desert studies (22), the vast majority of the iden-
tified viruses (95+%) belong to the family Caudovirales, which
includes both virulent and temperate members. Thus, we cannot
exclude the presence of a large number of undetected prophages
that might stay dormant for long periods of time.
Finally, we investigated in situ genome replication rates of
organisms via a genome-resolved metagenomics approach (23)
of samples retrieved from YU and ME. For YU, we recon-
structed a draft genome of the most dominant organism (uncul-
tivated Actinobacteria) with an estimated completeness of 92%
A
BC
Fig. 3. Genome-resolved metagenomics analyses and results. (A) Work flow
and main results from genome-resolved metagenomics. For details please
see SI Appendix,Read-Based Metagenomics, Genome-Resolved Metage-
nomics and in Situ Replication Rates. Genome replication forks are symbolic.
(B) Overview of iRep values retrieved from the four genomes from the YU
and ME sites (color codes correspond to those in A). Dashed line at value 1
marks threshold at which no replication occurs. Dashed line at value 2 marks
where each genome of a population has on average bidirectional repli-
cation taking place (24). (C) Rank-abundance curves based on rpS3 genes.
Colored genomes correspond to those in Aand B. For the YU site (Left rank-
abundance curve) the most dominant organism was reconstructed, and all
other genomes were fragmented. For the ME site (Right rank-abundance
curve) three genomes were reconstructed. The three most abundant organ-
isms were Actinobacteria, which were similar in GC and abundance.
based on single-copy genes (Fig. 3). The iRep value (24) of
the genome was 1.57, which is indicative of its slow replication.
For the ME site, we retrieved three high-quality draft genomes
belonging to members of the phyla Chloroflexi,Actinobacteria,
and Saccharibacteria (completeness 86–98%; Fig. 3). The in situ
replication rates of these genomes varied between 1.86 and 3.31.
The lower replication rates compare with literature values of
a wide array of organisms across multiple phyla, but the iRep
value of 2.48 for the Chloroflexi indicates that each genome in the
population has on average one bidirectional replication ongo-
ing (24). The genome replication rate for the Actinobacteria was
extremely high, which indicates that each genome of this popu-
lation had several replication forks at the time of sampling, thus
providing strong evidence for microbial activity.
A Transitory Habitat? The continuous decline of nonstructural
water at 20–30 cm depth at YU, from 2.7% by weight in 2015
to 0.2% and 0.1% in 2016 and 2017, respectively, suggests
temporarily favorable conditions for the activity of specialized
microorganisms after the rare precipitation event until water
activity fell again beneath a critical threshold (Fig. 4A). Miner-
alogical data confirmed a desiccation process in the later years
as some of the gypsum at YU 20–30 cm dehydrated to anhy-
drite (Fig. 4B). The steep decline of recovered iDNA by three
to five orders of magnitudes (Fig. 4 Cand D) indicates that the
sampling campaign in 2015, shortly after a major and very rare
rainfall event, tapped into a temporary, time-constrained habi-
tat, rather than a permanent one. ATP analyses, indicative of
active organisms, also support that assessment. The iATP values
follow that trend, declining by more than three orders of magni-
tude in the YU surface soil (Fig. 4E), but remain constant in the
deeper soil layer at YU (Fig. 4F), pointing to a longer retention
of microbial activity. Possibly some water released by the desicca-
tion of gypsum to anhydrite remains accessible to a specific part
of the microbial community. This possibility is supported by iso-
topic evidence. The δD values for the waters in the hydrous sul-
fate minerals suggest that small amounts of water accessible to
microorganisms might be available even in these hyperarid soils
(SI Appendix, Table S4), e.g., in the form of thin H2O films at
mineral surfaces (25) or as a product of mineral–water exchange
reactions (26).
Two other rainfall events occurred in August 2015 and June
2016 (each 6.7 mm at Antofagasta), but it is unclear how much
rain fell at YU. No indication of that rainfall event was observed
in our sharply declining iDNA and iATP values for the surface
soils from April 2015 to January 2017. This suggests that both the
August 2015 and June 2016 events were either insufficient to trig-
ger temporarily habitable conditions and a microbial response
or, since they occurred several months before our next sampling
round, were too small and subsided by the time we resampled.
Davis et al. (27) estimated that 2 mm or more precipitation are
needed to provide free water for the support of biological activity
in the soil. In previous studies, Navarro-Gonzalez et al. (7) were
not able to recover any DNA from the YU site, and Warren-
Rhodes et al. (28) reported on the virtual absence of hypolithic
cyanobacteria. Certainly, the literature data can provide only a
qualitative assessment about the presence or activity of microor-
ganisms, because of both the methodologies used and the spatial
heterogeneity of the sites. In contrast to our study, it appears
that previous sampling campaigns did not tap into habitable
conditions.
Discussion
The Atacama Desert soil microbiome has evolved as a result of
the prevailing environmental conditions. While the soil surface
was dominated by desiccation and UV-resistant species (Geo-
dermatophilaceae and Rubrobacter), deeper layers with higher
salt content were dominated by halophilic bacteria such as
4 of 6 |www.pnas.org/cgi/doi/10.1073/pnas.1714341115 Schulze-Makuch et al.
EARTH, ATMOSPHERIC,
AND PLANETARY SCIENCES
ECOLOGY
Fig. 4. Comparison of sampling events of April 2015, February 2016, and
January 2017 at YU. (A) Available nonstructural water decreases significantly
from 2015 to 2017. (B) Some of the gypsum at YU 20–30 desiccated and
formed anhydrite. (Cand D) Intracellular DNA amounts indicative of living
organisms drop by several orders of magnitudes at 0–5 cm and 20–30 cm
depths. (Eand F) Intracellular ATP amounts indicative of active organisms
drop by several orders of magnitudes at 0–5 cm, but stay constant at 20–
30 cm depth.
Betaproteobacteria (Comamonadaceae) or Firmicutes (Bacillaceae,
Alicyclobacillaceae) (SI Appendix, Fig. S7) and halophilic Archaea
(i.e., Halobacteria) at CS 20–30 cm (SI Appendix, Fig. S5C).
Notably, microbiomes associated with the hyperarid soils were
dominated by Bacteria rather than Archaea, consistent with an
assessment of the global distribution of archaeal abundances in
soils (29). The amount of unique OTUs in the iDNA pool of
the surface and subsurface soils of the hyperarid localities ME
and YU was much lower than at the moister sites. OTUs shared
between iDNA recovered from the surface and eDNA from
deeper layers (Fig. 2B) and between iDNA from the subsurface
and eDNA from the surface (Fig. 2C) drastically increased com-
pared with those in CS, indicating distinct microbial populations
at different depths with increasing dryness. This indicates that
selection pressures for microorganisms were much higher in the
hyperarid surface soils than in the wetter coastal area, resulting
in species well adapted to the extreme dryness and UV radiation.
However, some salt-tolerant bacteria such as Acidimicrobiales,
Comamonadaceae, and Bacillaceae potentially survive in deeper
soil layers after being buried (SI Appendix, Fig. S7), e.g., by ongo-
ing atmospheric deposition of salts and sediments or by halo- and
thermoturbation of soils. Alternatively, microbial communities
might have persisted in the subsurface since the onset of deserti-
fication, or an initial community successively changed over geo-
logical time to cope with altered environmental conditions (5).
Our results suggest that incoming microbial “newcomers” have
at least been exposed to passive environmental selection, but
also maintain transient activity even in the deeper soil layers and
sustain viability in the Atacama Desert for very long time peri-
ods. However, it remains questionable whether the organisms
found in this environment are adapting to the harsh conditions
present. Bacteria reaching the Atacama Desert by atmospheric
processes have been exposed to desiccation and UV stress dur-
ing aerial transport, possibly for extended periods (30). This sug-
gests that environmental species filtering could be an impor-
tant factor contributing to shaping the indigenous microbial
communities. In line with this hypothesis, our shotgun metage-
nomics data revealed several genes associated with dehydra-
tion tolerance [e.g., groEL,dnaK,fadD,glgX-malZ,phaC (31)]
and radiation/desiccation tolerance [e.g., recQ (32)]. Immunoas-
says corroborated these metagenomic results by detecting ATP
synthase, GroEL, CspA, and DPS DNA-protecting proteins at
YU (50 cm), CS, and RS, and metaproteomic analyses of sam-
ples taken at YU also confirmed the presence of ATP synthase
and GroEL.
One additional challenge for microorganisms to persist at
both surface and subsurface locations is the low organic mat-
ter content characteristic of hyperarid soils. A higher TOC
and moisture content allowed a higher total microbial biomass
and diversity (Fig. 1 and SI Appendix, Fig. S6). For example,
chloromethane (CH3Cl) release during low-temperature ther-
molysis of surface soil samples, which is indicative of hetero-
bonded methyl groups of organic matter, was highest for CS
(300 ng·g1) and much lower at the hyperarid sites (1–
5 ng·g1) (SI Appendix, Fig. S10). Stable hydrogen isotope anal-
yses of the released chloromethane confirmed the biochemical
origin of the methyl group. The emission profiles of CH3Cl are
almost identical to observations made by the Curiosity rover on
Mars (33), where even harsher environmental conditions prevail
than in the hyperarid core of the Atacama Desert [lack of water,
scarcity of organic matter, high UV irradiation, and high salt con-
tent in the soils including bassanite and perchlorates (34)]. No
rain can fall from the Martian atmosphere today (35), but liq-
uid water can be present near the Martian surface in the form of
nightly snow storms/ice microbursts (36), fog (37), near-surface
groundwater (38), and possibly also from mineral dehydration
reactions (39). On Mars, the deeper soil layers with a higher
water activity and reduced exposure to environmental stresses
(e.g., UV irradiation, large daily temperature fluctuations) are
expected to be more suitable for supporting life. At YU this was
the case, with the gypsum-rich soil layer at a depth of 20–30 cm
containing a higher biomass and microbial diversity (Figs. 1 B
and Dand 2) and also retaining a similar level of activity beyond
2015 for at least 2 y more. Thus, we observe in the hyperarid core
of the Atacama Desert a transitory habitat with microorganisms
that are active for short periods of time and which can serve as a
reasonable working model for Mars.
Conclusions
Although both microbial biomass and diversity in the Atacama
Desert decrease with increasing aridity, our study shows that
even the lowest precipitation levels on Earth can sustain episodic
incidences of microbial activity. There is no single agreed-upon
method known to date reaching the bar of evidence for micro-
bial activity for such low-biomass environments. However, using
our complementary tool box of combining different method-
ologies, including unique genome-resolved metagenomics, we
have addressed the question of microbial activity and can answer
it positively for the sampling time after the major precipita-
tion event in 2015. Thereafter, the biomarkers for microbial
activity dropped dramatically, inferring that the transitory hab-
itable conditions have ended until the next major rain event may
occur, providing a sufficient amount of free water for the micro-
bial biota. The insights gained from the hyperarid core of the
Atacama Desert can serve as a working model for Mars, where
environmental stresses are even harsher. If life ever evolved
on Mars, the results presented here suggest that it could have
endured the transition from the early aquatic stage, through
increasing aridity cycles, and perhaps even found a subsurface
niche beneath today’s severely hyperarid surface.
Materials and Methods
Detailed methods, including a description of the sampling sites with numer-
ous figures and tables, are provided in SI Appendix. Two unique methods
were used. The e/i-DNA methodology is described in detail in an appropri-
ate subject journal (13), with some of the associated issues discussed else-
where (40). The validity of the e/i-DNA method is further supported by a
Schulze-Makuch et al. PNAS Latest Articles |5 of 6
positive correlation between microbial biomass and the Shannon index (SI)
calculated for iDNA (r=0.62), but not with either calcium or sulfate con-
centrations. Conversely, the SI for eDNA correlated with calcium and sulfate
soil concentrations (r=0.74 and 0.61, respectively), but not with biomass
(r=0.03). The other state-of-the-art method was used to measure in situ
replication rates of genomes by calculating the number of active replication
forks reconstructed from the metagenome sequences (15) (see SI Appendix,
Read-Based Metagenomics, Genome-Resolved Metagenomics and in Situ
Replication Rates for more details). All data reported in this paper are com-
piled in SI Appendix and have been archived at GenBank/EMBL under Bio-
Project ID PRJNA395196 and at EMBL-EBI under accession no. PRJEB20402
(sample IDs ERS1666624–ERS1666714).
ACKNOWLEDGMENTS. D.S.-M. acknowledges support by the European Re-
search Council Advanced Grant Habitability Of Martian Environments
(339231), which provided base funding for the study, including sample
collection. The fungal diversity assessment was supported by funding (to
H.-P.G.) through the Leibniz Senatsausschuss Wettbewerb Project MycoLink
and DFG Project Microprime (GR1540/23-1). F.K. received financial support
from the German Science Foundation (DFG KE 884/8-2). The 16S rRNA
gene amplicon (MiSeq) sequencing was financed through the Helmholtz
Research Program “Geosystem–The Changing Earth” and the data were
processed by Fabian Horn (GFZ German Research Center for Geosciences–
Helmholtz Center Potsdam). The stable isotopic composition of water was
carried out through the Europlanet 2020 Research Infrastructure supported
by the European Union’s Horizon 2020 research and innovation program
(654208). Endospore quantification benefited from funding by the Deep
Carbon Observatory through a Pilot Project (L.W.). Part of the organic geo-
chemical analyses were performed at Imperial College London, supported by
United Kingdom Space Agency Grant ST/N000560/1. V.P. and D.C.’s work was
supported by the Spanish Ministry of Economy and Competitiveness Grants
ESP2015-69540-R and RYC-2014-19446, respectively. G.V. was supported by
a Humboldt Research Fellowship for postdoctoral researchers. M.F. acknowl-
edges support from National Institute of Food and Agriculture Hatch Project
1014527. The Leibniz Institute of Freshwater Ecology & Inland Fisheries (IGB)
housed the workshop at which much of the presented work was coordi-
nated. We thank M. Degebrodt for technical assistance.
1. Ewing SA, et al. (2006) A threshold in soil formation at Earth’s arid-hyperarid transi-
tion. Geochim Cosmochim Acta 70:5293–5322.
2. Michalski G, Boehlke JK, Thiemens M (2004) Long term atmospheric deposition as the
source of nitrate and other salts in the Atacama Desert, Chile: New evidence from
mass-independent oxygen isotopic compositions. Geochim Cosmochim Acta 68:4023–
4038.
3. Davila AF, Schulze-Makuch D (2016) The last possible outposts for life on Mars. Astro-
biology 16:159–168.
4. Wierzchos J, et al. (2011) Microbial colonization of Ca-sulfate crusts in the hyperarid
core of the Atacama Desert: Implications for the search for life on Mars. Geobiology
9:44–60.
5. Crits-Christoph A, et al. (2013) Colonization patterns of soil microbial communities in
the Atacama Desert. Microbiome 1:28.
6. Azua-Bustos A, Caro-Lara L, Vicuna R (2015) Discovery and microbial content of the
driest site of the hyperarid Atacama Desert, Chile. Environ Microbiol Rep 7:388–394.
7. Navarro-Gonzalez R, et al. (2003) Mars-like soils in the Atacama Desert, Chile, and the
dry limit of microbial life. Science 302:1018–1021.
8. Stevenson A, et al. (2015) Multiplication of microbes below 0.690 water activity: Impli-
cations for terrestrial and extraterrestrial life. Environ Microbiol 17:257–277.
9. Bozkurt D, Rondanelli R, Garreaud R, Arriagada A (2016) Impact of warmer eastern
tropical Pacific SST on the March 2015 Atacama floods. Mon Weather Rev 144:4441–
4460.
10. Normand P (2006) Geodermatophilaceae fam. nov., a formal description. Int J Syst
Evol Microbiol 56:2277–2278.
11. Montero-Calasanz MdC, et al. (2013) Geodermatophilus tzadiensis sp. nov., a UV
radiation-resistant bacterium isolated from sand of the Saharan desert. Syst Appl
Microbiol 36:177–182.
12. Ewing SA, et al. (2007) Rainfall limit of the N cycle on Earth. Glob Biogeochem Cycles
21:GB3009.
13. Alawi M, Schneider B, Kallmeyer J (2014) A procedure for separate recovery of extra-
and intracellular DNA from a single marine sediment sample. J Microbiol Methods
104:36–42.
14. Levy-Booth DJ, et al. (2007) Cycling of extracellular DNA in the soil environment. Soil
Biol Biochem 39:2977–2991.
15. Robinson CK, et al. (2015) Microbial diversity and the presence of algae in halite
endolithic communities are correlated to atmospheric moisture in the hyper-arid zone
of the Atacama Desert. Environ Microbiol 17:299–315.
16. Finstad KM, et al. (2017) Microbial community structure and the persistence of
cyanobacterial populations in salt crusts of the hyperarid Atacama desert from
genome-resolved Metagenomics. Front Microbiol 8:1435.
17. Kuske C, et al. (1998) Small-scale DNA sample preparation method for field PCR detec-
tion of microbial cells and spores in soil. Appl Environ Microbiol 64:2463–2472.
18. Hertkorn N, et al. (2008) Natural organic matter and the event horizon of mass spec-
trometry. Anal Chem 80:8908–8919.
19. Rossello-Mora R, et al. (2008) Metabolic evidence for biogeographic isolation of the
extremophilic bacterium Salinibacter ruber. ISME J 2:242–253.
20. Maslov S, Sneppen K (2017) Population cycles and species diversity in dynamic Kill-
the-Winner model of microbial ecosystems. Sci Rep 7:39642.
21. Thingstad TF (2000) Elements of a theory for the mechanisms controlling abundance,
diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol
Oceanogr 45:1320–1328.
22. Fierer N, et al. (2007) Metagenomic and small-subunit rRNA analyses reveal the
genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Micro-
biol 73:7059–7066.
23. Tyson GW, et al. (2004) Community structure and metabolism through reconstruction
of microbial genomes from the environment. Nature 428:37–43.
24. Brown CT, Olm MR, Thomas BC, Banfield JF (2016) Measurement of bacterial replica-
tion rates in microbial communities. Nat Biotechnol 34:1256–1263.
25. Wilson SA, Bish DL (2011) Formation of gypsum and bassanite by cation exchange
reactions in the absence of free-liquid H2O: Implications for Mars. J Geophys Res
116:E09010.
26. Palacio S, Azor´
ın J, Montserrat-Mart´
ı G, Ferrio JP (2014) The crystallization water of
gypsum rocks is a relevant water source for plants. Nat Commun 5:4660.
27. Davis WL, de Pater I, McKay CP (2010) Rain infiltration and crust formation in the
extreme arid zone of the Atacama Desert, Chile. Planet Space Sci 58:616–622.
28. Warren-Rhodes KA, et al. (2007) Cyanobacterial ecology across environmental gra-
dients and spatial scales in China’s hot and cold deserts. FEMS Microbiol Ecol 61:
470–482.
29. Bates ST, et al. (2011) Examining the global distribution of dominant archaeal popu-
lations in soil. ISME J 5:908–917.
30. Smith DJ, Griffin DW, Schuerger AC (2010) Stratospheric microbiology at 20 km over
the Pacific Ocean. Aerobiologia 26:35–46.
31. Rajeev L, et al. (2013) Dynamic cyanobacterial response to hydration and dehydration
in a desert biological soil crust. ISME J 7:2178–2191.
32. Hua X, Huang L, Tian B, Hua Y (2008) Involvement of recQ in the ultraviolet damage
repair pathway in Deinococcus radiodurans. Mutat Res 641:48–53.
33. Ming DW, et al. (2014) Volatile and organic compositions of sedimentary rocks in
Yellowknife Bay, Gale crater, Mars. Science 343:1245267.
34. Neilson JW, et al. (2017) Arid soil microbiome: Significant impacts of increasing arid-
ity. mSystems 2:e00195.
35. Craddock RA, Lorenz RD (2017) The changing nature of rainfall during the early his-
tory of Mars. Icarus 293:172–179.
36. Spiga A, et al. (2017) Snow precipitation on Mars driven by cloud-induced night-time
convection. Nat Geosci 10:652–657.
37. M ¨
ohlmann DT, Niemand M, Formisano V, Savijrvi H, Wolkenberg P (2009) Fog phe-
nomena on Mars. Planet Space Sci 57:1987–1992.
38. Malin MC, Edgett KS (2000) Evidence for recent groundwater seepage and surface
runoff on Mars. Science 288:2330–2335.
39. Bish DL, Carey JW, Vaniman DT, Chipera SJ (2003) Stability of hydrous minerals on the
Martian surface. Icarus 164:96–103.
40. Vuillemin A, et al. (2017) Preservation and significance of extracellular DNA in ferrug-
inous sediments from Lake Towuti, Indonesia. Front Microbiol 8:1440.
6 of 6 |www.pnas.org/cgi/doi/10.1073/pnas.1714341115 Schulze-Makuch et al.
... 8), makes them fundamental to the global functioning of desert ecosystems. This is strengthened by recent experimental evidence suggesting that (hyper)arid hot desert soil microbial communities, even when desiccated, are active and functional (e.g., Angel et al. 2012;Gunnigle et al. 2014Gunnigle et al. , 2017Schulze-Makuch et al. 2018;León-Sobrino et al. 2019;Jordaan et al. 2020). ...
... It should, however, be noted that edaphic communities from the dunes and gravel plains of the hyperarid Namib Desert harbored from 10 to 25% of Crenarchaeota/Thaumarchaeota ( Lecanoromycetes > Archaeosporomycetes > M-Ascomycota > Leotiomycetes > Eurotiomycetes these some of the most archaeal-rich soils on the planet. It is noted that a deep soil community from the Atacama Desert was composed of >50% of Euryarchaeota (Schulze-Makuch et al. 2018), although other soils from the hyperarid Atacama showed only low relative abundances of archaeal phyla, with on average 0.03% Euryarchaeota and 0.01% Thaumarchaeota (Araya et al. 2019). At present, the ecological functions of hot desert archaea remain poorly understood, although they probably play important roles in N cycling. ...
... Hot desert soil viral communities, like most soils and independently of the technology used, have been found to be dominated by members of the dsDNA Caudovirales order (Prestel et al. 2012;Makhalanyane et al. 2015;Zablocki et al. 2016;Schulze-Makuch et al. 2018;Scola et al. 2018). Sahara Desert soil viral communities were particularly enriched in tailed viruses from the Myoviridae family (Prestel et al. 2012), while Namib Desert soils were in addition dominated by members of the Siphoviridae and Podoviridae families (Zablocki et al. 2017;Scola et al. 2018). ...
Chapter
Deserts are one of the major terrestrial biomes on Earth and, with the impacts of global climate change, are expanding. Given the fact that over two billion humans currently live in dryland areas, understanding how these major ecosystems function is particularly important. The poly-extreme environmental conditions of deserts, particularly (hyper)aridity, (hyper)oligotrophy, and high temperatures, limit the distribution and density of higher organisms, particularly plants. As a result, indigenous microbial communities in hot deserts are the dominant sources of primary productivity and other critical ecosystem services. Counterintuitively, hot desert surface soils, which are exposed to the harshest of abiotic conditions, exhibit high phylogenetic and functional microbial diversity. Independent of geographical localization, these soil communities are dominated by members of the bacterial Actinobacteria and Proteobacteria phyla. Furthermore, community assembly is primarily driven by deterministic niche-partitioning and habitat-filtration processes, with evidence that biotic interactions also play a role. The functionality of desert soil communities is highly water dependent. However, despite the observations that these communities are strongly activated by water input, there is evidence that desert soil microbiomes retain functionality during dry periods, particularly driven toward nutrient and energy acquisition. Together, these studies clearly confirm that hot desert soil microbial communities are well adapted to water scarcity, oligotrophy, and resource patchiness.
... Rain and fog events occur between *1 and 10 times per year on average, respectively (McKay et al., 2003;Valdivia-Silva et al., 2012). Despite the infrequency of rain and fog events, viable cells are found in the top tens of cm in these soils (Navarro-Gonzalez et al., 2003;Valdivia-Silva et al., 2011;Schulze-Makuch et al., 2018). Little is known about the relationship between water input and microbial activity or microbial growth in these environments, except that-counter intuitively-major inputs of water (e.g., during El Niño events) can negatively affect the microbial community by driving certain microbial species locally adapted to hyperarid conditions to extinction and favoring a select minority that is capable of tolerating osmotic-shock and hypersaline brines (Azua-Bustos et al., 2018). ...
... Given that other environments can stimulate biological activity through WVA (McHugh et al., 2015), and the direct evidence for the presence of microbes in Atacama soils (Navarro-Gonzalez et al., 2003;Valdivia-Silva et al., 2011Schulze-Makuch et al., 2018, it seems possible that WVA contributes at least partially to the habitability of Atacama soils. Taken together, it seems reasonable to conclude that future missions to Mars could fruitfully investigate the subsurface RH and water cycle. ...
Article
Water is necessary for all life on Earth. Water is so critical that organisms have developed strategies to survive in hyperarid environments. These regions with extremely low water availability are also unique analogs in which to study the physico-chemical conditions of extraterrestrial environments such as Mars. We have identified a daily, sustainable cycle of water vapor adsorption (WVA) and desorption that measurably affects soil water content (SWC) in the hyperarid region of the Atacama Desert in southern Perú. We pair field-based soil temperature and relative humidity soil profiles with laboratory simulations to provide evidence for a daily WVA cycle. Using our WVA model, we estimate that one adsorptive period-one night-increases SWC by 0.2-0.3 mg/g of soil (∼30 μm rainfall). We can plausibly rule out other water inputs during our field campaign that could account for this water input, and we provide evidence that this WVA cycle is driven by solar heating and maintained by atmospheric water vapor. The WVA may also serve to retain water from infrequent rain events in these soils. If the water provided by WVA in these soils is bioavailable, it could have significant implications for the microorganisms that are endemic to hyperarid environments.
... We suggest that sites should be targeted where organic carbon, water, and photoautotrophs are limited and the utilization of atmospheric gases by microbial communities is well documented (King, 2003;Lynch et al., 2012Lynch et al., , 2014. This includes volcanic deposits as well as additional cold and hot deserts, such as the McMurdo Dry Valleys (Babalola et al., 2009;Van Goethem et al., 2016), Namib (van der Walt et al., 2016;Gunnigle et al., 2017), Thar (Rao et al., 2016), and Atacama (Lynch et al., 2014;Schulze-Makuch et al., 2018). Finally, this study highlights the genetic potential of microbial communities residing in cold oligotrophic deserts across the globe to conduct atmospheric chemosynthesis and FIGURE 5 | Spearman correlations between the relative abundance of the two target genes, rbcL1E and hhyL, against all 26 measured physicochemical parameters for the 117 Antarctic and high Arctic soils. ...
Article
Soil microbiomes within oligotrophic cold deserts are extraordinarily diverse. Increasingly, oligotrophic sites with low levels of phototrophic primary producers are reported, leading researchers to question their carbon and energy sources. A novel microbial carbon fixation process termed atmospheric chemosynthesis recently filled this gap as it was shown to be supporting primary production at two Eastern Antarctic deserts. Atmospheric chemosynthesis uses energy liberated from the oxidation of atmospheric hydrogen to drive the Calvin-Benson-Bassham (CBB) cycle through a new chemotrophic form of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), designated IE. Here, we propose that the genetic determinants of this process; RuBisCO type IE (rbcL1E) and high affinity group 1h-[NiFe]-hydrogenase (hhyL) are widespread across cold desert soils and that this process is linked to dry and nutrient-poor environments. We used quantitative PCR (qPCR) to quantify these genes in 122 soil microbiomes across the three poles; spanning the Tibetan Plateau, 10 Antarctic and three high Arctic sites. Both genes were ubiquitous, being present at variable abundances in all 122 soils examined (rbcL1E, 6.25 × 103 –1.66 × 109 copies/g soil; hhyL, 6.84 × 103 –5.07 × 108 copies/g soil). For the Antarctic and Arctic sites, random forest and correlation analysis against 26 measured soil physicochemical parameters revealed that rbcL1E and hhyL genes were associated with lower soil moisture, carbon and nitrogen content. While further studies are required to quantify the rates of trace gas carbon fixation and the organisms involved, we highlight the global potential of desert soil microbiomes to be supported by this new minimalistic mode of carbon fixation, particularly throughout dry oligotrophic environments, which encompass more than 35% of the Earth’s surface.
... Groundwater and the moisture contribution from its sub-surface veins can be a determinant of microbial activity on long timescales (∼100 year scale) (Gamboa et al., 2019). There are reports detecting the growth of microbial communities after very rare rainfall events (1-10 year scale) (Schulze-Makuch et al., 2018). Therefore, we consider that water-soluble organic matter, which supports microbial growth, is correlated with the total amount of rainfall and the degree of solubility of sedimentary matrix. ...
Article
Full-text available
Microbiological activities can be detected in various extreme environments on Earth, which suggest that extraterrestrial environments, such as on Mars, could host life. There have been proposed a number of biomarkers to detect extant life mostly based on specific molecules. Because terrestrial organisms have catalytic proteins (enzymes), enzymatic activity may also be a good indicator to evaluate biological activities in extreme environments. Phosphatases are essential for all terrestrial organisms because phosphate esters are ubiquitously used in genetic molecules (DNA/RNA) and membranes. In this study, we evaluated microbial activity in soils of the Atacama Desert, Chile, by analysing several biomarkers, including phosphatase activity. Phosphatases extracted with Tris buffer were assayed fluorometrically using 4-methylumbelliferyl phosphate as a substrate. The horizontal distribution of phosphatase activity and other parameters in soils from the Atacama Desert showed that phosphatase activity was positively correlated with amino acid concentration and colony-forming units and negatively correlated with precipitation amount. We found consistent that biochemical indicators including phosphatase significantly decreased in the extreme hyper-arid zone where rainfall of <25 mm year ⁻¹ . The results were compared with phosphatase activities detected in extreme environments, such as submarine hydrothermal systems and Antarctic soils, as well as soils from ordinary environments. Overall, our results suggested that phosphatase activity could be a good indicator for evaluating biological activities in extreme environments.
... The microbial abundances of regolith samples from the Qaidam Basin were comparable to those in soils from the Atacama Desert (Lester et al., 2007) and the Antarctic Desert (Smith et al., 2006), and the concentrations of crude DNA extract from samples in this study were also comparable to those from soils in the Antarctic Desert (Smith et al., 2006). Aridity has been shown to have significant impacts on shaping soil microbial communities in deserts, with microbial diversity decreasing as desiccation increases in general (Crits-Christoph et al., 2013;Neilson et al., 2012;Schulze-Makuch et al., 2018). In this study, we note that microbial biomass and diversity were positively correlated with the moisture and TOC contents (Table S2), indicating that water and organic carbon availability are essential constraints for the proliferation of microbial life in the Qaidam Basin. ...
Article
The Qaidam Basin on the northern Tibetan Plateau, China, is one of the driest deserts at high elevations, and it has been considered a representative Mars analogue site. Despite recent advances in the diversity of microbial communities in the Qaidam Basin, our understanding of their genomic information, functional potential and adaptive strategies remains very limited. Here, we conducted a combination of physicochemical and metagenomic analyses to investigate the taxonomic composition and adaptive strategies of microbial life in the regolith across the Qaidam Basin. 16S ribosomal RNA (rRNA) gene‐based and metagenomic analyses both reveal that microbial communities in the Qaidam Basin are dominated by the bacterial phylum Actinobacteria. The low levels of moisture and organic carbon contents appear to have essential constraints on microbial biomass and diversity. A total of 50 high‐quality metagenome‐assembled genomes were reconstructed and analysed. Our results reveal the potential of microorganisms to use ambient trace gases to meet energy and carbon needs in this nutrient‐limited desert. Furthermore, we find that DNA repair mechanisms and protein protection are likely essential for microbial life in response to stressors of hyperaridity, intense ultraviolet radiation and tremendous temperature fluctuations in this Mars analogue. These findings shed light on the diversity and survival strategies of microbial life inhabiting Mar‐like environments, which provide implications for potential life on early Mars.
... 3-9; Cowan et al. 2020). Even the harshest of desert ecosystems, such as in the most hyperarid regions of the Atacama and Namib Deserts, are colonized by a wide range of active microbial taxa (Gunnigle et al. 2014Schulze-Makuch et al. 2018;León-Sobrino et al. 2019;Chaps. 4 and 9). ...
Chapter
Deserts are the most dominant terrestrial environments as they cover over a third of the Earth’s emerged surface. These arid ecosystems further influence global biogeochemical cycling particularly via the emission of dust. These dust clouds can travel thousands of kilometers and fertilize very distant environments as well as intensify global warming. This is concerning as desert surfaces are expanding with climate change. This concluding chapter therefore briefly discusses possible novel research avenues that desert microbial ecologist could follow in the context of climate change.
Article
The pulse–reserve paradigm (PRP) is central in dryland ecology, although microorganismal traits were not explicitly considered in its inception. We asked if the PRP could be reframed to encompass organisms both large and small. We used a synthetic review of recent advances in arid land microbial ecology combined with a mathematically explicit theoretical model. Preserving the PRPs core of adaptations by reserve building, the model considers differential organismal strategies to manage these reserves. It proposes a gradient of organisms according to their reserve strategies, from nimble responders (NIRs) to torpid responders (TORs). It predicts how organismal fitness depends on pulse regimes and reserve strategies, partially explaining organismal diversification and distributions. After accounting for scaling phenomena and redefining the microscale meaning of aridity, the evidence shows that the PRP is applicable to microbes. This modified PRP represents an inclusive theoretical framework working across life-forms, although direct testing is still needed.
Article
The search for life elsewhere in the Universe goes together with the search for liquid water. Life as we know it requires water; however, it is possible for microbial life to exist under hyperarid conditions with a minimal amount of water. We report on the ability of two typical terrestrial bacteria (Escherichia coli B and Eucapsis sp) and two extremophiles (Gloeocapsa-20201027-1 sp and Planococcus halocryophilus) to grow and survive in three martian soil (regolith) simulants (Mohave Mars Simulant-1 [MMS-1] F, Mars Global Simulant-1 [MGS-1], and JSC Mars-1A [JSC]). Survival and growth were assessed over a 21-day period under terrestrial conditions and with water:soil (vol:wt) ratios that varied from 0.25:1 to 5:1. We found that Eucapsis and Gloeocapsa sp grew best in the simulants, MMS and JSC, respectively, while P. halocryophilus growth rates were better in the JSC simulant. As expected, E. coli did not show significant growth. Our results indicate that these martian simulants and thus martian regolith, with minimal or no added nutrients or water, can support the growth of extremophiles such as P. halocryphilus and Gloeocapsa. Similar extremophiles on early Mars may have survived to the present in near-surface ecological niches analogous to those where these organisms exist on Earth.
Preprint
Full-text available
Background Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics. Results In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Variations in the antimicrobial resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure. Conclusions Comparative analyses of MAGs and whole genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low dose irradiation compared to the evolution of microbes here on Earth.
Chapter
Desert ecosystems are a key repository for important Mars analog habitats and the extant or extinct life within them. We provide an overview of four main desert habitat types—soils, sediments, salts, and rocks—and the extreme microbiology living within them, with a particular focus on the hyperarid Atacama Desert and Dry Valleys of Antarctica, the driest and coldest limits for life on Earth. We construct habitat maps of Mars from an ecological perspective and the first estimates of study sample sizes of key habitats from historical and recent Mars orbiter and lander imagery and data. We review the lessons that can be drawn for the search for life on Mars from decades of microbial ecology work in end-member terrestrial deserts.
Article
Full-text available
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites. This is in stark contrast to the extremely high sample specificity of most other community members. Only present at the highest moisture site is a genomically characterized Thermoplasmatales archaeon (Marine Group II) and six Nanohaloarchaea, one of which is represented by a complete genome. Parcubacteria (OD1) and Saccharibacteria (TM7), not previously reported from hypersaline environments, were found at low abundances. We found no indication of a N2 fixation pathway in the communities, suggesting acquisition of bioavailable nitrogen from atmospherically derived nitrate. Samples cluster by site based on bacterial and archaeal abundance patterns and photosynthetic capacity decreases with increasing distance from the ocean. We conclude that moisture level, controlled by coastal fog intensity, is the strongest driver of community membership.
Article
Full-text available
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.
Article
Full-text available
We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.
Article
Full-text available
Several explanations have been proposed for the temporal differences in geologic processes associated with the modification of martian impact craters, which occurred throughout the Noachian, and the formation of valley networks, which occurred during the Noachian/Hesperian transition. Here we show that it could be a result of the changing nature of rainfall as the primordial atmospheric pressure on Mars waned through time. We calculate the terminal velocity and resulting kinetic energy from raindrops >0.5 mm in diameter that would impact the surface of Mars in a CO2-rich atmosphere ranging in pressure from 0.5 to 10 bars. Our analyses indicate that the primordial atmosphere of Mars could not have exceeded ∼4.0 bars as raindrop sizes would have been limited to <3 mm and surface erosion from rain splash and subsequent crater modification would not have occurred. At pressures between ∼3.0 and 4.0 bars, sediment transport from rain splash could occur, but surface runoff would have been limited, which could explain the modification of impact craters. Once atmospheric pressures waned to ∼1.5 bars, rainfall intensity could begin to exceed the infiltration capacity of most soils, which would be necessary to initiate martian valley network formation. Due to the lower gravity, a storm on Mars that occurred in a 1 bar atmosphere could generate raindrops with a maximum diameter of ∼7.3 mm compared to 6.5 mm on the Earth. However, rainfall from such a storm would be only be ∼70% as intense on Mars, primarily due to the lower martian gravity and resulting lower terminal velocities of the rain drops.
Article
Full-text available
Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity.
Article
Full-text available
Northern Chile hosts the driest place on Earth in the Atacama Desert. Nonetheless, an extreme precipitation event affected the region on 24-26 March 2015 with 1-day accumulated precipitation exceeding 40 mm in several locations and hourly mean rainfall rates higher than 10 mm h⁻¹, producing floods and resulting in casualties and significant damage. The event is analyzed using ERA-Interim, surface station data, sounding observations, and satellite-based radar. Two main conditions favorable for precipitation were present at the time of the event: (i) a cutoff low (COL) off the coast of northern Chile and (ii) positive sea surface temperature (SST) anomalies over the eastern tropical Pacific. The circulation driven by the COL was strong but not extraordinary. Regional Climate Model, version 4 (RegCM4), is used to test the sensitivity of precipitation to SST anomalies by removing the warm SST anomaly in the eastern tropical Pacific. The cooler simulation produced very similar COL dry dynamics to that simulated in a control run (with observed SST), but suppressed the precipitation by 60%-80% over northern Chile and 100% in parts of the Atacama Desert due to the decreased availability of precipitable water. The results indicate that the warm SST anomaly over the eastern Pacific, favored by the onset of El Niño 2015/16, was instrumental to the extreme precipitation event by providing an anomalous source of water vapor transported to Atacama by the circulation ahead of the COL.
Article
Although it contains less water vapour than Earth’s atmosphere, the Martian atmosphere hosts clouds. These clouds, composed of water-ice particles, influence the global transport of water vapour and the seasonal variations of ice deposits. However, the influence of water-ice clouds on local weather is unclear: it is thought that Martian clouds are devoid of moist convective motions, and snow precipitation occurs only by the slow sedimentation of individual particles. Here we present numerical simulations of the meteorology in Martian cloudy regions that demonstrate that localized convective snowstorms can occur on Mars. We show that such snowstorms—or ice microbursts—can explain deep night-time mixing layers detected from orbit and precipitation signatures detected below water-ice clouds by the Phoenix lander. In our simulations, convective snowstorms occur only during the Martian night, and result from atmospheric instability due to radiative cooling of water-ice cloud particles. This triggers strong convective plumes within and below clouds, with fast snow precipitation resulting from the vigorous descending currents. Night-time convection in Martian water-ice clouds and the associated snow precipitation lead to transport of water both above and below the mixing layers, and thus would affect Mars’ water cycle past and present, especially under the high-obliquity conditions associated with a more intense water cycle.
Article
H₂O, CO₂, SO₂, O₂, H₂, H₂S, HCl, chlorinated hydrocarbons, NO and other trace gases were evolved during pyrolysis of two mudstone samples acquired by the Curiosity rover at Yellowknife Bay within Gale crater, Mars. H₂O/OH-bearing phases included 2:1 phyllosilicate(s), bassanite, akaganeite, and amorphous materials. Thermal decomposition of carbonates and combustion of organic materials are candidate sources for the CO₂. Concurrent evolution of O₂ and chlorinated hydrocarbons suggest the presence of oxychlorine phase(s). Sulfides are likely sources for S-bearing species. Higher abundances of chlorinated hydrocarbons in the mudstone compared with Rocknest windblown materials previously analyzed by Curiosity suggest that indigenous martian or meteoritic organic C sources may be preserved in the mudstone; however, the C source for the chlorinated hydrocarbons is not definitively of martian origin.
Article
Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies.
Article
The evolution of habitable conditions on Mars is often tied to the existence of aquatic habitats and largely constrained to the first billion years of the planet. Here, we propose an alternate, lasting evolutionary trajectory that assumes the colonization of land habitats before the end of the Hesperian period (ca. 3 billion years ago) at a pace similar to life on Earth. Based on the ecological adaptations to increasing dryness observed in dryland ecosystems on Earth, we reconstruct the most likely sequence of events leading to a late extinction of land communities on Mars. We propose a trend of ecological change with increasing dryness from widespread edaphic communities to localized lithic communities and finally to communities exclusively found in hygroscopic substrates, reflecting the need for organisms to maximize access to atmospheric sources of water. If our thought process is correct, it implies the possibility of life on Mars until relatively recent times, perhaps even the present. Key Words: Life-Mars-Evolution-Desert-Land ecosystems-Deliquescence. Astrobiology 16, xxx-xxx.